Latest Articles from Research Ideas and Outcomes Latest 63 Articles from Research Ideas and Outcomes https://riojournal.com/ Fri, 29 Mar 2024 09:21:09 +0200 Pensoft FeedCreator https://riojournal.com/i/logo.jpg Latest Articles from Research Ideas and Outcomes https://riojournal.com/ Strengthening the 2018 EU Bioeconomy Strategy through Microbiome Analysis and Synthetic Microbial Consortia Technologies https://riojournal.com/article/120994/

DOI: 10.3897/arphapreprints.e121032

Authors: Jens Krömer, Gabriela Popova, Katja Bühler, Peter Lindblad

Abstract: The 2018 EU Bioeconomy Strategy aims to create a sustainable, circular, and low-emissions economy, based on the use of renewable biological resources. The strategy focuses on the development of new biobased products and markets, the promotion of sustainable and efficient use of resources, and the support of research, innovation, and skills development in the bioeconomy sector. The main objectives of the strategy are to: - Accelerate the deployment of bio-based products and services to reduce Europe’s dependence on fossil fuels and promote the transition to a circular economy; - Optimise the use of renewable biological resources to ensure food security, while also protecting the environment and biodiversity; - Promote sustainable and efficient use of natural resources, reduce waste, and minimize greenhouse gas emissions; - Develop innovative, sustainable, and competitive bio-based industries and value chains that create jobs and support economic growth, particularly in rural areas; - Support research, innovation, and skills development in the bioeconomy sector to drive technological advancements, enhance the competitiveness of the EU’s bio-based industries, and address societal challenges such as climate change, food security, and public health. The EU Horizon 2020 PROMICON project is a pioneering initiative that directly addresses the objectives of the 2018 EU Bioeconomy Strategy. By focusing on the production of biopolymers, energy carriers, feedstocks, and antimicrobial molecules from natural microbiomes, the project is promoting the sustainable production and use of renewable biological resources while also supporting research and innovation in the bioeconomy sector.

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Policy Brief Mon, 19 Feb 2024 09:15:05 +0200
PaNOSC/ExPaNDS Science Projects for EOSC Future (WP6.3): Demonstrating EOSC Value through cross-domain Research Science Projects https://riojournal.com/article/107226/

DOI: 10.3897/arphapreprints.e116674

Authors: Miguel Angel Gonzalez, Rudolf Dimper, Patrick Fuhrmann, Fra Schluenzen, Gianluca Santoni, Jordi Bodera, Jayesh Wagh, Irina Safiulina, Paolo Mutti, Arianna D'Angelo, Paul Millar, Krisztian Pozsa, Leonardo Sala, Alun Ashton, Giuseppe La Rocca

Abstract: Photon and Neutron (PaN) user facilities serve a large variety of scientific user communities using x-rays and/or neutrons in their research projects in order to understand the structure and function of matter. The current proposal presents two concrete scientific cases intended to demonstrate the utility of FAIR data and automatic workflows in the specific domain of biological structures and processes, simplifying the access and manipulation of large sets of data and the combination of experimental and modelling tools. The final objective consists in reducing the level of expertise required to analyze and interpret data acquired at large scale neutron and synchrotron facilities.

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Grant Proposal Tue, 5 Dec 2023 12:45:39 +0200
Open Imaging Data Sharing in EOSC: COVID-19 as Demonstrator https://riojournal.com/article/110376/

DOI: 10.3897/arphapreprints.e116672

Authors: Reagon Karki, Andrea Zaliani, Philip Gribbon, Carolina Simon, Jose Ramon Macias, Bugra Özdemir, Aastha Mathur

Abstract: This Science Project (SP) brings together three different domains of life sciences with the aim to create reproducible workflows, tools and web-services for data visualization. This SP focuses in building resources for handling data from bioimaging, structural and bio-chemical studies. The Euro-Bioimaging will implement a community standard cloud compatible open image data format and data submission workflow for high-throughput screening data. Whereas, Instruct-ERIC will develop a user-friendly web-service to access to multi-dimensional structural and imaging data. Lastly, EU-OpenScreen/Fraunhofer ITMP will create reproducible workflow for generating Knowledge Graphs that represent phenotype-chemotype of diseases. While these resources are being developed, the collaborators will also simultaneously harmonize the resources right from the beginning to enable FAIR data principles. This SP uses COVID-19 as a demonstrator, however the resources will be generalized for any disease of interest.

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Grant Proposal Tue, 5 Dec 2023 12:35:16 +0200
Tracing bio-structures with serial crystallography: Facilitating the access to high-throughput macromolecular x-ray crystallography techniques. https://riojournal.com/article/110441/

DOI: 10.3897/arphapreprints.e116671

Authors: Miguel Angel Gonzalez, Rudolf Dimper, Patrick Fuhrmann, Gianluca Santoni, Jordi Bodera, Jayesh Wagh, Irina Safiulina, Arianna D'Angelo, Paolo Mutti, Paul Millar, Krisztian Pozsa, Leonardo Sala, Alun Ashton, Giuseppe La Rocca

Abstract: Serial (femtosecond) X-ray-Crystallography (SFX) is a special variant of macromolecular X-ray crystallography aiming at rapid structural studies at room temperature. This highly innovative technology permits investigation of bio-structures not tractable with conventional X-ray crystallography, and is capable of studying fast in-situ biochemical processes. The method is still relatively new, but it is already one of the most prominent applications of free-electron lasers (FELs), and increasingly also of very brilliant synchrotron radiation sources. One of the unique characteristics of this type of experiments is the extremely high repetition rate combined with a quite moderate success rate. A crucial task in the rather complex data processing pipeline is the rapid and accurate classification of images: typically, only a few percent of the images contain a diffraction pattern suitable for subsequent integration and structure refinement. AI-supported image classification is hence particularly suited for drastic data reduction, saving precious storage space, compute cycles and processing time. The experimental techniques and methodologies are rapidly evolving, and the integration of emerging tools into the processing pipeline is an essential task. SFX data sets are big, require substantial storage, and computational power. The main goal of this SP is to establish and develop a data processing platform, which integrates services and developments from PaNOSC/ExPaNDS. The platform should provide integrated processing pipelines for well-established and cutting-edge applications, so that cross-disciplinary users with modest expertise gain rapid and convenient access to tools and documentation of newest developments. On the other hand, it should also provide convenient access to FAIR SFX-data, to foster developments and strengthen collaboration between experimentalists and developers of new algorithms and software implementations. This approach is of very high relevance for all PaN synchrotron and FEL facilities and their users.

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Grant Proposal Tue, 5 Dec 2023 12:30:49 +0200
Following biological processes combining small angle neutron and x-ray scattering and modelling techniques https://riojournal.com/article/110452/

DOI: 10.3897/arphapreprints.e116670

Authors: Miguel Angel Gonzalez, Irina Safiulina, Arianna D'Angelo, Paolo Mutti, Jordi Bodera, Gianluca Santoni, Rudolf Dimper, Jayesh Wagh, Patrick Fuhrmann, Paul Millar, Krisztian Pozsa, Leonardo Sala, Alun Ashton, Giuseppe La Rocca

Abstract: Small-angle scattering techniques are widely used in scientific communities to determine the shape, distribution, and uniformity of particles in solution. New developments and faster acquisition will also allow for tracking the dynamics of the particles themselves. Small-Angle X-ray or Neutron Scattering (SAXS or SANS, respectively) can be very effective tools for studying, for example, the time dependence of genome release from phages, investigating entire viral life cycles, or the assembly of macromolecular complexes, providing deep insights into infection pathways. Neutrons and X-rays can be applied in a complementary mode, as is the case for the joint SANS-SAXS proposal between the ESRF and the ILL.This strategic plan aims to advance the field by providing an EOSC-based platform, enabling FAIR data and software, unified data processing pipelines featuring robust scaling algorithms for the two different sources, supporting reproducibility and automated validation, and integrating with other relevant structural databases (e.g., electron microscopy/tomography or protein structural and ligand databases).

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Grant Proposal Tue, 5 Dec 2023 12:25:21 +0200
BatchConvert: A command-line tool for parallelised conversion of image collections into the standard bioimage file formats OME-TIFF and OME-Zarr. https://riojournal.com/article/112650/

DOI: 10.3897/arphapreprints.e116669

Authors: Bugra Özdemir, Aastha Mathur, Johanna Bischof, John E. Eriksson, Jean-Karim Hériché, Josh Moore, Christian Tischer, Antje Keppler

Abstract: File formats incompatibility has become a major obstacle in biological imaging, complicating downstream processes such as image processing and analysis. One way to address this challenge is to convert the acquired image data into standard image file formats. Here we introduce BatchConvert, a command line tool for parallelised conversion of image collections into OME-TIFF or OME-Zarr using the workflow management system Nextflow. BatchConvert offers functionalities such as remote input-output support, optional execution on Slurm clusters and pattern-based filtering of input files. Conversion can be coupled to image concatenation, allowing selected images to be merged along specified dimensions. Support for remote locations includes an option to submit the output data to S3-compatible object stores or public archives such as BioImage Archive. Overall, BatchConvert is a flexible tool for researchers who are routinely managing and analysing large multidimensional image data that is either locally or remotely stored.

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Software Description Tue, 5 Dec 2023 12:20:54 +0200
A Jupyter notebook to explore protein conformations: An output of PaNOSC SP8 case https://riojournal.com/article/112700/

DOI: 10.3897/arphapreprints.e116668

Authors: Irina Safiulina, Miguel Angel Gonzalez, Paolo Mutti, Giuseppe La Rocca, Enol Fernández

Abstract: Small-angle scattering techniques are widely employed across scientific communities to elucidate the morphology, spatial distribution, and uniformity of particles within liquid solutions. Recent advancements and accelerated data acquisition capabilities have extended the utility of these techniques to probe the dynamic behavior of particles over time. Small-Angle X-ray Scattering (SAXS) and Small-Angle Neutron Scattering (SANS) emerge as powerful tools in this realm, enabling the investigation of phenomena such as the time-dependent release of genomes from phages, the comprehensive exploration of viral life cycles, and the assembly dynamics of macromolecular complexes. This tandem application of X-rays and neutrons, exemplified by the collaborative SANS-SAXS initiative between the European Synchrotron Radiation Facility (ESRF) and the Institut Laue-Langevin (ILL), yields complementary insights into complex infection pathways.In this report, we present the outcomes of a software development project undertaken as part of Science Project 8: "PaNOSC Dynamics of Biological Processes" within the EOSC Future framework. The project's deliverables include a Jupyter Notebook and accompanying Python scripts, specifically sas_helper.py. The primary objective of Science Project 8 is to expand the accessibility of open Small-Angle Neutron Scattering (SANS) and Small-Angle X-ray Scattering (SAXS) data to a broader scientific community. This endeavor underscores the profound transformative potential of open-science data analysis within the European Open Science Cloud (EOSC) framework while advocating for the adoption of FAIR (Findable, Accessible, Interoperable, and Reusable) principles in scientific research. 

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Project Report Tue, 5 Dec 2023 12:15:12 +0200
The impacts of multiple stressors on managed bees: Novel insights from the PoshBee project https://riojournal.com/article/114828/

DOI: 10.3897/arphapreprints.e115172

Authors: Mark Brown, Matthias Albrecht, Pilar De la Rúa, Sara Hellström, Alexandra-Maria Klein, Denis Michez, Francesco Nazzi, Robert Paxton, Edward Straw, Dimitry Wintermantel, Simon Potts

Abstract: Managed bees and other pollinators are exposed to a wide variety of stressors and these often act in combination. Historically, most risk assessments and research have focused on the impacts of individual stressors on honey bees. However, there is broad scientific consensus that there is a need for a systems-based risk assessment approach and a post-approval monitoring system. This should consider: multiple interacting stressors; a variety of pollinator species (including different subspecies, sexes, castes and life history stages); field studies as well as laboratory studies; and a diversity of end-points (molecular, physiological, behavioural, developmental, reproductive and colony health). The PoshBee project has made a significant step in our understanding of how the interactions between agrochemicals, pathogens and nutrition impact different bee species.

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Policy Brief Mon, 6 Nov 2023 08:49:50 +0200
Mitigating multiple stressors on managed pollinators: Effectiveness and feasibility of implementing response options https://riojournal.com/article/112381/

DOI: 10.3897/arphapreprints.e112382

Authors: Bryony Willcox, Deepa Senapathi, Mark Brown, Simon Potts

Abstract: In the real world, pollinators face multiple interacting pressures, and so response options must be tailored to this. To date, most attention has been on characterising the risks to managed pollinators from single stressors, though recently more attention has been paid to risks from multiple stressors (e.g., pesticides, pathogens and poor nutrition). The PoshBee project has developed a policy brief providing recommendations on options that mitigate against multiple stressors.

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Policy Brief Fri, 8 Sep 2023 10:23:11 +0300
PoshBee Toolbox: A portfolio of high quality methodologies, tools, and practice guides for pollinators https://riojournal.com/article/112170/

DOI: 10.3897/arphapreprints.e112175

Authors: Mark Brown, Philippe Bulet, Marie-Pierre Chauzat, Alexandra-Maria Klein, Anina Knauer, Marika Mand, Denis Michez, Francesco Nazzi, Robert Paxton, Oliver Schweiger, Jane Stout, Orlando Yanez, Simon Potts

Abstract: Policies and management practices for managed bees and other pollinators are increasingly reliant on the availability of high quality data in order to inform them. This in turn requires the widespread adoption of state-of-the-art standardised methods and approaches so that new data and knowledge are both robust and trustworthy. The PoshBee project has developed, tested, and validated a wide range of new tools. These include, but are not limited to: experimental protocols, monitoring tools, technological tools and practice guides. The wide scale application of these, and other tools will help ensure that researchers, risk assessors, policymakers, beekeepers, and agri-food industry are producing data to the highest standards in a way that increases comparability and transparency.

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Policy Brief Tue, 5 Sep 2023 08:44:37 +0300
Improving COVID-19 metadata findability and interoperability in the European Open Science Cloud https://riojournal.com/article/107280/

DOI: 10.3897/arphapreprints.e107873

Authors: Christian Ohmann, Steve Canham, Kurt Majcen, Petr Holub, Gary Saunders, Jing Tang, Tanushree Tunstall, Philip Gribbon, Reagon Karki, Mari Kleemola, Katja Moilanen, Walter Daelemans, Pieter Fivez, Daan Broeder, Franciska de Jong, Maria Panagiotopoulou

Abstract: This publication details the workplan of the Science Project (SP) “COVID-19 metadata findability and interoperability in EOSC” (short: META-COVID) that is part of the Horizon Europe funded project EOSC Future. The COVID-19 pandemic has generated a huge variety of research activities, studies, and policies across both the life sciences (LS) and the social sciences and humanities (SSH). Useful insights from combining the data and conclusions from these different forms of research are, however, hampered by the lack of a common metadata framework with which to describe them. This is because different scientific disciplines have different ways of organising research activities. For example, the type of the research (e.g., hypothesis testing versus hypothesis generating) and the methodology chosen (e.g., experimental, survey, cohort, case study) are key elements in understanding the data generated and in supporting its secondary use. Another issue to be tackled is the integration of various sources of metadata related to parliamentary and social media metadata. In META-COVID, scientists from the LS and SSH domains gathered to discuss ways in which metadata could go beyond the description of the data itself to include the basic elements of the research process (“contextual metadata”) within the frame of the European Open Science Cloud (EOSC). The main outcomes of the SP will be: i) An inventory of metadata schemas applied across infrastructures and domains; ii) The development of a framework for a metadata model characterising the research approach and workflow across research infrastructures; iii) The application of the framework to selected COVID-19 use cases; iv) The development of an ontology of COVID-19 related topics from parliamentary data and social media.

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Grant Proposal Wed, 14 Jun 2023 11:20:57 +0300
Climate Change Impact on Biodiversity and Ecosystems in Europe: Assessing the impact of Non-Indigenous Invasive Species (NIS) in European ecosystems https://riojournal.com/article/106388/

DOI: 10.3897/arphapreprints.e106475

Authors: Christos Arvanitidis, Alberto Basset, Thierry Carval, Katrina Exter, Nicola Fiore, Alessandra Giorgetti, Juan Miguel González-Aranda, Mark Hebden, Georgios Kotoulas, Joaquín López Lérida, Rory Meyer, Nikos Minadakis, Matthias Obst, Nicolas Pade, Christina Pavloudi, Marc Portier, Ioulia Santi, Dick Schaap, Peter Thijsse, Lucia Vaira, Cristina Huertas Olivares

Abstract: This Science Project (SP) contributes to the estimation of the impacts of the invasive species on the European Biodiversity and Ecosystems. This topic is important for European Green Deal and the new European Biodiversity Strategy. The SP is also linked with the socio-economic issues because of the NIS implications to the local ecosystems and their services, and their societal goods and services. Since many of the above impacts may be of local scale, they may alter common practices in circular economies. The SP is implemented by: (a) Combining different sources of data and information; (b) Using a dual workflow to analyse the data; (c) Integrating its resources with core EOSC services and potentially horizontal services available; (d) Engaging the relevant scientific communities. The users will be able to: (a) Analyse distribution patterns of invasive species from different sources of data; (b) Compare the above patterns; (c) Provide managerial suggestions to relevant authorities; (d) Build on the existing infrastructure to address more complex questions (e.g. future scenarios).

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Grant Proposal Tue, 16 May 2023 10:15:00 +0300
EOSC Future: Design and implementation of community engagement through Science Projects https://riojournal.com/article/106368/

DOI: 10.3897/arphapreprints.e106369

Authors: Christos Arvanitidis, Ron Dekker, Andreas Petzold, Niklas Blomberg, Giovanni Lamanna, Rudolf Dimper, Cristina Isabel Huertas Olivares, Ana Mellado, Matthew Viljoen, Sally Chambers, Montserrat González, Sophie Viscido

Abstract: The Special Collection of articles on the Science Projects of the EOSC Future project, funded by the European Commission, refers to one of the essential components of the project. This editorial article explains how the Science Projects fit to the EOSC Future, the way their concept has been developed and evolved during the preparation and the implementation of the project and it also makes an introduction to the templates developed by the Science Projects as a plan to carry out their activities.

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Editorial Mon, 15 May 2023 17:03:13 +0300
Bending the curve of biodiversity loss requires rewarding farmers economically for conservation management https://riojournal.com/article/104874/

DOI: 10.3897/arphapreprints.e104881

Authors: David Kleijn, Ignasi Bartomeus, Vincent Bretagnolle, Kati Häfner, Felix Herzog, Jochen Kantelhardt, Erik Öckinger, Simon Potts, Giulia Riedo, Anna Sapundzhieva, Lena Luise Schaller, Nikol Yovcheva

Abstract: Agricultural expansion and intensification are key drivers of biodiversity decline. There is mounting evidence that modern farming impacts the effectiveness of protected areas as one of the key instruments of biodiversity conservation through, for example, eutrophication, pesticide emissions or increasing access to remote areas [1]. This is increasingly acknowledged and in many countries conservation efforts now include farmed lands and engage farmers to enhance biodiversity on their lands. This benefits farmland biodiversity which, especially in Eurasia, supports some highly threatened species groups [2]. However, farmland biodiversity is also functionally important as it provides a wide range of ecosystem services. Examples are natural pest regulation, pollination, carbon sequestration, human well-being, water purification and cultural services. Agricultural management influences the provision of a wide range of ecosystem services and therefore, contributes to food security and mankind’s ability to sustain itself in the mid to long term. There is clear evidence that enhancing farmland biodiversity promotes the delivery of specific ecosystem services [3]. For example, enhancing wild pollinators and natural enemies through the provision of semi-natural habitat enhances productivity of many crops [4, 5]. However, only a few ecosystem services, such as pollination, pest control and nutrient cycling, may provide private benefits to farmers. Other services, such as carbon sequestration, biodiversity conservation, health benefits and water purification, are public goods which are poorly captured by markets [6].

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Policy Brief Thu, 13 Apr 2023 09:47:11 +0300
Deliverable D3.1 Project logo, marketing pack and website design and development https://riojournal.com/article/102610/

DOI: 10.3897/arphapreprints.e102613

Authors: Slavena Peneva, Kristina Hristova, Anna Sapundzhieva, Boris Barov, Pavel Stoev, Margarita Grudova, Iva Kostadinova

Abstract: This document presents BiCIKL’s recognizable visual identity, including the project logo, visual identity guide, brochure, poster, document, presentation templates and website design and functionality developed in the first three months. These materials will ensure that BiCIKL is communicated effectively and professionally with the aim to raise awareness and build a community from the start of the project.The modern and user-friendly public website (bicikl-project.eu) provides an easy-to-navigate, continuously updated platform allowing fast access to general information about BiCIKL and its activities, operating on several levels. It also prominently features the participating project partners and Research Infrastructures and their extensive service portfolio.

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Project Report Fri, 24 Feb 2023 16:50:06 +0200
Deliverable D6.4 Applications for interoperable access to OpenBiodiv through semantically enhanced queries https://riojournal.com/article/102611/

DOI: 10.3897/arphapreprints.e102612

Authors: Lyubomir Penev, Mariya Dimitrova, Georgi Zhelezov, Teodor Georgiev

Abstract: To the best of our knowledge, OpenBiodiv is the first production-stage  semantic  system running on top  of  a  reasonably-sized biodiversity knowledge graph. It stores biodiversity data in  a semantic interlinked format and offers facilities for working with it (Senderov et Penev 2016, Senderov et al.   2018, Penev et al. 2019, Dimitrova et al. 2021). It is a dynamic system that continuously updates its database as new biodiversity information becomes available by several international biodiversity publishers. It also allows its users to ask complex queries via SPARQL (a query language for semantic graph databases) and a simplified semantic search interface.OpenBiodiv was created during two EU-funded Marie Sklodowska-Curie PhD projects: BIG4 (Grant Agreement No 642241) and IGNITE (Grant Agreement No 764840). During those projects, the backend Ontology-0, the first versions of RDF converters and the basic website functionalities have been created (see Dimitrova et al. 2021 for overview).After the start of the BiCIKL project, the entire workflow for processing and RDF conversion of full-text articles in XML and Plazi’s treatments in XML has been re-built using up-to-date technological solutions (such as Apache Kaka  and  Elasticsearch)  to  fully  automatise  and speed up the conversion process and to make it trackable and efficient. As a result, the entire graph content has been re-processed and indexed. New user applications described  in Milestone MS27 App specifications have been discussed and implemented.The present deliverable describes the newly built workflow and tools for data extraction, conversion and indexing and the user applications, created in the BiCIKL project.

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Project Report Fri, 24 Feb 2023 16:49:01 +0200
Deliverable D12.9 Data Management Plan https://riojournal.com/article/102608/

DOI: 10.3897/arphapreprints.e102609

Authors: Lyubomir Penev, Teodor Georgiev, Boris Barov, Pavel Stoev, Kristina Hristova

Abstract: The  main goal of the BiCIKL project is to improve, for the first time, seamless access, linking and usage tracking of data within a network of Research Infrastructures managing different data classes (literature, specimens, samples, occurrences, sequences, taxon names and Operational Taxonomic Units (OTU)), ultimately represented also in a biodiversity knowledge graph. To achieve this, the consortium members will operate with huge amount of data during and after the end of the project.As a Horizon 2020 project, BiCIKL conforms to the Open Research Data Pilot (ORDP)1 and   Article 29.3 of the H2020 Model Grant Agreement by default, hence the consortium aims to improve and maximise access, sharing, linking and reuse of FAIR Open Research Data (ORD), generated or managed by the project. A detailed Data Management Plan is a critical part of   the ORDP. The DMP described in the present document is developed in BiCIKL within the first  six months of the project and it will evolve as a “living document” during the lifetime of the project and beyond in order to present the status of the project's reflections on data management.The BiCIKL DMP outlines the handling of research data and provides the basis of the project consortium’s data management life cycle for the data collected, generated and processed by the participants in the project. The DMP also covers the methodologies and standards previously developed for data sharing and open access, curation  and  preservation.  The subject of the DMP is the management of research data. Personal data management  is covered by deliverable D9.1 Protection of Personal Data.The BiCIKL DMP was developed in close collaboration with all project partners and involved Research Infrastructures (RI) who provided information on their data management practices and policies in a questionnaire and planned generation, collection, and processing of data for the purposes of building a resilient data management strategy of the project which meets all criteria for open research.This DMP aims to adhere to the FAIR (Findable, Accessible, Interoperable, Reusable) data management criteria of Horizon 20202.

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Data Management Plan Fri, 24 Feb 2023 16:46:45 +0200
Feedback report from the first ParAqua hybrid meeting - with considerations on challenges and advantages of mixed events https://riojournal.com/article/102002/

DOI: 10.3897/arphapreprints.e102047

Authors: Serena Rasconi

Abstract: The fist hybrid meeting and workshop of the COST Action “Applications for zoosporic parasites in aquatic systems” was held from 4th to 7th of July 2022 at the Multifunctional Center for Social Activities and Welfare of the Larnaka Municipality in Larnaca, Cyprus. 22 participants from 11 countries and 15 institutions attended on site, 26 participants from 9 countries and 26 institutions attended online. The activities included presentations, open discussions and collaborative work.This report presents the results of the feedback survey send to participants after the event. The survey was anonymous and included multiple choice responses (checkboxes) and short answers to complete and provide arguments to the checkboxes answers. 16 surveys were collected from the 54 participants, 13 from onsite and 3 from virtual attendees. Based on feedbacks and comments from the participants, the report will also include some considerations on challenges and advantages of mixed events.The report will contribute to set-up an active network and effective communication strategy for ParAqua, by describing advantages and limitations of different settings based on the Action experience and provide tips and hints to foster collaboration and effective work in hybrid mode.

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Workshop Report Mon, 20 Feb 2023 12:04:15 +0200
Milestone 15 Protocols for semi-field and field experiments https://riojournal.com/article/101313/

DOI: 10.3897/arphapreprints.e101323

Authors: Matthew J Allan, Robin Dean, Alexandra-Maria Klein, Dimitry Wintermantel, Matthias Albrecht, Janine Schwarz, Anina Knauer

Abstract: Under the terms of the PoshBee agreement, the members tasked with delivering Work Package 7 carried out semi-field and field studies on honey bees, bumble bees and solitary bees. These studies involved the exposure of the bees to more than one stressor, for example a fungicide and an insecticide or a fungicide and a nutritional deficiency. This is in contrast to the conventional study design where one stressor or product alone is assessed.These studies built upon recommendations by the European and Mediterranean Plant Protection Organisation (EPPO), European Food Safety Authority (EFSA), Prevention of Honeybee Colony Losses (COLOSS), and the Organisation of Economic Co-operation and Development (OECD). The team of researchers incorporated several innovative approaches in designing and carrying out the studies. In the authors’ view both the quality and quantity of data required for ecotoxicology studies can be improved by adoption of novel methods, including electronic means and artificial intelligence, and the design, manufacture and use of equipment specifically for such studies. Several examples are described.It is the intention of the team to include in this document practical advice for workers who are not familiar with such studies.

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Project Report Mon, 6 Feb 2023 10:31:16 +0200
Policies Handbook on Using Molecular Collections https://riojournal.com/article/98356/

DOI: 10.3897/arphapreprints.e98432

Authors: Astrid de Mestier, Daniel Mulcahy, David J. Harris, Nadja Korotkova, Sarah Long, Eva Häffner, Alan Paton, Edmund Schiller, Frederik Leliaert, Jacqueline Mackenzie-Dodds, Tim Fulcher, Gunilla Stahls, Thomas von Rintelen, María P. Martín, Robert Lücking, China Williams, Christopher Lyal, Anton Güntsch, Heléne Aronsson, Magalie Castelin, Anna Pielach, Peter Poczai, Yolanda Ruiz León, Isabel Sanmartin Bastida, Marco Thines, Gabriele Droege

Abstract: The access to molecular collections worldwide greatly improves the quality of scientific research by making a growing number of data available for investigation. The efforts on digitization also aim at facilitating the exchange of material between institutions and researchers that must follow regulations in place and respect best practice. The handbook presented here proposes a workflow to follow to safely exchange materials, in accordance with international laws and legislations. We make numerous recommendations here to help the institutions and researchers to navigate the legal and administrative procedures, to manage molecular collections in the best way possible. 

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Project Report Fri, 9 Dec 2022 14:16:32 +0200
Europa Biodiversity Observation Network: integrating data streams to support policy https://riojournal.com/article/81102/

DOI: 10.3897/arphapreprints.e81207

Authors: Henrique M. Pereira, Jessi Junker, Néstor Fernández, Joachim Maes, Pedro Beja, Aletta Bonn, Tom Breeze, Lluís Brotons, Helge Bruelheide, Marcel Buchhorn, César Capinha, Cher Chow, Karolin Dietrich, Maria Dornelas, Grégoire Dubois, Miguel Fernandez, Mark Frenzel, Nikolai Friberg, Steffen Fritz, Ivelina Georgieva, Anne Gobin, Carlos Guerra, Sigrid Haande, Sergi Herrando, Ute Jandt, W. Daniel Kissling, Ingolf Kühn, Christian Langer, Camino Liquete, Anne Lyche Solheim, David Martí, Juliette G. C. Martin, Annett Masur, Ian McCallum, Marit Mjelde, Jannicke Moe, Hannah Moersberger, Alejandra Morán-Ordóñez, Francisco Moreira, Martin Musche, Laetitia M. Navarro, Alberto Orgiazzi, Robert Patchett, Lyubomir Penev, Joan Pino, Gabriela Popova, Simon Potts, Anna Ramon, Leonard Sandin, Joana Santana, Anna Sapundzhieva, Linda See, Judy Shamoun-Baranes, Bruno Smets, Pavel Stoev, Leho Tedersoo, Liis Tiimann, Jose Valdez, Sara Vallecillo, Roy H. A. Van Grunsven, Ruben Van De Kerchove, Dani Villero, Piero Visconti, Claudia Weinhold, Annika M. Zuleger

Abstract: Observations are key to understand the drivers of biodiversity loss, and the impacts on ecosystem services and ultimately on people. Many EU policies and initiatives demand unbiased, integrated and regularly updated biodiversity and ecosystem service data. However, efforts to monitor biodiversity are spatially and temporally fragmented, taxonomically biased, and lack integration in Europe. EuropaBON aims to bridge this gap by designing an EU-wide framework for monitoring biodiversity and ecosystem services. EuropaBON harnesses the power of modelling essential variables to integrate different reporting streams, data sources, and monitoring schemes. These essential variables provide consistent knowledge about multiple dimensions of biodiversity change across space and time. They can then be analyzed and synthesized to support decision-making at different spatial scales, from the sub-national to the European scale, through the production of indicators and scenarios. To develop essential biodiversity and ecosystem variables workflows that are policy relevant, EuropaBON is built around stakeholder engagement and knowledge exchange (WP2). EuropaBON will work with stakeholders to identify user and policy needs for biodiversity monitoring and investigate the feasibility of setting up a center to coordinate monitoring activities across Europe (WP2). Together with stakeholders, EuropaBON will assess current monitoring efforts to identify gaps, data and workflow bottlenecks, and analyse cost-effectiveness of different schemes (WP3). This will be used to co-design improved monitoring schemes using novel technologies to become more representative temporally, spatially and taxonomically, delivering multiple benefits to users and society (WP4). Finally, EuropaBON will demonstrate in a set of showcases how workflows tailored to the Birds Directive, Habitats Directive, Water Framework Directive, Climate and Restoration Policy, and the Bioeconomy Strategy, can be implemented (WP5).

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Grant Proposal Wed, 26 Jan 2022 18:15:00 +0200
Dataset for Mosquitoes (Diptera: Culicidae) from Cross Key, Monroe County, Florida, USA https://riojournal.com/article/73768/ Research Ideas and Outcomes 7: e73768

DOI: 10.3897/rio.7.e73768

Authors: Lawrence J. Hribar

Abstract: The Florida Keys Mosquito Control District deploys dry ice-baited light traps to monitor mosquito populations throughout the Florida Keys. Cross Key is an island directly north of Key Largo and via bridges it serves as a link between Key Largo and mainland Florida.This paper describes a data set compiled from trap collections on Cross Key, Florida, between September 23, 2002 and March 1, 2016.

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Data Paper (Biosciences) Fri, 22 Oct 2021 09:00:00 +0300
Identifying SOX2-OT transcript that is responsible for regulating SOX2 in cancer cells and embryonic stem cells https://riojournal.com/article/69726/ Research Ideas and Outcomes 7: e69726

DOI: 10.3897/rio.7.e69726

Authors: Dao-Yin Dong, Pu-Yu Li

Abstract: SOX2 overlapping transcript (SOX2-OT) is an evolutionarily conserved long non-coding RNA (lncRNA) whose intronic region contains the transcript of pluripotency gene SRY-box transcription factor 2 (SOX2). It has been suggested that SOX2-OT can regulate its overlapping gene, SOX2. Studies demonstrated that elevated SOX2-OT promotes SOX2 expression in cancer cells, whereas levels of SOX2-OT are inversely correlated with levels of SOX2 in embryonic stem cells. It is not clear why there is a tremendous discrepancy in the regulation of SOX2 by SOX2-OT in cancer cells and embryonic stem cells. Due to the diversified transcription of the SOX2-OT gene, we hypothesize that differential expression of transcripts of the SOX2-OT gene in cancer cells and embryonic stem cells may contribute to the divergence in the regulatory relationship of SOX2-OT and SOX2. A CRISPR screening platform can be leveraged to systemic evaluate which transcript of the SOX2-OT gene may be responsible for upregulation or downregulation of SOX2 in cancer cells and embryonic stem cells, respectively.

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Short Communication Tue, 8 Jun 2021 17:00:00 +0300
Georeferencing for Research Use (GRU): An integrated geospatial training paradigm for biocollections researchers and data providers https://riojournal.com/article/32449/ Research Ideas and Outcomes 4: e32449

DOI: 10.3897/rio.4.e32449

Authors: Katja Seltmann, Sara Lafia, Deborah Paul, Shelley James, David Bloom, Nelson Rios, Shari Ellis, Una Farrell, Jessica Utrup, Michael Yost, Edward Davis, Rob Emery, Gary Motz, Julien Kimmig, Vaughn Shirey, Emily Sandall, Daniel Park, Christopher Tyrrell, R. Sean Thackurdeen, Matthew Collins, Vincent O'Leary, Heather Prestridge, Christopher Evelyn, Ben Nyberg

Abstract: Georeferencing is the process of aligning a text description of a geographic location with a spatial location based on a geographic coordinate system. Training aids are commonly created around the georeferencing process to disseminate community standards and ideas, guide accurate georeferencing, inform users about new tools, and help users evaluate existing geospatial data. The Georeferencing for Research Use (GRU) workshop was implemented as a training aid that focused on the creation and research use of geospatial coordinates, and included both data researchers and data providers, to facilitate communication between the groups. The workshop included 23 participants with a wide background of expertise ranging from students (undergraduate and graduate), professors, researchers and educators, scientific data managers, natural history collections personnel, and spatial analyst specialists. The conversations and survey results from this workshop demonstrate that it is important to provide opportunities for biocollections data providers to interact directly with the researchers using the data they produce and vice versa.

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Workshop Report Mon, 17 Dec 2018 09:24:57 +0200
Building and hacking open source hardware https://riojournal.com/article/31701/ Research Ideas and Outcomes 4: e31701

DOI: 10.3897/rio.4.e31701

Authors: Simone Monachino, Eric James McDermott, Andre Maia Chagas

Abstract: The first edition of the Aspects of Neuroscience Brainhack took place at the Department of Physics at University of Warsaw, Poland between November 17th and 19th 2017. This hackathon was one of the satellite events of the Aspects of Neuroscience conference, it was organized by the Brainhack organization to promote interaction between researchers, encouraging open (neuro)science and collaborations on projects related to the study of the nervous system. The event had a total of nine projects on many different topics including functional connectivity research, white matter tractography, classification of brain-ageing biomarkers through machine learning, presentation of a portable one channel EEG registration device and a do it yourself 3D-printed neurobiology lab. The latter is highlighted in this paper.

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Workshop Report Tue, 11 Dec 2018 11:29:31 +0200
Cafebr - Citation Amender/Formatter for Biological Research https://riojournal.com/article/29773/ Research Ideas and Outcomes 4: e29773

DOI: 10.3897/rio.4.e29773

Authors: Daisuke Tsugama

Abstract:

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Software Description Wed, 26 Sep 2018 08:55:46 +0300
Rethinking schizophrenia through the lens of evolution: shedding light on the enigma https://riojournal.com/article/28459/ Research Ideas and Outcomes 4: e28459

DOI: 10.3897/rio.4.e28459

Authors: Ariel Cariaga-Martinez, Kilian Gutiérrez, Raúl Alelú-Paz

Abstract: Schizophrenia refers to a complex psychiatric illness characterized by the heterogenic presence of positive, negative and cognitive symptoms occurring in all human societies. The fact that the disorder lacks a unifying neuropathology, presents a decreased fecundity of the affected individuals and has a cross-culturally stable incidence rate, makes it necessary for an evolutionary explanation that fully accounts for the preservation of “schizophrenic genes” in the global human genepool, explaining the potential sex differences and the heterogeneous cognitive symptomatology of the disorder and is consistent with the neuropsychological, developmental and evolutionary findings regarding the human brain. Here we proposed a new evolutionary framework for schizophrenia that is consistent with findings presented in different dimensions, considering the disorder as a form of brain functioning that allows us to adapt to the environment and, ultimately, maintain the survival of the species. We focus on the epigenetic regulation of thalamic interneurons as a major player involved in the development of the clinical picture characteristic of schizophrenia.

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Research Idea Thu, 19 Jul 2018 09:41:44 +0300
PhytoAuthent: Molecular authentication of complex herbal food supplements for safety and efficacy https://riojournal.com/article/26986/ Research Ideas and Outcomes 4: e26986

DOI: 10.3897/rio.4.e26986

Authors: Mihael Ichim, Gianina Crisan, Carmen Tebrencu, Hugo de Boer

Abstract: The PhytoAuthent project was structured to gather, test, develop and apply, in real life case scenarios, molecular techniques, such as biochemical fingerprinting and DNA sequence-based methods, for plant identification of constituents in complex herbal products. The project had a strong focus on applied aspects like protecting consumers from health risks associated with product substitution and contamination of herbal products.

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Project Report Wed, 30 May 2018 08:56:47 +0300
Task-based assessment of visualization tools for the comparison of biological taxonomies https://riojournal.com/article/25742/ Research Ideas and Outcomes 4: e25742

DOI: 10.3897/rio.4.e25742

Authors: Lilliana Sancho-Chavarria, Fabian Beck, Daniel Weiskopf, Erick Mata-Montero

Abstract: Maintenance and curation of large-sized biological taxonomies are complex and laborious activities. Information visualization systems use interactive visual interfaces to facilitate analytical reasoning on complex information. Several approaches such as treemaps, indented lists, cone trees, radial trees, and many others have been used to visualize and analyze a single taxonomy. In addition, methods such as edge drawing, animation, and matrix representations have been used for comparing trees. Visualizing similarities and differences between two or more large taxonomies is harder than the visualization of a single taxonomy. On one hand, less space is available on the screen to display each tree; on the other hand, differences should be highlighted. The comparison of two alternative taxonomies and the analysis of a taxonomy as it evolves over time provide fundamental information to taxonomists and global initiatives that promote standardization and integration of taxonomic databases to better document biodiversity and support its conservation. In this work we assess how ten user visualization tasks for the curation of biological taxonomies are supported by several visualization tools. Tasks include the identification of conditions such as congruent taxa, splits, merges, and new species added to a taxonomy. We consider tools that have gone beyond the prototype stage, that have been described in peer-reviewed publications, or are in current use. We conclude with the identification of challenges for future development of taxonomy comparison tools.

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Research Article Thu, 12 Apr 2018 09:30:47 +0300
Transmission Mechanism of Lewy Body-Like α-Synucleinopathies in Dopaminergic Neurons Derived from Human Induced Pluripotent Stem Cells https://riojournal.com/article/25423/ Research Ideas and Outcomes 4: e25423

DOI: 10.3897/rio.4.e25423

Authors: Cheng Lin

Abstract: Grafting of cells in Parkinson's disease (PD) results in a prion-like infection, exhibiting a Lewy body-like pathology, caused by the recipient cells. The transmission mechanism of Lewy bodies is not completely understood. Therefore, a research idea with a novel experimental strategy is proposed to investigate the transmission mechanism of α-synuclein pathology using PD patient-derived human induced pluripotent stem cells (hiPSC) in an in vitro human cellular and molecular PD model and in vivo mouse PD model for dopaminergic neuron transplantation.

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Research Idea Tue, 10 Apr 2018 09:07:45 +0300
FIIND: Ferret Interactive Integrated Neurodevelopment Atlas https://riojournal.com/article/25312/ Research Ideas and Outcomes 4: e25312

DOI: 10.3897/rio.4.e25312

Authors: Roberto Toro, Rembrandt Bakker, Thierry Delzescaux, Alan Evans, Paul Tiesinga

Abstract: The first days after birth in ferrets provide a privileged view of the development of a complex mammalian brain. Unlike mice, ferrets develop a rich pattern of deep neocortical folds and cortico- cortical connections. Unlike humans and other primates, whose brains are well differentiated and folded at birth, ferrets are born with a very immature and completely smooth neocortex: folds, neocortical regionalisation and cortico-cortical connectivity develop in ferrets during the first postnatal days. After a period of fast neocortical expansion, during which brain volume increases by up to a factor of 4 in 2 weeks, the ferret brain reaches its adult volume at about 6 weeks of age. Ferrets could thus become a major animal model to investigate the neurobiological correlates of the phenomena observed in human neuroimaging. Many of these phenomena, such as the relationship between brain folding, cortico-cortical connectivity and neocortical regionalisation cannot be investigated in mice, but could be investigated in ferrets. Our aim is to provide the research community with a detailed description of the development of a complex brain, necessary to better understand the nature of human neuroimaging data, create models of brain development, or analyse the relationship between multiple spatial scales. We have already started a project to constitute an open, collaborative atlas of ferret brain development, integrating multi-modal and multi-scale data. We have acquired data for 28 ferrets (4 animals per time point from P0 to adults), using high-resolution MRI and diffusion tensor imaging (DTI). We have developed an open-source pipeline to segment and produce – online – 3D reconstructions of brain MRI data. We propose to process the brains of 16 of our specimens (from P0 to P16) using high-throughput 3D histology, staining for cytoarchitectonic landmarks, neuronal progenitors and neurogenesis. This would allow us to relate the MRI data that we have already acquired with multi-dimensional cell-scale information. Brains will be sectioned at 25 μm, stained, scanned at 0.25 μm of resolution, and processed for real-time multi-scale visualisation. We will extend our current web-platform to integrate an interactive multi-scale visualisation of the data. Using our combined expertise in computational neuroanatomy, multi-modal neuroimaging, neuroinformatics, and the development of inter-species atlases, we propose to build an open-source web platform to allow the collaborative, online, creation of atlases of the development of the ferret brain. The web platform will allow researchers to access and visualise interactively the MRI and histology data. It will also allow researchers to create collaborative, human curated, 3D segmentations of brain structures, as well as vectorial atlases. Our work will provide a first integrated atlas of ferret brain development, and the basis for an open platform for the creation of collaborative multi-modal, multi-scale, multi-species atlases.

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Grant Proposal Fri, 30 Mar 2018 13:28:50 +0300
The DIARS toolbox: a spatially explicit approach to monitor alien plant invasions through remote sensing https://riojournal.com/article/25301/ Research Ideas and Outcomes 4: e25301

DOI: 10.3897/rio.4.e25301

Authors: Carol X. Garzon-Lopez, Tarek Hattab, Sandra Skowronek, Raf Aerts, Michael Ewald, Hannes Feilhauer, Olivier Honnay, Guillaume Decocq, Ruben Van De Kerchove, Ben Somers, Sebastian Schmidtlein, Duccio Rocchini, Jonathan Lenoir

Abstract: The synergies between remote sensing technologies and ecological research have opened new avenues for the study of alien plant invasions worldwide. Such scientific advances have greatly improved our capacity to issue warnings, develop early-response systems and assess the impacts of alien plant invasions on biodiversity and ecosystem functioning. Hitherto, practical applications of remote sensing approaches to support nature conservation actions are lagging far behind scientific advances. Yet, for some of these technologies, knowledge transfer is difficult due to the complexity of the different data handling procedures and the huge amounts of data it involves per spatial unit. In this context, the next logical step is to develop clear guidelines for the application of remote sensing data to monitor and assess the impacts of alien plant invasions, that enable scientists, landscape managers and policy makers to fully exploit the tools which are currently available. It is desirable to have such guidelines accompanied by freely available remote sensing data and generated in a free and open source environment that increases the availability and affordability of these new technologies. Here we present a toolbox that provides an easy-to-use, flexible, transparent and open source set of tools to sample, map, model and assess the impact of alien plant invasions using two high-resolution remote sensing products (hyperspectral and LiDAR images). This online toolbox includes a real case dataset designed to facilitate testing and training in any computer system and processing capacity.

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Monitoring Schema Fri, 30 Mar 2018 10:03:27 +0300
FluoRAS Sensor - Online organic matter for optimising recirculating aquaculture systems https://riojournal.com/article/23957/ Research Ideas and Outcomes 4: e23957

DOI: 10.3897/rio.4.e23957

Authors: Adam Hambly, Colin Stedmon

Abstract: FluorRAS will develop a sensor that can save recycled fish farms 30% per year in water and energy consumption for water treatment, as well as optimize nitrogen removal. The sensor will be developed in a partnership between engineers (Krüger A / S) and researchers (DTU), and the product will be made available to the entire sector through Danish Aquaculture. Global aquaculture production is expected to double within the next 15 years. Recycling technology has a great potential for supporting environmentally and economically sustainable production. However, the technology has some challenges in balancing both the maintenance of necessary water quality and water treatment costs. Loss of production due to poor water quality is expensive and can be avoided with correct sensor systems. Accumulation of dissolved organic matter and nutrients in the water reduce the effectiveness of UV treatment, is a source of nutrition for opportunistic pathogens, and reduces the effectiveness of the biofilter's removing ammonia. Modern recycling systems are therefore dependent on a network of online sensors that monitor and respond to changes in water quality, but currently there is a need for a sensor to monitor the accumulation of organic matter. FluoRAS aims to fill this gap in technology by developing an online fluorescence sensor. The sensor is based on non-destructive, online optical technology that does not require chemicals and can run continuously.

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Grant Proposal Wed, 31 Jan 2018 10:36:43 +0200
PhytoAuthent: Molecular authentication of complex herbal food supplements for safety and efficacy https://riojournal.com/article/21710/ Research Ideas and Outcomes 3: e21710

DOI: 10.3897/rio.3.e21710

Authors: Mihael Ichim, Gianina Crisan, Carmen Tebrencu, Hugo de Boer

Abstract: The PhytoAuthent project was structured to gather, test, develop and apply, in real life case scenarios, molecular techniques, such as biochemical fingerprinting and DNA sequence-based methods, for plant identification of constituents in complex herbal products. The project had a strong focus on applied aspects like protecting consumers from health risks associated with product substitution and contamination of herbal products.

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Project Report Tue, 17 Oct 2017 16:01:18 +0300
Impaired Cognitive Processes Influence Expressive Language Skills In Attention Deficits https://riojournal.com/article/20662/ Research Ideas and Outcomes 3: e20662

DOI: 10.3897/rio.3.e20662

Authors: Callyn Villanueva

Abstract: This research idea investigates neural interactions by utilizing transcranial magnetic stimulation (TMS) to disrupt neural activities between the frontal and temporal left hemisphere cortices in individuals when performing language related task. The initial purpose is to thoroughly examine how impaired cognitive processes alter expressive language skills in attention deficit disorder and create an experimental design suited for examination.

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Research Idea Mon, 28 Aug 2017 17:10:34 +0300
Origin and diversification of hoverflies: a revision of the genera Asarkina and Allobaccha – A BIG4 Consortium PhD project https://riojournal.com/article/19860/ Research Ideas and Outcomes 3: e19860

DOI: 10.3897/rio.3.e19860

Authors: Trevor Burt, Ximo Mengual

Abstract: This BIG4 PhD project involves the overall taxonomic revision of the genera Allobaccha Curran and Asarkina Macquart (Diptera: Syrphidae). The revisions will be divided by biogeographic region (Afrotropical and Indomalayan) and published accordingly. The publications will be collated as a thesis for submission to the University of Bonn (Rheinische Friedrich-Wilhelms-Universität Bonn, Germany) doctoral program of biology. The goal of this project is to resolve alpha taxonomy and to infer the phylogenetic placement of these genera within the Syrphidae using Next-Generation Sequencing and Anchored Hybrid Enrichment techniques. The techniques undertaken in this project will be applied to future systematic problems in Diptera and testing future phylogenetic hypotheses.

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PhD Project Plan Mon, 7 Aug 2017 13:57:28 +0300
Tools Matter: Comparison of Two Surface Analysis Tools Applied to the ABIDE Dataset https://riojournal.com/article/13726/ Research Ideas and Outcomes 3: e13726

DOI: 10.3897/rio.3.e13726

Authors: Erin Dickie, Steven Hodge, R. Craddock, Jean-Baptiste Poline, David Kennedy

Abstract: We examine the similarity of outputs from Freesurfer version 5.1, Freesurfer version 5.3 and ANTS for the ABIDEI dataset.

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Project Report Wed, 17 May 2017 16:23:00 +0300
Semi-automated Robust Quantification of Lesions (SRQL) Toolbox https://riojournal.com/article/13395/ Research Ideas and Outcomes 3: e13395

DOI: 10.3897/rio.3.e13395

Authors: Kaori L Ito, Julia Anglin, Hosung Kim, Sook-Lei Liew

Abstract: Quantifying lesions in a reliable manner is fundamental for studying the effects of neuroanatomical changes related to recovery in the post-stroke brain. However, the wide variability in lesion characteristics across individuals makes manual lesion segmentation a challenging and often subjective process. This often makes it difficult to combine stroke lesion data across multiple research sites, due to subjective differences in how lesions may be defined. Thus, we developed the Semi-automated Robust Quantification of Lesions (SRQL; https://github.com/npnl/SRQL; DOI: 10.5281/zenodo.557114) 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. Here, we describe the methods implemented in the toolbox.

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Project Report Wed, 3 May 2017 14:30:53 +0300
Gradients of cortical hierarchy in Autism https://riojournal.com/article/13391/ Research Ideas and Outcomes 3: e13391

DOI: 10.3897/rio.3.e13391

Authors: Richard Bethlehem, Marcel Falkiewicz, Jan Freyberg, Owen Parsons, Seyedeh-Rezvan Farahibozorg, Charlotte Pretzsch, Bjoern Soergel, Daniel Margulies

Abstract: Autism is a developmental condition associated with altered functional connectivity. We propose to re-frame the functional connectivity alterations in terms of gradients that capture the functional hierarchy of cortical processing from sensory to default-mode network regions. We hypothesized that this hierarchy will be altered in ASD. To test that, we compared the scale of gradients in people with autism and healthy controls. The present results do not support our hypothesis. There are two alternative implications: either the processing hierarchies are preserved in autism or the scale of the gradients does not capture them. In the future we will attempt to settle which alternative is more likely.

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Project Report Tue, 2 May 2017 11:09:15 +0300
Developing predictive imaging biomarkers using whole-brain classifiers: Application to the ABIDE I dataset https://riojournal.com/article/12733/ Research Ideas and Outcomes 3: e12733

DOI: 10.3897/rio.3.e12733

Authors: Swati Rane, Eshin Jolly, Anne Park, Hojin Jang, Cameron Craddock

Abstract: We designed a modular machine learning program that uses functional magnetic resonance imaging (fMRI) data in order to distinguish individuals with autism spectrum disorders from neurodevelopmentally normal individuals. Data was selected from the Autism Brain Imaging Dataset Exchange (ABIDE) I Preprocessed Dataset.

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Project Report Mon, 20 Mar 2017 09:13:25 +0200
Noise paradoxically increases reliability metrics https://riojournal.com/article/12641/ Research Ideas and Outcomes 3: e12641

DOI: 10.3897/rio.3.e12641

Authors: Jingyuan Chen, Deepika Bagga

Abstract: Lower signal to noise ratio (SNR) of the scanning environment is generally considered to exert a negative impact on the inter-/intra-subject consistency of resting state functional connectivity (RSFC) metrics. Here, we show through simulations that this assumption is not always true - poor SNR may paradoxically increase reliability metrics of RSFC under certain circumstances, due to the reduced senstivity to dynamic changes in brain connectivity.

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Project Report Mon, 13 Mar 2017 10:40:58 +0200
Cluster-viz: A Tractography QC Tool https://riojournal.com/article/12394/ Research Ideas and Outcomes 3: e12394

DOI: 10.3897/rio.3.e12394

Authors: Kesshi Jordan, Anisha Keshavan, Maria Luisa Mandelli, Roland Henry

Abstract: Cluster-viz is a web application that provides a platform for cluster-based interactive quality-control of tractography algorithm outputs. This tool facilitates the creation of white matter fascicle models by employing a cluster-based approach to allow the user to select streamline bundles for inclusion/exclusion in the final fascicle model. This project was started at the 2016 Neurohackweek and BrainHack events and is still under development. We welcome contributions to the Cluster-viz github repository (https://github.com/kesshijordan/Cluster-viz).

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Project Report Fri, 24 Feb 2017 10:24:32 +0200
Loading and plotting of cortical surface representations in Nilearn https://riojournal.com/article/12342/ Research Ideas and Outcomes 3: e12342

DOI: 10.3897/rio.3.e12342

Authors: Julia Huntenburg, Alexandre Abraham, João Loula, Franziskus Liem, Kamalaker Dadi, Gaël Varoquaux

Abstract: Processing neuroimaging data on the cortical surface traditionally requires dedicated heavy-weight software suites. Here, we present an initial support of cortical surfaces in Python within the neuroimaging data processing toolbox Nilearn. We provide loading and plotting functions for different surface data formats with minimal dependencies, along with examples of their application. Limitations of the current implementation and potential next steps are discussed.

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Project Report Thu, 23 Feb 2017 20:12:08 +0200
Laminar Python: tools for cortical depth-resolved analysis of high-resolution brain imaging data in Python https://riojournal.com/article/12346/ Research Ideas and Outcomes 3: e12346

DOI: 10.3897/rio.3.e12346

Authors: Julia Huntenburg, Konrad Wagstyl, Christopher Steele, Thomas Funck, Richard Bethlehem, Ophélie Foubet, Benoit Larrat, Victor Borrell, Pierre-Louis Bazin

Abstract: Increasingly available high-resolution brain imaging data require specialized processing tools that can leverage their anatomical detail and handle their size. Here, we present user-friendly Python tools for cortical depth resolved analysis in such data. Our implementation is based on the CBS High-Res Brain Processing framework, and aims to make high-resolution data processing tools available to the broader community.

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Project Report Thu, 23 Feb 2017 20:09:52 +0200
Mindcontrol: Organize, quality control, annotate, edit, and collaborate on neuroimaging processing results https://riojournal.com/article/12276/ Research Ideas and Outcomes 3: e12276

DOI: 10.3897/rio.3.e12276

Authors: Anisha Keshavan, Christopher Madan, Esha Datta, Ian McDonough

Abstract: 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.

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Project Report Wed, 15 Feb 2017 09:35:20 +0200
Semi-automated Robust Quantification of Lesions (SRQL) Toolbox https://riojournal.com/article/12259/ Research Ideas and Outcomes 3: e12259

DOI: 10.3897/rio.3.e12259

Authors: Kaori Ito, Julia Anglin, Sook-Lei Liew

Abstract: 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.

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Project Report Tue, 14 Feb 2017 11:10:59 +0200
Can video improve grant review quality and lead to more reliable ranking? https://riojournal.com/article/11931/ Research Ideas and Outcomes 3: e11931

DOI: 10.3897/rio.3.e11931

Authors: Michael Doran, Adrian Barnett, Joan Leach, William Lott, Katie Page, Will Grant

Abstract: 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”.

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Small Grant Proposal Wed, 1 Feb 2017 13:43:17 +0200
Technical aspects of preprint services in the life sciences: a workshop report https://riojournal.com/article/11825/ Research Ideas and Outcomes 3: e11825

DOI: 10.3897/rio.3.e11825

Authors: John Chodacki, Thomas Lemberger, Jennifer Lin, Maryann Martone, Daniel Mietchen, Jessica Polka, Richard Sever, Carly Strasser

Abstract:

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Workshop Report Mon, 16 Jan 2017 17:32:18 +0200
Data Management Plan for a Biotechnology and Biological Sciences Research Council (BBSRC) Tools and Resources Development Fund (TRDF) Grant https://riojournal.com/article/11624/ Research Ideas and Outcomes 3: e11624

DOI: 10.3897/rio.3.e11624

Authors: Laurent Gatto

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Data Management Plan (Biosciences) Thu, 5 Jan 2017 10:46:27 +0200
Data Management Plan for Moore Investigator in Data Driven Discovery Grant https://riojournal.com/article/10708/ Research Ideas and Outcomes 2: e10708

DOI: 10.3897/rio.2.e10708

Authors: Ethan White

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Data Management Plan (Biosciences) Tue, 4 Oct 2016 09:06:38 +0300
Functional characterization of the several splice variants of Fmr1 https://riojournal.com/article/10593/ Research Ideas and Outcomes 2: e10593

DOI: 10.3897/rio.2.e10593

Authors: Megha Abbey

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Research Idea Wed, 28 Sep 2016 10:22:21 +0300
Improved understanding of brain morphology through 3D printing: A brief guide https://riojournal.com/article/10398/ Research Ideas and Outcomes 2: e10398

DOI: 10.3897/rio.2.e10398

Authors: Christopher Madan

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Methods Thu, 8 Sep 2016 11:58:18 +0300
Migration of legacy data to new media formats for long-time storage and maximum visibility: Modern pollen data from the Canadian Arctic (1972/1973) https://riojournal.com/article/10269/ Research Ideas and Outcomes 2: e10269

DOI: 10.3897/rio.2.e10269

Authors: Harvey Nichols, Susann Stolze

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Data Management Plan (NSF Generic) Thu, 25 Aug 2016 08:02:29 +0300
Improved understanding of brain morphology through 3D printing: A brief guide https://riojournal.com/article/10266/ Research Ideas and Outcomes 2: e10266

DOI: 10.3897/rio.2.e10266

Authors: Christopher Madan

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Methods Tue, 23 Aug 2016 12:32:35 +0300
Chimeric spider silk production in microalgae: a modular bionanomaterial https://riojournal.com/article/9342/ Research Ideas and Outcomes 2: e9342

DOI: 10.3897/rio.2.e9342

Authors: João Vitor Molino, Tiago Lubiana Alves, Livia Ferreira-Camargo, Miguel Croce, Allan Tanaka, Felipe Buson, Pedro Ribeiro, Antony Campos-Salazar, Eduardo Antonio, André Maizel, Viviane Siratuti, Claudia Costa, Samarina Wlodarczyk, Raquel de Souza Lima, Fabio Mello, Stephen Mayfield, João Carvalho

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Research Idea Thu, 23 Jun 2016 10:33:17 +0300
Benefits and costs of aphid phenological bet-hedging strategies https://riojournal.com/article/9580/ Research Ideas and Outcomes 2: e9580

DOI: 10.3897/rio.2.e9580

Authors: Jens Joschinski

Abstract: 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.

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PostDoc Project Plan Fri, 17 Jun 2016 14:30:10 +0300
Open Neuroimaging Laboratory https://riojournal.com/article/9113/ Research Ideas and Outcomes 2: e9113

DOI: 10.3897/rio.2.e9113

Authors: Katja Heuer, Satrajit Ghosh, Amy Robinson Sterling, Roberto Toro

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Small Grant Proposal Sun, 8 May 2016 10:02:42 +0300
The influence of religion on science: the case of the idea of predestination in biospeleology https://riojournal.com/article/9015/ Research Ideas and Outcomes 2: e9015

DOI: 10.3897/rio.2.e9015

Authors: Aldemaro Romero Jr.

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Research Article Wed, 27 Apr 2016 11:45:46 +0300
Brain Graph Interface https://riojournal.com/article/8817/ Research Ideas and Outcomes 2: e8817

DOI: 10.3897/rio.2.e8817

Authors: Arno Klein

Abstract: 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.

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NIH Grant Proposal Tue, 19 Apr 2016 15:08:27 +0300
A game for crowdsourcing the segmentation of BigBrain data https://riojournal.com/article/8816/ Research Ideas and Outcomes 2: e8816

DOI: 10.3897/rio.2.e8816

Authors: Arno Klein

Abstract: 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.

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NIH Grant Proposal Tue, 19 Apr 2016 15:08:24 +0300
A Million Brains in the Cloud https://riojournal.com/article/8812/ Research Ideas and Outcomes 2: e8812

DOI: 10.3897/rio.2.e8812

Authors: Arno Klein, Satrajit Ghosh

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Research Idea Mon, 18 Apr 2016 22:10:45 +0300
Collection of informatics proposals from 2007 https://riojournal.com/article/8813/ Research Ideas and Outcomes 2: e8813

DOI: 10.3897/rio.2.e8813

Authors: Arno Klein

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Research Idea Fri, 15 Apr 2016 15:10:51 +0300
Concurrence Topology: Finding High-Order Dependence in Neuropsychiatric Data https://riojournal.com/article/8815/ Research Ideas and Outcomes 2: e8815

DOI: 10.3897/rio.2.e8815

Authors: Arno Klein, Steven Ellis

Abstract: 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.

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NIH Grant Proposal Wed, 13 Apr 2016 10:27:52 +0300