DOI: 10.3897/arphapreprints.e181365

Authors: Marie Alavi, Pascal Koch, Laura MacDonald, Katharina Miller, Gustav Nilsonne, Julia Priess-Buchheit, Jörg Scherer, Lea Škorić, Pavel Stoev, Dina Vrkic, Stephen Wyber, Nikol Yovcheva, Cemre Yucebalkan

Abstract: Advancing knowledge valorisation to enable transdisciplinary and cross-sector knowledge circulation is key to upgrading the European research landscape, resulting in economic, digital, ecological, and social benefits. That is why IP4OS advocates for a concerted Intellectual Property (IP) and Open Science (OS) approach: A complementary and supportive link between agile and fitting IP tools and the sharing of Findable, Accessible, Interoperable, and Re-usable (FAIR) research outputs (data, results, codes, etc.). IP4OS's overall goal is to empower multi-professionals and their organisations with awareness, knowledge, skills, and advocacy to valorise FAIR research outputs with effectively fitting IP tools.Firstly, IP4OS will publish a sound Synergy Framework - a Best Practice Manual mapping the relationship between IP and OS, providing recommendations for best practices. Secondly, IP4OS raises 50% more awareness in the Community of Practice (CoP) by informing about advocates, facts and figures on IP tools that support OS practices. Furthermore, IP4OS will reach 300 trained professionals and additionally (at least) 27 multipliers for multi-professional teams from all European countries via several easy-to-use and sustainable educational resources using the Synergy Framework and the Synergy Core Curriculum. Through all of IP4OS’s activities, the project builds a new CoP for IP management to support OS and addresses 15 specific professions in training who are actors, intermediaries, educators, and learners in the R&I landscape.With this approach, IP4OS is fully in line with the objectives and impact expectations of the call, namely (1) to identify the complementary synergy of IP management and OS practices by building on existing resources and practices as well as through a co-creative process of a Multi-Professional Community of Practice including experts and actors of the R&I landscape and (2) to anchor these findings in practice-oriented learning resources and bring them into practice through specialised courses to a broad community. With this process, IP4OS follows the call's core objective: the cross-over empowerment of multi-professionals and their organisations to enrich their IP practices with useful OS principles, thus emphasising value creation and utilisation in IP management and increasing European Research Area’s (ERA) benefits.IP4OS comprises a consortium with complementary expertise from IP management, knowledge transfer and education, research, libraries, and experts from small and medium-sized enterprises (SME) covering legal aspects and dissemination activities. The International Expert Advisory Board (IEAB) comprises renowned representatives from IP and industry, OS, reproducibility, training, knowledge transfer, and entrepreneurship to support the consortium. IP4OS can meet its ambitious goals due to its consortium’s and advisory board’s IP and OS experience, their already established crossover networks and infrastructures, and outstanding expertise.

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DOI: 10.3897/arphapreprints.e176591

Authors: Beatrice Bock

Abstract: Fungi exhibit diverse trophic strategies, ranging from obligate symbiosis to saprotrophy, with some taxa capable of occupying multiple ecological roles. Manually identifying trophic versatility from literature is time-consuming and difficult to scale. Here, we present a pilot workflow that automates the classification of fungal trophic modes using transformer-based language models. A curated dataset of 56 fungal ecology abstracts was manually labelled as dual (occupying multiple trophic modes) or solo (restricted to one mode) and used to fine-tune four models: BioBERT, BERT-base-cased, BERT-base-uncased and BiodivBERT. Stratified 5-fold cross-validation revealed that BioBERT and BERT-base-cased performed equally well (~ 89% accuracy, balanced precision and recall), highlighting the importance of case sensitivity in taxonomic text. BiodivBERT and uncased BERT models underperformed, indicating that domain adaptation alone is not sufficient. This pilot study emphasises reproducibility, transparency and open data integration, offering a generalisable proof-of-concept for linking literature-derived ecological information to existing fungal trait databases such as FUNGuild and FungalTraits. All code and data are openly available to support reuse and scaling to larger datasets.

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DOI: 10.3897/arphapreprints.e174548

Authors: Luciana Chavez Rodriguez, Guilherme Oyarzabal, Bruno Eleres Soares, Alejandra Guzmán Luna, César Marín

Abstract: A brain drain phenomenon, i.e., the migration of highly skilled professionals, has represented and still represents a severe loss of intellectual capital for Global South countries. Factors driving this migration include limited research infrastructure, funding constraints, political instability, and the lack of scientific career prospects in the Global South, and the consequences are multifaceted. While this can hinder local development in the Global South, it simultaneously enriches research ecosystems in the Global North, exacerbating existing global inequalities in science and technology. Under this scenario, scientific diasporas represent an effort to counterbalance the brain drain scenario through initiatives that aim to increase science and technology, which are led by self-organized expat professionals and scientists. While we can find some successful examples of international cooperation driven by scientific diasporas, without a proper organization and full participation of the governments of the countries of origin, scientific diasporas can become dysfunctional and can promote more migration upon training. We, five early-career scientists, discuss our perspectives and personal reflections on scientific diasporas. We describe three migration models of highly skilled professionals, starting with a brain drain model, scientific diaspora, and dysfunctional scientific diaspora, and provide some ideas to help the implementation of successful scientific diasporas. We believe that migration must be a personal decision seeking scientific growth and professional development, and not the only option we should have to pursue a fulfilling career in science.

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DOI: 10.3897/arphapreprints.e168447

Authors: David Kinyonyi, Johnson Mwebaze

Abstract: This research focused on the development of a cost-effective IoT-enabled smart agriculture system meant to address the specific challenges that smallholder farmers are facing in Butaleja District (Uganda). The challenges included limited resources, dependence on traditional farming methods and vulnerability to climate change. The proposed system integrated low-cost IoT sensors to monitor critical environmental parameters such as soil moisture, temperature and weather conditions combined with cloud-based and offline edge analytics. It further provided real-time actionable insights to farmers via SMS (Short Message Service) and user-friendly platforms enabling improved irrigation management, optimized resource usage and enhanced crop productivity. Usability was prioritized through designing the system with the ability to operate in low-connectivity environments and ensuring ease of usage for farmers with minimal technical expertise. The system’s design and functionality were validated through the execution of multiple simulations proving its ability to accurately monitor environmental parameters, predict when irrigation is to happen using a machine learning model ensuring efficient irrigation management. The simulation also highlighted the effectiveness of integrating SMS notifications and real-time analytics, ensuring accessibility for farmers with minimal technological expertise. By addressing the unique needs of smallholder farmers, the study offers a scalable, sustainable and impactful solution for transforming agriculture in resource-constrained regions with potential applications beyond Uganda. Future work is intended to explore scaling the system to diverse agricultural contexts, assessing its socio-economic impacts and integrating renewable energy solutions to enhance sustainability.

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DOI: 10.3897/arphapreprints.e165146

Authors: Priscila Gil

Abstract: Latent viral infections, such as those caused by Herpes Simplex Virus (HSV), Human Immunodeficiency Virus (HIV), and Epstein-Barr Virus (EBV), remain a major obstacle to achieving complete viral eradication. These pathogens establish dormancy within host cells, effectively evading immune detection and undermining standard antiviral therapies. This research proposal outlines a three-phase strategy that integrates nanotechnology and molecular biology to selectively reactivate latent viruses and eliminate them through targeted capture and neutralization mechanisms. By employing biomimetic nanostructures and phase-specific activation triggers, this approach seeks to minimize off-target effects and collateral damage, offering a controlled and replicable platform for treating chronic viral infections.

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DOI: 10.3897/arphapreprints.e163819

Authors: Laurel Haak, Katherine Skinner, Kristen Ratan

Abstract: Research activities utilise and depend on interlocking infrastructures – tools, standards, protocols, and other systems and structures at local, national, and international scales that enable researchers to collaborate, analyze and share data and software, and discuss their research findings. Despite growing policy momentum towards open science, a significant challenge persists: a substantial portion of research infrastructure remains inherently closed or restrictive. This lack of openness undermines transparency, integrity, limits reproducibility, and constrains researchers’ ability to fully engage with each other. In this paper, we examine how research infrastructures can be designed to embed open principles throughout their development and operation, borrowing elements from Manufacturing Principles, Systemic Service Design, and Open Science frameworks. We propose an open-by-design reference framework for infrastructure builders and guidance for enabling, making visible, and incentivizing specific elements of “openness” within research infrastructures that are prerequisites for a thriving research and knowledge ecosystem.

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DOI: 10.3897/arphapreprints.e157676

Authors: Davide Raho, Andrea Tarallo, Ilaria Rosati

Abstract: This poster presents the ParAqua database, the first structured initiative aimed at centralising and harmonising data on zoosporic parasites of algae by integrating in situ observations, genetic data from NCBI, and literature sources. The database includes standardised information on parasite and host taxonomy, observation variables, genetic identifiers, and bibliographic metadata. Built with controlled vocabularies (Darwin Core, LifeWatch Traits Thesaurus, Dublin Core), the platform features a user-friendly web application offering structured query tools, a navigable data table, CSV downloads, and a stateless RESTful API for programmatic access. This resource supports researchers in identifying knowledge gaps and advancing parasitological and ecological studies. This work was presented as a poster at the CNR-IRET Conference held in Rome, February 18–19, 2025.

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DOI: 10.3897/arphapreprints.e144181

Authors: Manfred Asiedu, Gideon Twieku, Rhoda Lims

Abstract: We propose to explore an eco-friendly and sustainable approach to malaria control by employing fish as biological agents to reduce mosquito populations. Given the rising challenges of insecticide resistance and the environmental concerns associated with chemical interventions, this project investigates the effectiveness of fish species in consuming mosquito larvae, thereby lowering the prevalence of malaria vectors. Through a combination of laboratory experiments, ecological assessments and community engagement in malaria-endemic regions, the project will identify optimal fish species for this purpose, assess their impact on local ecosystems and gauge community perspectives on adopting fish-based malaria control methods. Key objectives include evaluating predation efficiency, determining ecological compatibility, quantifying the reduction in malaria transmission and fostering local involvement to enhance sustainability. This innovative approach has the potential to provide a scalable, environmentally conscious solution for malaria management, contributing to global public health efforts and advancing sustainable disease control strategies.

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DOI: 10.3897/arphapreprints.e139375

Authors: Lane Rasberry, Daniel Mietchen

Abstract: Various sources describe Wikipedia's popularity in different ways, including by count of its users, frequency of use, and its utility as an information resource in many fields of knowledge. The Wikimedia Foundation has claimed that Wikipedia has reached billions of readers; commercial web traffic services have ranked Wikipedia as a top-10 website by popularity; and researchers analyzing demographic surveys and user behavior metrics have described Wikipedia readers in enough detail to identify general trends. Researchers note that Wikipedia traffic data is public for examination, and also that the Wikipedia volunteer editorial community invites transparency by developing ethical guidelines to encourage analysis of Wikipedia's impact. Although Wikipedia is popular and its audience metrics are accessible, Wikipedia is unlike comparable media platforms and services in that it is rarely the target of professional, expert, or sponsored content development. We review the literature describing Wikipedia, and offer commentary on the dual nature of Wikipedia as simultaneously a popular communication channel and a media outlet with little documented recognition for its success in reaching audiences.

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DOI: 10.3897/arphapreprints.e127906

Authors: James Morris

Abstract: Community tutelary shrines in Taiwan have been identified as excellent resources for grassroots-level heritage. As community ritual assemblages, they are able to encode data about a settlement’s social, political, and economic history in their material composition, aesthetic choices, artifacts, displays, and orientations. This data paper previews a first edition dataset related to 752 such shrines found throughout the greater Taipei area in northern Taiwan. It explores the basis for such a dataset, how it can be used, and what has been produced. This dataset is available on the depositar research data repository, operated out of the Institute of Information Sciences at Academia Sinica in Taipei, and is publicly available for download.

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DOI: 10.3897/arphapreprints.e124344

Authors: Milos Stupar, Wejden Gongi, Silke Van den Wyngaert, Alexandra Kraberg, Albert Reñé, Serena Rasconi

Abstract: The objective of this methodological paper is to outline a microscopy protocol for detecting and observing fungal zoosporic parasites of phytoplankton in natural environments, with potential applications in algal biotechnology to enhance the success and sustainability of algal cultivation endeavors. The fluorescent dual staining with wheat germ agglutinin (WGA) and Calcofluor White (CFW) showcased during the Training School "Identification and detection of zoosporic parasites" in Neuglobsow (Germany) from 16th till 18th of May 2023 and organized and funded by COST Action ParAqua (European Cooperation in Science and Technology) illustrated its ease of implementation and suitability for diverse natural and artificial systems.

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DOI: 10.3897/arphapreprints.e124141

Authors: Yousef Gaballah

Abstract: This research proposal aims to replacement of N2 molecule (instead of O2) as a final electron receptor in micro-organisms so that they can produce NH3, which is important industrially, instead of H2O. This idea is based on the hypothesis that replacement of the central atom in gas-carrying compounds in living organisms such as chlorophyll, heme and hemocyanin would replace the fixed gas. However, NH3 is an expensive product because it is produced using Haber-Bosch reaction technique which requires high temperature and pressure. Therefore, it is predictable here to produce NH3 so simply in bioreactors which is a great economic benefit.

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DOI: 10.3897/arphapreprints.e120910

Authors: Maame Ekua Acquah, Frank Aboagye, Yvonne Ashong, Lydia Mosi

Abstract: Schistosomiasis is a neglected tropical disease that affects more than 200 million people and 45% of infections have been shown to occur in school-aged children. A large percentage of the disease burden lies in Africa. In 2012, the WHO outlined a roadmap for the elimination of schistosomiasis by 2020; however, this was not achieved. Treatment for schistosomiasis is by the use of Praziquantel, a drug in use for over 30 years and there is a concern for emerging drug resistance. There are several species of the genus Schistosoma causing infection in humans. For this study, Schistosoma mansoni which causes intestinal schistosomiasis will be investigated. There are reports of lowering cure rates and suboptimal response to praziquantel following several cycles of mass drug administration (MDA). Praziquantel resistance has also been reported in some countries and laboratory-bred schistosome experiments. To address the concerns of resistance, this study aims to employ a two-part approach to assess the prevalence of S. mansoni. praziquantel resistance among school-aged children in schistosomiasis endemic communities in Ghana and develop a diagnostic tool to aid in field assessment of infections. To achieve this, the study will attempt to answer the following research questions: 1. Is there developing S. mansoni praziquantel resistance in communities that have undergone several mass drug administrations? 2. Is there an interplay between intermediate host exposure to praziquantel and the development of praziquantel drug resistance in the definitive host?

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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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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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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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DOI: 10.3897/arphapreprints.e116667

Authors: Benjamin Beuster, Hilde Orten

Abstract: The paper focuses on the technical workflow description of EOSC Future’s Science Project 9 'Climate Neutral and Smart Cities', using reputable data sources such as the European Social Survey (ESS), the European Environmental Agency (EEA), and Copernicus ERA5.A significant contribution of this project to the European Open Science Cloud (EOSC) is its demonstration of cross-domain data integration using the DDI-CDI metadata standard. This serves as a practical example of how the DDI-CDI Process model can offer a standardised methodology for detailing integration processes, thereby ensuring clarity for researchers dealing with integrated data and computed variables.The paper outlines the key elements of the CDI-Process model selected for this approach, which includes around 10 classes such as 'Activity,' 'Step,' and 'Parameter.' These classes form the structural framework for the data integration steps.Additionally, a tool developed under the project visualises the entire workflow as outlined in the CDI workflow description

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DOI: 10.3897/arphapreprints.e113335

Authors: Rebecca Dikow, Corey DiPietro, Michael Trizna, Hanna BredenbeckCorp, Madeline Bursell, Jenna Ekwealor, Richard Hodel, Nilda Lopez, William Mattingly, Jeremy Munro, Richard Naples, Candace Oubre, Drew Robarge, Sara Snyder, Jennifer Spillane, Melinda Tomerlin, Luis Villanueva, Alexander White

Abstract: Applications of artificial intelligence (AI) and machine learning (ML) have become pervasive in our everyday lives. These applications range from the mundane (asking ChatGPT to write a thank you note) to high-end science (predicting future weather patterns in the face of climate change), but because they rely on human-generated or mediated data, they also have the potential to perpetuate systemic oppression and racism. For museums and other cultural heritage institutions, there is great interest in automating the kinds of applications at which AI and ML can excel, e.g., tasks in computer vision including image segmentation, object recognition (labeling or identifying objects in an image), and natural language processing (e.g. named-entity recognition, topic modeling, generation of word and sentence embeddings) in order to make digital collections and archives discoverable, searchable, and appropriately tagged.A coalition of staff, fellows, and interns working in digital spaces at the Smithsonian Institution, who are either engaged with research using AI or ML tools, or working closely with digital data in other ways, came together to discuss the promise and potential peril of applying AI and ML at scale and this work results from those conversations. Here we present the process that has led to the development of an AI Values Statement and an implementation plan, including the release of datasets with accompanying documentation to enable these data to be used with improved context and reproducibility (dataset cards). We plan to continue releasing dataset cards, and for AI and ML applications, model cards, in order to enable informed usage of Smithsonian data and research products.

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DOI: 10.3897/arphapreprints.e109429

Authors: Felix Bach, Kerstin Soltau, Sandra Göller, Christian Bonatto Minella, Stefan Hofmann

Abstract: Effective research data management solutions and infrastructures are crucial for ensuring the long-term preservation, accessibility, and reusability of research data, not only to facilitate the verification and validation of discoveries but also to reduce or even avoid experimental redundancy. We present our first implementation steps of the Fair Digital Object Framework for RADAR, a generic research data repository, and discuss our experience with several approaches as well as their benefits and shortcomings. By embedding signposted typed link headers in our landing pages we increased the interoperability by making them machine-readable and -actionable, enabling the new data visiting paradigm additionally to metadata harvesting using the Open Archives Initiative Protocol for Metadata Harvesting.

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DOI: 10.3897/arphapreprints.e108908

Authors: Ulrich Schwardmann, Tibor Kálmán

Abstract: Based on the notion of a FAIR Digital Object (FDO) record, which is consised of key-value pairs as attributes that are precisely defined in a Data Type Registry and selected in a profile, we show three examples of FDOs from different viewpoints how FDO records can be implemented as Handle PID records. As references to the attribute definitions, the keys determine the value space of the attribute. In the first two examples the profiles enable human readable keys and legacy digital objects to be integrated into FDO records. How legacy metadata from IANA media types can be transformed into structured metadata of appropriate attribute definitions that then can be applied in profiles and FDO records, is described in the third example.

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DOI: 10.3897/arphapreprints.e108817

Authors: Anne Fouilloux, Elisa Trasatti, Federica Foglini, Alejandro Coca-Castro, Jean Iaquinta

Abstract: The numerous benefits of Open Science (OS) and of the four FAIR foundational principles -Findable, Accessible, Interoperable and Reusable- are increasingly valued in academia, although what OS and FAIR entail is still largely misunderstood. In such conditions putting in practice OS and applying the FAIR principles is challenging and underrated. However, realising OS is perfectly within grasp provided that an infrastructure supporting the management of the research lifecycle is available. RoHub is precisely a Research Object (RO) management platform implementing three complementary technologies: Research Objects, Data Cubes and Artificial Intelligence-based Text Mining services. RoHub enables researchers to collaboratively manage, share and preserve their research while they are still working on it (rather than after the work is finished). In this paper, three communities from Earth Sciences, namely Geohazards, Sea Monitoring and Climate Change, demonstrate how RoHub helped them to understand each other and to work openly, and more importantly how communities of practice play an important role in facilitating reuse and interdisciplinary collaboration. These findings are illustrated with several use cases from these various communities.

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DOI: 10.3897/arphapreprints.e107394

Authors: Tina Heger, Jonathan Jeschke, Maud Bernard-Verdier, Camille Musseau, Daniel Mietchen

Abstract: The enemy release hypothesis is a major and well-known hypothesis in invasion biology. Building on a summary of different previous definitions, we provide the following revised definition: “A reduced pressure by enemies in the non-native range positively affects invasion success.” Further, we suggest formalizing the hypothesis in the basic form ‘subject - relationship - object’ to allow for disambiguating the different existing meanings and enhancing their usability by machines.

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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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DOI: 10.3897/arphapreprints.e105207

Authors: Dylan Nguyen

Abstract: With an alarmingly high rate of Long COVID, it is essential to address the lack of understanding of the pathogenesis and susceptibility to Long COVID. This study aims to investigate how symptoms and immunological markers of Long COVID are correlated in order to develop better biomarkers and inform strategies to accurately identify patients at high risk for developing Long COVID. It has been found that underlying health conditions increase the likelihood of developing Long COVID. Additionally, certain symptoms during COVID-19 infection have been linked to Long COVID. However, the immune system activity has not been well investigated for its correlation to the susceptibility and severity of Long COVID symptoms. In our study, human subjects from the United States and United Kingdom will be followed for a year, where they will be tested weekly for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), draw blood for immune system activity analysis, and report symptoms bidaily. Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) will be used to detect and quantify the presence of SARS-CoV-2. Qualitative information about participants will be collected via the ZOE Health Study app to enable the collection of clinical metadata such as symptoms. This study’s unique and sizeable prospective cohort will provide critical knowledge about the susceptibility of patients to Long COVID by pre-existing symptomatology and immune markers. Moreover, we will better understand the possible mechanisms and pathogenesis of the disease.

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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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DOI: 10.3897/arphapreprints.e96718

Authors: Heidi Murray

Abstract: The Florida Keys Mosquito Control District (FKMCD) is an independent taxing district in Monroe County, Florida. The mission of FKMCD is to protect the community and visitors of the Florida Keys from mosquito-borne disease and prevent nuisance mosquitoes from impacting the quality of life of its citizens and the local economy. The State of Florida requires mosquito control programs to provide recorded evidence of mosquito activity prior to pesticide application. Surveillance is an appropriate method to record the abundance and mosquito species present in an area to determine if adulticide applications are necessary. Mosquito surveillance traps have been set by FKMCD since 1998. Trapping is conducted throughout the District to document species composition and abundance.  Mosquito surveillance is used for operational decisions for both nuisance mosquitoes and disease vectors.This data set includes previously unreported mosquito trapping results in Monroe County, Florida. This data set includes trap results collected from CDC light traps and BG Sentinel traps set weekly on Vaca Key, Flamingo Island, Key Colony Beach, Fat Deer Key, Crawl Key, Long Point Key, Grassy Key, Long Key, and Lower Matecumbe Key from January 1, 2018 through December 31, 2021.

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DOI: 10.3897/arphapreprints.e94687

Authors: Shweata Hegde, Ayush Garg, Peter Murray-Rust, Daniel Mietchen

Abstract: Ethical aspects of research are steadily receiving more attention, from descriptions of research that is proposed to be done to the documentation of ongoing research to reports about research already performed. One of the ways in which this trend manifests itself is the increasingly common addition of ethics statements to publications in fields like biomedicine, psychology or ethnography. Such ethics statements in publications provide the reader with a window into some of the practical yet typically hidden aspects of research ethics. As more and more publications are becoming available in full text and in machine readable formats through repositories like Europe PubMed Central, we propose to mine the literature for ethics statements and to extract information about the various aspects of research ethics that they address. The more standardized these statements are, the better the mined materials can be converted into structured and queryable information that can in turn be used to inform efforts towards higher levels of standardization in research ethics. This paper sketches out the motivation for such mining and outlines some methodological approaches that could be leveraged towards this end.

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DOI: 10.3897/arphapreprints.e94590

Authors: Serena Rasconi, Hans-Peter Grossart, Alena Gsell, Bastiaan Willem Ibelings, Dedmer van de Waal, Ramsy Agha, Ariola Bacu, Maija Balode, Meryem Beklioğlu, Maja Berden Zrimec, Florina Botez, Tom Butler, Slawomir Cerbin, Angela Cortina, Michael Cunliffe, Thijs Frenken, Esther Garcés, Laura Gjyli, Yonatan Golan, Tiago Guerra, Ayis Iacovides, Antonio Idà, Maiko Kagami, Veljo Kisand, Jovica Leshoski, Pini Marco, Natasa Mazalica, Takeshi Miki, Maria Iasmina Moza, Sigrid Neuhauser, Deniz Özkundakci, Kristel Panksep, Suzana Patcheva, Branka Pestoric, Maya Petrova Stoyneva, Diogo Pinto, Juergen Polle, Carmen Postolache, Joaquín Pozo Dengra, Albert Reñé, Pavel Rychtecky, Dirk S. Schmeller, Bettina Scholz, Géza Selmeczy, Télesphore Sime-Ngando, Kálmán Tapolczai, Orhideja Tasevska, Ivana Trbojevic, Blagoy Uzunov, Silke Van den Wyngaert, Ellen van Donk, Marieke Vanthoor, Elizabeta Veljanoska Sarafiloska, Susie Wood, Petr Znachor

Abstract: Zoosporic parasites (i.e. fungi and fungi-like aquatic microorganisms) constitute important drivers of natural populations, causing severe host mortality. Economic impacts of parasitic diseases are notable in the microalgae biotech industry, affecting production of food ingredients, biofuels, pharma- and nutraceuticals.While scientific research on this topic is gaining traction by increasing studies elucidating the functional role of zoosporic parasites in natural ecosystems, we are currently lacking integrated and interdisciplinary efforts for effectively detecting and controlling parasites in the microalgae industry. To fill this gap we propose to establish an innovative, dynamic European network connecting scientists, industries and stakeholders to optimize information exchange, equalize access to resources and to develop a joint research agenda. ParAqua aims at compiling and making available all information on the occurrence of zoosporic parasites and their relationship with hosts, elucidate drivers and evaluate impacts of parasitism in natural and man-made aquatic environments. We aim to implement new tools for monitoring and prevention of infections, and to create protocols and a Decision Support Tool for detecting and controlling parasites in the microalgae biotech production. Applied knowledge on zoosporic parasites can feed back from industry to ecology, and we therefore will explore whether the developed tools can be applied for monitoring lakes and reservoirs. Short-Term Scientific Missions and Training Schools will be organised specifically for early stage scientists and managers – with a specific focus on ITC – with the aim to share and integrate both scientific and applied expertise and increase exchange between basic and applied researchers and stakeholders.

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DOI: 10.3897/arphapreprints.e89458

Authors: Ritesh Bhirud

Abstract: Oral cancer is a cancerous growth in the oral cavity. More than 90% of all oral cancers are squamous cell carcinoma. Oral squamous cell carcinoma has the highest mortality ratio compared to other carcinomas. The high mortality rate is mainly due to detection of the cancer in an advanced stage on account of its initial asymptomatic nature. In addition, the methods currently in place for oral cancer detection involve expensive complex laboratory procedures and usually longer wait times for patients leading to late diagnosis. Further, the treatments for advanced staged cancers are costly and less effective in terms of the post-treatment survival rates. Thus, society needs an easy-to-use tool for assessing oral cancers at an early stage. The aim of the project is to develop an easily accessible point-of-care kit which will assist in early detection of oral cancer at a low cost. The kit will consist of a complete home-based test which could be easily operated by vulnerable individuals. The test will be based on the patient’s salivary sample and to obtain an oral cancer risk-analysis with detailed statistics on an app. Furthermore, the app will also feature a digital pathology test for an analysis of potential malignancies based on image(s) of the oral cavity. The chemical aspect of the tool will be based on a thermal reaction of formulated Thiobarbituric Acid reagent along with a spectroscopy sensor. The app will be connected to the sensor via Bluetooth and the image screening will be based on deep learning using deep convolutional neural network. 

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DOI: 10.3897/arphapreprints.e86743

Authors: Urmas Kõljalg, R. Henrik Nilsson, Arnold Tobias Jansson, Allan Zirk, Kessy Abarenkov

Abstract: Species have intrinsic value but also partake in a long range of ecosystem services of major economic value to humans. These values have proved hard to quantify precisely, making it all too easy to dismiss them altogether. We outline the concept of the species stock market (SSM), a system to provide a unified basis for valuation of all living species. The SSM amalgamates digitized information from natural history collections, occurrence data, and molecular sequence databases to quantify our knowledge of each species from scientific, societal, and economical points of view. The trading system will necessarily be unlike that of the regular stock market, but the looming biodiversity crisis implores us to finally put an open and transparent price tag on symbiosis, deforestation, and pollution

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DOI: 10.3897/arphapreprints.e79014

Authors: Prasanth Sambaraju

Abstract: Solver is a Microsoft Excel add-in program which is used to find an optimal value for a formula in the objective cell. Solver accomplishes this either by maximizing, minimizing or setting the objective cell value to a specific value. The article presents the utility of in built worksheet events in Excel VBA to save the value of objective cell from each iteration when solver is used for optimization.

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