DOI: 10.3897/rio.12.e202621

Authors: Mohammad Mahfuzur Rahman, James Ojiambo Were

Abstract: This policy brief examines the contribution of brick kilns to Dhaka’s severe air-pollution crisis and argues that persistent emissions reflect failures of governance, enforcement and regulatory coordination rather than a lack of technological alternatives. Drawing on recent epidemiological studies, atmospheric modelling and policy evidence from Bangladesh and across Asia, the brief analyses how seasonal brick production intensifies winter PM2.5 concentrations and contributes to major public-health and economic losses. Although Bangladesh has enacted ambitious environmental legislation, weak institutional capacity, fragmented oversight and entrenched political-economic incentives continue to undermine implementation. The brief evaluates three policy pathways: universal Zigzag 2.0 kiln conversion, substitution towards non-fired construction materials and enforcement intensification through satellite-based monitoring. It recommends a phased five-year national strategy integrating cleaner kiln technology, demand-side reform, targeted enforcement and regional airshed cooperation. Effective implementation could substantially reduce pollution exposure, improve life expectancy and strengthen long-term environmental governance in Bangladesh.

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DOI: 10.3897/rio.12.e193918

Authors: Erica Zaja, Will Brownlie, Rajabu Hamisi, Maja Arsic, Adelaide Asante, Hilary Barraclough, André Bationo, Martin Blackwell, Dana Cordell, James Elser, Oluwole Fatunbi, Kwame Frimpong, Elise Gallois, Enam Gbekor, Kailyn Harris-Gilliam, Philip Haygarth, Ludwig Hermann, Kenneth Irvine, Issy Lewis, Ning Liu, Vincent Logah, Kaushik Majumdar, Muneta Grace Manzeke-Kangara, Eric Mensah, Malika Mezeli, Michael Miyittah, Innocent Muhwezi, Frederick Otu-Larbi, Richard Padi, Kasper Reitzel, Seth Robinson, Collins Tay, Francis Tetteh, Louis Tetteh, Shamie Zingore, Bryan Spears

Abstract: Phosphorus sustains global food production and is, therefore, of crucial importance to human nutrition and health. However, its mismanagement can lead to water pollution and environmental degradation in addition to low crop yields. In many parts of sub-saharan Africa, phosphorus deficiency constrains agricultural productivity and exacerbates food insecurity. Despite these challenges, phosphorus remains a fragmented topic in global and African policy. To address these issues, the 8th Sustainable Phosphorus Summit (SPS8) was convened in Africa for the first time. SPS8 took place in Accra, Ghana, between 30th September and 3rd October 2025. The Summit was an international collaboration, with co-conveners from the Council for Scientific and Industrial Research (CSIR) – Ghana, the Forum for Agricultural Research in Africa (FARA), The UK Centre for Ecology & Hydrology West Africa Office, Lancaster University and Rothamsted Research. In this paper, we give a detailed overview of the key messages and insights that emerged from highlight talks, lectures, working groups and field trips. We also discuss and reflect on the challenges of delivering an inclusive summit, from designing solutions to benefit-sharing. SPS8 demonstrates that inclusive, cross-sector knowledge-exchange events are crucial to support and enable phosphorus sustainability on the continent of Africa and globally and to enable the next generation of interdisciplinary phosphorus researchers.

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DOI: 10.3897/rio.12.e194808

Authors: Nicolae Manta, Cristina Preda, Laurentiu Rozylowicz, Steluta Manolache, Ioana-Minodora Sirbu, Marius Skolka, Cristian Ioja, Iulia Miu, Andreea Nita, Mihai Nita, Iulian Niculae, Mihaela Urziceanu, Eugenia Nagoda, Alina Cislariu, Petronela Camen-Comanescu, Marian Mirea, Lavinia Pindaru, Marius Matache, Paulina Anastasiu

Abstract: Invasive alien species (IAS) represent one of the most significant threats to biodiversity in Romania and across the European Union. Despite the adoption of EU Regulation 1143/2014 on the prevention and management of the introduction and spread of IAS, its effective implementation at national level requires substantial institutional, scientific and operational capacity building. Here, we present a comprehensive national project, COMPLIAS Consolidarea Sistemului National de Management al Speciilor Alogene Invazive din Romania in Conformitate cu Cerintele UE / Strengthening the National Management System for Invasive Alien Species in Romania in Compliance with EU Requirements, SMIS 337191, funded under the Sustainable Development Programme (PDD/216, Priority 2, Specific Objective RSO 2.7) and implemented by the University of Bucharest in partnership with the Ministry of Environment, Waters and Forests of Romania. The project addresses all major obligations under EU Regulation 1143/2014 through seven interconnected work packages: (WP1) updating the regulatory and strategic framework, including the revision of the Invasive Alien Species Action Plan (IAS action plan); (WP2-WP4) comprehensive inventory and mapping of invasive alien species (plants, vertebrates and invertebrates) across Romania; (WP5) developing an early detection and border control system for IAS; (WP6) species distribution modelling, impact assessment and piloting eradication and control techniques for priority IAS; and (WP7) public awareness and stakeholder engagement campaigns. The project will also produce legally binding outputs, including a revised IAS action plan approved by Ministerial Order and mandatory country reports to the European Commission. This paper describes the project's objectives, methodological approach, expected outcomes and its contribution to the EU Biodiversity Strategy for 2030.

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DOI: 10.3897/rio.12.e177555

Authors: Jordy van den Berg

Abstract: The relationship between self-efficacy and self-leadership has been widely explored, with research indicating that higher perceived self-efficacy is positively associated with effective self-leadership. Self-leadership has been a focus of attention in recent studies, particularly with the increasing emphasis on the context of knowledge work, where self-leadership is associated with job performance, motivation and job satisfaction. As organisations shift towards less hierarchical and more team-based organisations, self-leadership, which involves guiding oneself through internal drive rather than external leadership, has become significant. However, much is unknown about early self-leadership development, especially as it pertains to contextual factors, such as childhood exposure to domestic violence. Specifically, prior work suggests that childhood exposure to domestic violence negatively impacts self-efficacy, but the long-term impact on self-leadership is unclear.This study explores the influence of childhood experiences with domestic violence on adult self-leadership and self-efficacy. The findings show a small, but not significant difference in the self-efficacy and self-leadership of individuals who experienced childhood domestic violence versus those who did not. This research extends leadership development research by exploring early life contextual factors as potential influences on self-efficacy and self-leadership. Practically, this study emphasises the value of trauma-informed leadership development initiatives and highlights that certain factors may buffer the long-term impacts of childhood trauma.

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DOI: 10.3897/rio.12.e183261

Authors: Enriko Kroon, Ricardo Borges, Rômulo de Jesus, Stefan Kuhn

Abstract: It has been shown that it is possible to train a (simple) neural network to classify nuclear magnetic resonance spectra by a substructures either being part of the chemical structure measured or not. We now explore the interpretability of such models using techniques from explainable AI, specifically Grad-CAM. We show that those techniques do not give ideal results in the context of NMR, which would be able to identify individual peaks. On the other hand, they enable a better interpretation of the results than those metrics just based on "right or wrong". We can also confirm the result from our previous work, that the trained network performs well for pure compounds, but its generalisability to mixtures is questionable, a limitation that could only be assumed in the original study.

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DOI: 10.3897/arphapreprints.e182926

Authors: Richard Marijnissen, Dirk S. van Maren, Luis Garrote, David Santillan, Ana Iglesias, Subbiah Bharathi, Xavier Sánchez-Artús, Vicente Gracia, Manuel Espino, Agustín Sánchez-Arcilla, Luciana Villa Castrillon, Benjamin Jacob, Johannes Pein, Wei Chen, Joanna Staneva, Pushpa Dissanayake, Dennis Oberrecht, Andreas Wurpts, Reinier Schrijvershof, R.J.A van Weerdenburg, Frederica Zennaro, Fabienne Horneman, Elisa Furlan, Silvia Torresan, Andrea Critto, Christophe Briere, Julien Fornasari, Rémi Caillibotte, Claire Mahe, Alexis Beudin, Rosaria Ester Musumeci, Massimiliano Marino, Sofia Nasca, Ahmad Alkharoubi, Luca Cavallaro, Enrico Foti, Nikolay Valchev, Petya Eftimova, Elitsa Hineva, Nataliya Andreeva, Grzegorz Różyński, Morgane Jolivet, Thomas Faraon, Olivier Boutron, Mathis Cathala

Abstract: Within this portfolio of restoration interventions, we present a range of model-based projections assessing the impact of large-scale Nature-based Solutions (NbS) on enhancing Eco System Services (ESS) in various coastal systems. This deliverable applies these models to detail how these systems respond to climate change and nature-based interventions intended to mitigate climate change impacts under different Sea Level Rise (SLR) scenarios. The models range from hydro-morphological simulations of future conditions to a machinelearning approach, all aimed at demonstrating the ESS provided by restoration in the future.

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DOI: 10.3897/arphapreprints.e182685

Authors: Aafke Schipper

Abstract: The EU Biodiversity Strategy for 2030 aims to put biodiversity on the path to recovery by 2030. A key component of the Strategy is the development of a coherent Trans-European Nature Network (TEN-N), to increase the coherence of the existing network of Natura 2000 sites and other nationally designated protected areas by addressing gaps in the coverage of priority habitats and species. The NaturaConnect project supports the design of a TEN-N, amongst others by designing and developing a future-proof blueprint through spatial conservation prioritisation. In this context, it is key to consider multifunctionality, that is, to ensure that the TEN-N addresses not just ecological representativeness but also the ability of nature to meet societal needs or demands through the provisioning of ecosystem services (ES).The present deliverable of NaturaConnect (D4.2) provides a set of ES layers aligned with present and potential future land and climate conditions, designed for use in spatial conservation prioritisation. We generated layers for a selection of regulating and cultural ES, with a focus on climate change mitigation (carbon storage and sequestration) and adaptation (e.g., improving soil retention considering expected increases in the magnitude and frequency of heavy rainfall events), food security (crop pollination, pest control), as well as the capacity of nature to improve people’s mental and physical health by offering opportunities for recreation and experiencing nature. We quantified all ES based on common input data with regard to land systems and climate, to ensure compatibility. Where possible and relevant, we considered ES supply, demand and flow separately.We quantified carbon storage and sequestration according to a book-keeping approach, assigning typical values of the amounts of carbon stored (MgC/ha) and sequestred (MgC/ha/yr) to each land system. We considered only the supply of carbon storage and sequestration, reasoning that the demand for this service is global and considerably larger than the supply. The amounts of carbon stored and sequestered are based on values from the scientific literature and existing datasets which indicate how much carbon is stored and sequestered per land system, and how this would change if the land system underwent a transition (e.g. from forest to cropland). Output maps revealed that forests and wetlands, especially in northern Europe, are characterised by the highest carbon storage and sequestration rates. Croplands are characterised by negative sequestration rates, hence act as sources of emission.We quantified the supply of soil retention based on the ability of vegetation to prevent soil erosion induced by heavy rainfall events, using the universal soil loss equation (RUSLE) to assess soil erosion. Specifically, we quantified the soil retention service (t/ha/yr) based on how much soil loss is prevented by the current vegetation cover, defined per land system, as compared to a counterfactual situation without vegetation. We also quantified the potential additional prevention of soil loss (t/ha/yr) if the vegetation were restored from its current state to a maximum cover. We defined soil retention demand based on the amount of soil loss to be prevented in order to ensure that losses would not exceed the natural soil formation rate. Output maps revealed hotspots of actual and potential additional soil retention demand, supply and flow mainly in mountainous regions, reflecting the key role of terrain slope in determining erodibility as well as the importance of vegetation for reducing it.We modelled the supply of crop pollination based on the potential of pollinator habitat to provide pollinators and the demand based on the presence of nearby cropland in need of pollination. Using observational data from scientific literature and existing databases, we first established a quantitative relationship that estimates wild pollinator abundance in pollinator-dependent cropland (n/m2) based on various ecologically relevant covariates, including the proportion of pollinator habitat within 3 km from the cropland cell. We used this relationship to map pollinator abundance in croplands across Europe, which we subsequently attributed to the cells with pollinator habitat (i.e., the service-providing units) within 3 km from each focal cropland cell, to facilitate application of the model results in spatial conservation prioritisation. Output maps reveal high pollinator abundance values for habitat cells located in areas dominated by cropland, as these habitat cells serve multiple cropland cells, and low values when multiple habitat cells surround a single cropland cell.To assess forest recreational potential, we developed a spatial model based on people’s preferences for forests with different structural characteristics, expressed through the willingness-to-travel (WTT) indicator. Using data from a large-scale visual choice experiment conducted in 12 European countries, we estimated WTT as a function of forest management classes, combined with spatial data on canopy height and tree species diversity. The result is the first Europe-wide map of forest recreational potential, revealing particularly high values in regions with taller, more diverse, and structurally complex forests.We modelled landscape recreational potential based on the recreational opportunities associated with the land systems surrounding each grid cell. We quantify supply based on the number and diversity of land systems that provide recreational opportunities within a given distance from each focal grid cell, and the demand based on the number of potential beneficiaries within a certain distance. Well-supplied areas encompass, among others, the western Iberian peninsula (Portugal) and the Pyrenees, the Auvergne, Rhone-Alpes, and the Provence-Alpes-Cote d’Azur in France, Ireland, Scotland, the Alps and Dinarides as well as the Baltics (Estonia, Latvia), and large parts of the Scandinavian Peninsula and Finland. Demand is particularly high for the European megacities and the various conurbations and metropolitan areas.Finally, we modelled nine regulating and five cultural species-based ecosystem services provided by terrestrial vertebrate species, including, among others, carrion removal, control of pest species (bark beetles, mosquitoes) and evolutionary heritage. For each service, we modelled supply based on the number of specific vertebrate species able to provide a certain service and demand based on the land system in a grid cell assumed to be in need of the service. Resulting maps show distinct patterns for the different ES, revealing the richness of provider species in areas with demand for each service.The ES layers described in this report were primarily developed to support broad-scale spatial conservation or restoration prioritisation efforts, i.e., efforts to identify and rank planning units (in this case grid cells) based on features considered in need of conservation or restoration. In the NaturaConnect project, the ES layers will be used together with layers of other relevant variables, such as biodiversity features, habitat connectivity and the costs of conservation, to identify pan-European conservation priorities. Beyond NaturaConnect, we expect our layers to be useful in particular for national and sub-national governmental and non-state authorities responsible for land planning, as our maps can help in identifying sites where ES supply or flow are high (indicating a need for conservation) or where demand is high yet supply is low (indicating a need for restoration). This way, we expect the layers and underlying code to be useful for informing land management and conservation planning also beyond the project.

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DOI: 10.3897/arphapreprints.e180508

Authors: Christopher John Topping, Noa Simon Delso, James Henty Williams, Johan Axelman

Abstract: EU chemical regulation remains slow, costly, and prone to “ecological surprises” such as unforeseen negative impacts, delayed neonicotinoid bans and ongoing pollinatordecline. Current approaches create silos, overlook cumulative impacts, and trap decisions in binary “safe/unsafe” categories.A systems-first, tools-second approach can deliver faster, cheaper, and more effective decisions by prioritising simulation and systems understanding before developing regulatory tools forEnvironmental Risk Assessment (ERA). Horizon Europe’s PollinERA project demonstrates how this can work in practice: building a prototype One Systemworkflow with interoperable data and models for pollinator risk assessment; an approach that can be expanded to other environmental domains.

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DOI: 10.3897/rio.11.e176120

Authors: Christos Arvanitidis, Olga Ameixa, Alberto Basset, Eva Chatzinikolaou, Claudia Coman, Berta Companys, Francesco De Leo, Klaas Deneudt, Federico Drago, John Eriksson, Tiziana Ferrari, Teodor Georgiev, Giovanni Giuliano, Stefan Gruber, Jens Habermann, Katharina Heil, Tim Hubbard, Cristina Huertas Olivares, Georgios Kotoulas, Dimitris Koureas, Natalia Manola, Vanessa Marrocco, Nicolas Pade, Ana Portugal Melo, Antonello Provenzale, Fotis Psomopoulos, Niels Raes, Susie Robinson, Patrick Ruch, Dick Schaap, Adrian Stanica, Tassos Stavropoulos, Heliana Teixeira, Peter van Tienderen, Costas Tsigenopoulos, Robert Waterhouse, Giuseppe Aprea, Michel Boër, Ana Casino, Laurent Delauney, Jonathan Ewbank, Ana Lillebø, Michael Mirtl, Jana Pavlic-Zupanc, Lyubomir Penev, Jaume Piera, Paraskevi Pitta, Ingrid Puillat, David Richter, Diana Stepanyan, Anton Ussi, Jan Węsławski, Gabriela Zuquim

Abstract: The interdependence of human, animal, plant and ecosystem health necessitates systemic, cross-domain collaboration to address global challenges, such as emerging diseases, climate change and biodiversity severe change. Through the Crete Declaration, Europe’s (e-)infrastructures, organisations and projects that focus on the functioning of our biosphere commit to jointly advancing the One Health approach. In doing so, the signatories aim to strengthen Europe’s resilience and leadership through the sharing of data and expertise, the development of innovative solutions and the promotion of evidence-based policies.

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DOI: 10.3897/rio.11.e164067

Authors: Sara Klingenfuß, Manuel John, Tuulikki Halla, Theresa Klara Loch, Philipp Mack, Barbara Meyers, Ronja Mikoleit, Taru Peltola

Abstract: The forest understory plays a central role in ecological processes and human experiences of forests, yet it often remains overlooked in forest management and conservation. In this interdisciplinary workshop, researchers from Finland and Germany came together to explore the understory through multiple lenses—ecological, cultural, social, and sensory. The participants acknowledged and discussed diverse forms of knowledge related to the understory, from scientific to traditional and place-based, to better understand the many ways people relate to it. Through shared readings, discussion, and direct engagement in the forest, we reflected on how the understory shapes foraging practices, sense of place, human–nature relationships, and alternative forest economies. We discussed what it means to "know" the understory, who holds this knowledge, and how it influences forest governance. This report brings together the key themes, questions, and ideas that emerged, highlighting the understory not only as a biological layer, but as a space where ecological, cultural and political dimensions meet. In doing so, we aim to provoke rethinking dominant forest perspectives and encourage more inclusive and relational ways of valuing and managing European forests.

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DOI: 10.3897/arphapreprints.e167392

Authors: Anita Franco, Katie Smyth, Michael Elliott

Abstract: Marine biodiversity is adversely affected by many human activities and their pressures. As such, there is the need for a cause-consequence-response method to objectively address the risks associated with those adverse changes. Such a method is the ISO-accredited Bow-tie technique as an objective and structured approach giving the causes, preventative control measures, mitigation and compensation measures and consequences of changes to biodiversity. Here, the Bow-tie method underpinned by the cause-consequence-response DAPSI(W)R(M) framework was used and adapted to help managers map out risks to biodiversity requiring management of the human activities and their relevant pressures, in specific case study areas (termed Broad Belt Transects, BBTs). Instead of using restrictive proprietary software, a more-flexible template framework was developed in Microsoft PowerPoint to allow a broad user base. This employed standardised lists of elements (and further adapted during the application process) allowing the development of unique, but standardised and directly comparable Bow-ties for all BBTs. The methods of developing the template and standardised lists are described together with the techniques used to help quantify this usually qualitative approach. The successful application of the Bow-tie method in case studies from the European seas shows the adaptability of this approach in ways wider than the original policy-driven risk-assessment use. Although designed for European seas, the approach and standardised lists are sufficiently generic for adoption in wider areas worldwide.

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DOI: 10.3897/arphapreprints.e166451

Authors: Lorenzo Latini, Giorgio Massaro, Stefania Coppa, Jacopo Giampaoletti, Giuseppe de Lucia, Alessia Dinoi, Paolo Magni

Abstract: The Gulf of Oristano Area, located on the central-western coast of Sardinia (Italy, Mediterranean Sea), is a highly diverse and ecologically valuable region. This area features a mosaic of habitats, supports rich biodiversity, and sustains traditional fishing practices. It is also protected under various international and EU conservation frameworks. However, despite its ecological importance, the Gulf Area faces growing pressures from human activities such as overfishing, eutrophication, habitat loss, and the introduction of non-native species. This study applies a bow-tie risk analysis framework to identify key drivers, pressures, and consequences associated with three central ecological events: species decline and loss, habitat change, and increased competition with non-native species. Stakeholder consultations and standardized classification systems inform the assessment, highlighting the interplay between legal fishing, tourism, aquaculture, pollution, and infrastructure development. The analysis identifies both prevention and mitigation measures, such as spatial planning, environmental monitoring, citizen science, and sustainable tourism and fisheries initiatives. While the environmental regulation of the Gulf of Oristano Area provides a basis for ecosystem protection, persistent challenges – such as enforcement, fragmented governance, and low stakeholder engagement – hinder effectiveness. To ensure ecological integrity and socio-economic resilience in the central-western Sardinian coast, this study underscores the need for strengthened integrated coastal zone management, alignment with EU strategies, and investment in adaptive and participatory conservation approaches.

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DOI: 10.3897/rio.11.e152094

Authors: Frank Twum Aboagye, Mawutor Kwame Ahiabu, Maame Ekua Acquah, Queenstar Quarshie, Naa Kumah, Hannah Akahoho, Nfayem Imoro, Abena Enninful, Bill Egyam, Yvonne Ashong

Abstract: The emergence of COVID-19, caused by SARS-CoV-2, led to the widespread use of antigen rapid diagnostic tests (AgRDTs) due to their speed, affordability and ease of use. However, the diagnostic sensitivity of AgRDTs has been inconsistent across emerging SARS-CoV-2 variants, with some variants exhibiting reduced detection rates. Thus, AgRDTs have been unreliable in detecting the different variants of SARS-CoV-2. This study explores the molecular mechanisms responsible for this variability, focusing on structural changes in the viral spike (S) and nucleocapsid (N) proteins and how these changes affect antigen-antibody interactions. Using structural biology techniques, such as X-ray crystallography and cryo-electron microscopy, molecular virology approaches like whole genome sequencing, immunoassays including ELISA and surface plasmon resonance (SPR) and computational modelling tools for molecular dynamics simulations, this research will uncover specific mutations that impact diagnostic sensitivity. The results of this study will provide information for the development of next-generation AgRDTs with enhanced sensitivity across diverse viral variants, thereby supporting global efforts in pandemic surveillance and control.

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DOI: 10.3897/rio.11.e156738

Authors: Max Korbmacher

Abstract: In the proposed project, we expect to improve diagnosis and treatment for patients suffering from neurodegenerative diseases by establishing a new biomarker based on deep learning and big data outputs. We will use brain age, a neuroimaging-derived marker of brain health which has previously rarely been tested longitudinally, but not in neurodegenerative disorders. The analyses will help to assess treatment response as well as stratifying and sub-typing neurodegenerative disease, based on brain structural characteristics in addition to multiple other markers of disease expression.

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DOI: 10.3897/rio.11.e156054

Authors: Mihael Ichim, Ruxandra Crețu, Valentin Grigoras, Madalina Popa, Ancuța Raclariu-Manolică, Camelia Stefanache

Abstract: Herbal food supplements produced from medicinal and aromatic plants (MAPs) are becoming increasingly popular to complement synthetic pharmaceuticals. This category of products is regulated under more lenient food product regulations rather than the stringent rules applicable to medicines. The effectiveness and safety of these products rely on various factors, including the varying phytochemical composition of the original plant material, potential adulteration, substitution and contamination from biological and chemical sources. The SAFEMAPS scientific research project aims to provide integrated analytical solutions that enhance the compliance and quality of food supplements derived from aromatic and medicinal plants. This project seeks to improve the safe use of these products by consumers, while promoting the sustainable exploitation of plant biodiversity. Within this project, an experimental model will be developed to assess the identity, authenticity, traceability and quality of herbal food supplements. This model includes analytical solutions that integrate phytochemical and molecular genetic analyses. The proposed solutions will prioritise the needs of the food supplements industry, particularly regarding the quality and compliance of herbal products sold in Romania and across the European single market. These solutions will also tackle various aspects of the supply chain, including growers or collectors of medicinal and aromatic plants, processors, importers and final consumers.

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DOI: 10.3897/arphapreprints.e148125

Authors: Serena Rasconi, Laura Garzoli, Ana Gavrilović

Abstract: Abstracts of talks presented at ParAqua Conference held in Dubrovnik (Croatia), 16-17 April 2024

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DOI: 10.3897/rio.10.e134189

Authors: Vixey Douglas

Abstract: Animal-transmitted diseases such as rabies represent a barrier to successful rewilding and threaten continued human-wildlife co-existence. In North America, population growth and human settlement expansion lead to encounters with wild mammals which have the potential to transmit rabies to domestic dogs and humans. The recent development of gene drives mediated by CRISPR-Cas9 allows for ecosystem engineering at unprecedented scales given the potential to spread new traits through wild populations with biased inheritance exceeding the pattern of classical Mendelian dominant genes. This study of a possible red fox rabies immunity gene drive project contributes a novel proposal to the existing academic conversation about suitable applications of gene drive technology in wild animal populations, such as projects to fight malaria and Lyme disease. Noting the unique characteristics of rabies, such as the dire mortality rate in humans once symptoms arise, as well as the tendency for rabid wild animals to lose their fear of humans, it appears to be a suitable target for eventual eradication via gene drive to spread immunity through wild mammal reservoir populations. Introducing heritable rabies immunity into North American red fox populations through gene drive represents a strategy to both battle rabies and adjust the ecology of (sub)urban environments. Given this review of the project's possible implementation and expected outcomes, providing inherited rabies immunity to wild red fox populations in North America via gene drive appears both feasible and sensible. Similar projects may be used to eradicate comparable infectious diseases from other wild animal populations, with likely benefits to human patients, wildlife and ecosystems.

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DOI: 10.3897/rio.10.e133454

Authors: Yann Hautier, Kathryn Barry, Mariet Hefting, Marijke van Kuijk, Edwin Pos, Betty Verduyn, Rola Johannes, George Kowalchuk, Merel Soons

Abstract: Extreme climate events such as floods and droughts are becoming increasingly frequent and intense across the world. Future climate scenarios predict both an increase in individual extreme events, as well as chronic changes in climatic seasonality. Yet, the combined and relative effects of these pressures on ecosystems remain unknown. Concurrently, human-induced ecological disruption is accelerating species extinction rates, which are estimated to be 100 to 1000 times greater than pre-human levels. This is alarming as greater biological diversity is thought to buffer ecosystem functioning against extreme climate events, thereby safeguarding the provisioning of essential ecological services that contribute to human well-being. However, how and to what extent biodiversity buffers ecosystems against climate variability remains unclear. We recently constructed experimental grassland communities in a mesocosm-based field design representing a realistic gradient of plant diversity. Both extreme events (drought and flood) and a change in seasonality of precipitation are manipulated in a full factorial design to quantify the effects of future seasonal shifts and extremes in precipitation. We will: 1) determine to what extent higher biological diversity ensures that grasslands can continue to provide multiple ecosystem services even in the context of climate change and 2) unravel the fundamental mechanisms by which this is achieved including species asynchrony and positive species interactions. Results of our experimental approach will advance our understanding of the buffering potential of plant diversity and contribute to the development of strategies for sustainable service provisioning of our ecosystems in the face of climate change.

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DOI: 10.3897/rio.10.e125508

Authors: Mawutor Kwame Ahiabu, Frank Aboagye

Abstract: Several water assessments of some rivers affected by illegal mining (locally known as galamsey) activities in Ghana have recorded high levels of heavy metals and metalloids (such as lead, cadmium, copper, arsenic, mercury, iron and zinc); this poses significant health threats to communities served by affected rivers. To the best of our knowledge, the haematological study by Armah and colleagues is the only one that revealed staggering folds of blood metal concentrations beyond the WHO-required levels in inhabitants of the Tarkwa Nsuaem Municipality and Prestea-Huni Valley District of Ghana. As inhabitants of communities near galamsey sites are constantly exposed to heavy metals since some individuals rely on polluted rivers for domestic purposes, it is necessary to investigate and understand the threat of hypertension and renal damage associated with this unfortunate situation. We share our perspective and a proposed study to elucidate the exact hypertensive and renal damage associated with heavy metal exposure in galamsey-polluted rivers in Ghana. Onsite/human studies should provide important information about blood metal concentrations and current hypertension, renal function and genetic status of individuals exposed to heavy metals in specific galamsey-infested areas. Experimental studies using Sprague-Dawley rat models should determine the proportion of anthropogenic contribution to the levels of heavy metals in the bloodstream. Furthermore, the experimental studies should determine the extent (concentrations and time) and the possible mechanisms/pathways of galamsey-related heavy metals that trigger the pathogenesis and pathophysiology of hypertension and renal damage.

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DOI: 10.3897/arphapreprints.e134026

Authors: Claudia Fornarini, Alessandra D'Alessio, Jeremy Dertien, Néstor Fernández, Francisco Moreira, Anandi Sarita Namasivayam, Louise O'Connor, Henrique Pereira, Peter Verburg, Carlo Rondinini

Abstract: A key goal of the EU Biodiversity Strategy for 2030 is the design of a connected Trans European Nature Network (TEN-N), that helps to build a coherent and resilient network of protected areas across Europe. The TEN-N will need to consider and integrate societal perspectives on future biodiversity protection in Europe, accounting for multiple values and perspectives of nature. The NaturaConnect project, through a process of co-design with stakeholders, is developing narratives on future nature protection in Europe using the Nature Futures Framework (NFF). In this framework. three value perspectives of nature are presented at each corner of a triangle: Nature for Nature, Nature as Culture, and Nature for Society. By using this framework, NaturaConnect aligns with global efforts on scenario development auspicated by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES). This report outlines the development of scenario narratives for Europe of the NaturaConnect project. The development of the narratives considered the global and European policy context as a starting point, and included a stakeholder engagement process conducted to elicit stakeholders' preferences and visions in relation to future nature conservation and management in Europe. These narratives present contrasting perspectives and priorities for seven themes: Protected areas, Connectivity and Restoration, Forestry, Freshwater ecosystems, Urban system, Agriculture, Energy. These topics are key to building a more positive future for nature and people. Besides specificities for each narrative, we also identify commonalities across the three perspectives, including macroeconomic trend assumptions, biodiversity strategic goals of the European Union and shared solutions that are necessary to achieve any positive nature future.

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DOI: 10.3897/rio.10.e125086

Authors: Bekir Afsar, Kyle Eyvindson, Tuomas Rossi, Martijn Versluijs, Otso Ovaskainen

Abstract: Forests are crucial in supporting biodiversity and providing ecosystem services. Understanding forest biodiversity dynamics under different management strategies and climate change scenarios is essential for effective conservation and management. This paper introduces the Forest Biodiversity Dynamics Prototype Digital Twin (pDT), integrating forest and biodiversity models to predict the effects of management options on forest ecosystems. The primary objective is to identify optimal management strategies that promote biodiversity, focusing on conservation and adaptation to different climate conditions. We start with the case of Finnish forests and bird species and plan to expand to include more European countries and a variety of species as the pDT is further developed.

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DOI: 10.3897/rio.10.e125450

Authors: Simon Rolph, Chris Andrews, Dylan Carbone, Julian Lopez Gordillo, Tomáš Martinovič, Nick Oostervink, Dirk Pleiter, Kata Sara-aho, John Watkins, Christoph Wohner, Will Bolton, Jan Dick

Abstract: Digital twin approaches have the potential to revolutionise usage, planning and management of cultural ecosystem services i.e. the non-material benefits people obtain from ecosystems, including recreation, tourism, intellectual development, spiritual enrichment, reflection and aesthetic experiences.Here, we outline our blueprint for a prototype digital twin (pDT) for cultural ecosystem services. The pDT consists of two modelling components; a recreation potential model to quantify the cultural ecosystem services of the physical landscape and species distribution models to quantify the biodiversity component.It is envisaged that the digital twin will be used primarily by two user types: 1. those who wanted to enjoy the area and potentially contribute to citizen science programmes and 2. people who want to inform or make evidence-based management decisions (land managers, policy-makers, researchers).

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DOI: 10.3897/rio.10.e127123

Authors: Nico Eisenhauer, Cordula Vogel, Luiz A. Domeignoz Horta, Ana Bonato Asato, Zarah Janda, Simone Cesarz

Abstract: Soil is the basis for life on Earth as we know it. Healthy and stable soil is a prerequisite for well-functioning terrestrial ecosystems and has, thus, been proposed to play a key role in plant diversity–ecosystem functioning relationships. The overall objective of this sub-project is to study multidimensional soil stability as affected by plant diversity in a long-term plant diversity experiment. We designed three coordinated work packages (WPs) to comprehensively assess soil multistability to environmental fluctuations and climate extremes by considering the biological, chemical and physical dimensions that are key for soil functioning. We will use all unique facilities and approaches of the Jena Experiment Research Unit by combining synthesis of long-term data in the Main Experiment and the ΔBEF Experiment with performing new soil analyses in the DrY Experiment, the ResCUE Experiment and a joint CoMic Experiment, to gain a better mechanistic understanding of plant diversity–ecosystem functioning relationships. In close collaboration with other sub-projects, we will assess biological, chemical and physical soil properties and stability indicators that will be used to calculate soil multifunctionality and multistability indices. In WP1, we will build on three unique datasets to explore short-term and long-term effects of plant diversity on the stability of soil (microbial) properties. In WP2, we will combine different datasets and approaches to explore if plant diversity effects on the magnitude and stability of soil properties increase with abiotic and biotic stresses. In WP3, we will combine measurements of the above-mentioned dimensions of soil stability to explore if plant diversity increases the stability of multiple soil properties under hot drought. This sub-project is at the heart of the Research Unit by testing the overarching hypotheses outlined in the Coordination Proposal of the Jena Experiment, contributing to all main experiments, sharing data and performing joint sampling campaigns with all sub-projects and, at the same time, introducing a novel concept of soil multistability as affected by plant diversity and climate extremes. We propose to use a combination of simple, high-throughput (e.g. bait-lamina test) and more sophisticated methods (e.g. extracellular polymeric substances analyses) to be able to investigate temporal dynamics of soil processes and their mechanistic basis. Taken together, the results of the three WPs will provide new insights into the stabilising mechanisms of soil properties in the long term and in relation to climate extremes through plant diversity.

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DOI: 10.3897/rio.10.e124177

Authors: Eunice Ayerakwa, Isawumi Abiola

Abstract: Neurocysticercosis, caused by the invasion of the central nervous system (CNS) by Taenia solium larvae, poses a significant global health burden. Despite its prevalence and severe neurological consequences, understanding of the molecular and signalling pathways facilitating parasite dissemination and CNS invasion is limited. The lack of comprehensive knowledge of host-parasite interactions and associated proteins involved in T. solium infection hinders the development of targeted interventions to mitigate its ability to cross the epithelia barrier. This is complicated by reduced oxygen availability in the intestine, a phenomenon called hypoxia. Hypoxia can result in epithelial barrier disruption and cell damage, thereby promoting the translocation and dissemination of T. solium. This study aims to establish the role of hypoxia in T. solium invasion and disseminated infections. The effect of hypoxia on the migration, viability and morphological characteristics of T. solium would be determined using transwell invasion assays, flow cytometry and microscopy. T. solium oncosphere development and dissemination under hypoxic and normoxic conditions will be monitored using animal models. Also, host-parasite transcriptome and proteome profiling will be performed to determine pathways triggered under hypoxic conditions. It is expected that hypoxia would promote the invasion and dissemination of T. solium by enhancing epithelial and endothelial cell permeability. , hypoxia will induce the expression of binding and adhesion proteins and other virulence markers such as enolase, serpin, and glutathione transferases that are involved in host invasion. Understanding the role of hypoxia in the translocation mechanism of T. solium can be leveraged to provide insights into host tissues dissemination and the development of appropriate interventions.

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DOI: 10.3897/rio.10.e116907

Authors: Tosin Senbadejo, Isawumi Abiola, Lily Paemka

Abstract: Uterine fibroid (UF) is the most prevalent benign tumour that affects millions of women globally, with a high incidence of 70% amongst women of reproductive age. UF has been associated with various complications, such as recurrent surgeries, infertility, anemia and pregnancy loss. Notably, women of African descent often experience more severe symptoms and complications. Although hormones, growth factors, and genetic alterations are widely associated with UF, the precise mechanism underlying its pathogenesis is not fully understood. Recent evidence suggests altered microbiota may serve as a potential risk factor for UF development. Altered microbiota can contribute to tumorigenesis via epigenetic changes to host cells or toxic effects from invasion. The lack of curative-drug treatment poses significant challenges to patients with UF. Patients often undergo surgeries that require the removal of the uterus or tumour, which can negatively impact fertility. Furthermore, uterine fibroids’ diagnosis relies on expensive imaging technologies such as ultrasound, which may not be readily available in developing countries. Moreso, diagnosis is often conducted only after patients’ symptoms become severe. Although late presentation may contribute to severe symptoms and complications among women with UF in Africa, other factors that influence severity and increase incidence in this population remain unknown. A comprehensive assessment of UF predisposing factors in high-risk populations such as Ghana could give better insights into disease pathogenesis. Hence, this study aims to assess: UF-associated demographic factors, the role of uterine microbiota dysbiosis on UF tumorigenesis; and molecular markers associated with UF in the Ghanaian population. Epidemiological data and clinical samples (tissues, blood and cervico-vaginal swabs) will be obtained. The characterization of samples will involve metagenomics, whole genome sequencing, functional validation of SNPs and SNP genotyping. The association of risk alleles with disease phenotypes will be assessed via regression analysis using PLINK v.1.9. The findings will provide information on potential disease markers that can be explored for better management strategies for UF in high-risk populations.

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DOI: 10.3897/arphapreprints.e125515

Authors: Simon Rolph, Chris Andrews, Dylan Carbone, Julian Lopez Gordillo, Tomas Martinovic, Nick Oostervink, Dirk Pleiter, Kata Sara-aho, John Watkins, Christoph Wohner, Jan Dick

Abstract: Digital twin approaches have the potential to revolutionise usage, planning and management of cultural ecosystem services i.e. the non-material benefits people obtain from ecosystems, including recreation, tourism, intellectual development, spiritual enrichment, reflection, and aesthetic experiences. Here we outline our blueprint for a prototype digital twin (pDT) for cultural ecosystem services. The pDT consists of two modelling components; a recreation potential model to quantify the cultural ecosystem services of the physical landscape and species distribution models to quantify the biodiversity component. It is envisaged that the digital twin will be used primarily by two user types 1. those who wanted to enjoy the area and potentially contribute to citizen science programs and 2. people who want to inform or make evidence-based management decisions (land managers, policy makers, researchers).

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DOI: 10.3897/rio.10.e120899

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 amongst 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/rio.10.e119782

Authors: Catherine Borremans, Jennifer Durden, Timm Schoening, Emma Curtis, Luther Adams, Alexandra Branzan Albu, Aurélien Arnaubec, Sakina-Dorothée Ayata, Reshma Baburaj, Corinne Bassin, Miriam Beck, Katharine Bigham, Rachel Boschen-Rose, Chad Collett, Matteo Contini, Paulo Correa, Carlos Dominguez-Carrió, Gautier Dreyfus, Graeme Duncan, Maxime Ferrera, Valentin Foulon, Ariell Friedman, Santosh Gaikwad, Chloe Game, Adriana Gaytán-Caballero, Fanny Girard, Michela Giusti, Mélissa Hanafi-Portier, Kerry Howell, Iryna Hulevata, Kiamuke Itiowe, Chris Jackett, Jan Jansen, Clarissa Karthäuser, Kakani Katija, Maxime Kernec, Gabriel Kim, Marcelo Kitahara, Daniel Langenkämper, Tim Langlois, Nadine Lanteri, Claude Jianping Li, Qi-Ran Li, Pierre-Olivier Liabot, Dhugal Lindsay, Ali Loulidi, Yann Marcon, Simone Marini, Ashley Marranzino, Miquel Massot-Campos, Marjolaine Matabos, Lenaick Menot, Bernabé Moreno, Marcus Morrissey, David Nakath, Tim Nattkemper, Monika Neufeld, Matthias Obst, Karine Olu, Alexa Parimbelli, Francesca Pasotti, Dominique Pelletier, Margaux Perhirin, Nils Piechaud, Oscar Pizarro, Autun Purser, Clara Rodrigues, Elena Ceballos Romero, Brian Schlining, Yifan Song, Heidi Sosik, Marc Sourisseau, Bastien Taormina, Jan Taucher, Blair Thornton, Loïc Van Audenhaege, Charles von der Meden, Guillaume Wacquet, Jack Williams, Kea Witting, Martin Zurowietz

Abstract: Imaging is increasingly used to capture information on the marine environment thanks to the improvements in imaging equipment, devices for carrying cameras and data storage in recent years. In that context, biologists, geologists, computer specialists and end-users must gather to discuss the methods and procedures for optimising the quality and quantity of data collected from images. The 4th Marine Imaging Workshop was organised from 3-6 October 2022 in Brest (France) in a hybrid mode. More than a hundred participants were welcomed in person and about 80 people attended the online sessions. The workshop was organised in a single plenary session of presentations followed by discussion sessions. These were based on dynamic polls and open questions that allowed recording of the imaging community’s current and future ideas. In addition, a whole day was dedicated to practical sessions on image analysis, data standardisation and communication tools. The format of this edition allowed the participation of a wider community, including lower-income countries, early career scientists, all working on laboratory, benthic and pelagic imaging.This article summarises the topics addressed during the workshop, particularly the outcomes of the discussion sessions for future reference and to make the workshop results available to the open public.

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DOI: 10.3897/rio.10.e116333

Authors: Katja Liebal, Vera Denzer, Nico Eisenhauer, Immo Fritsche, Ute Kunzmann, Linda Oña, Martin F. Quaas, Ingmar Staude, Christian Wirth

Abstract: Human activities and their consequences, such as environmental pollution, the exploitation of resources or deforestation, are major causes of biodiversity loss. However, humans depend on a biologically diverse and healthy environment in many ways, as it provides access to clean water, air and food. The loss of biodiversity is an ecological crisis that threatens human health, and ultimately their very existence. At the same time, there is an unwavering interest in the positive effects of "nature" on mental health. Although these examples point to a connection between biodiversity and health, little is known about the causal effects of different facets of biodiversity on mental health. Exploring these relationships and the underlying psychological mechanisms is a major goal of this project. We will build on the expertise of an interdisciplinary team involving scholars from psychology, biodiversity research, human geography, and behavioural economics and combine this expertise with a variety of methods, with a focus on quantitative research, experimental and intervention designs, and investigate participants from different age groups to understand the causal effects of different environments with varying degrees of biological diversity on mental health, and to identify the physical, social, and psychological boundary conditions of these causal effects.

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DOI: 10.3897/rio.10.e119243

Authors: Linda Bouquillon, Dot Bindman, Jos Hendriksen, Phillipe Collin, Janet Hoskin, Rory Conn, Chloe Geagan, Ros Quinlivan

Abstract: This workshop aimed at summarising knowledge and key issues in psychiatric prescribing and psychological testing in children and adults with Duchenne muscular dystrophy (DMD). It comprised clinicians and patient representatives from the UK and the Netherlands. The following topics were discussed: a model for capturing the range of non-motor problems in the domains of cognition, learning, emotion and behaviour; psychosocial screening tools for use with children and adults; assessing neurocognitive functioning in children and adults; parent and teacher perspectives on psychosocial needs; and psychopharmacological treatment for affective disorders, anxiety disorders, obsessive compulsive disorder, attention deficit hyperactivity disorder (ADHD) and insomnia. Some key considerations included: the need for tools used to assess behavioural and psychosocial functioning to consider motor aspects in DMD; to understand more about working memory performance; the need for early interventions for automatisation problems, which affect reading and arithmetic; appropriate selection of tests for neuropsychology assessments; in schools, acknowledging the range of psychosocial risks and gathering evidence of psychosocial needs; the suitability of selective serotonin reuptake inhibitors for mood and anxiety disorders; the use of stimulant medications for ADHD; melatonin use for insomnia; the cautious use of benzodiazepines; and the need for improving pathways for psychosocial care.

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DOI: 10.3897/rio.9.e109307

Authors: Marisa Conte, Allen Flynn, Philip Barrison, Peter Boisvert, Zach Landis-Lewis, Charles Friedman

Abstract: We present our work to develop digital objects to represent and convey a specific category of scientific knowledge: computable biomedical knowledge (CBK). Properly developed, validated, implemented and stewarded, CBK has the potential to accelerate the translation of actionable knowledge from scientific discovery to clinical application.Our research takes an infrastructural approach to CBK, initially by focusing on the creation of a conceptual model for packaging computable biomedical knowledge - the Knowledge Object (KO) - and on corresponding efforts to create an architecture for KO management and implementation. Additionally, our work is grounded in the FAIR principles, such that KO artefacts should be findable, accessible, interoperable and reusable and we are exploring aligning KOs with emerging best practices for FAIR Digital Objects (FDO).The outcomes of this work resonate in clinical contexts, health professions education, healthcare quality improvement, biomedical and translational research and population care. Our KO model is also of interest to researchers and practitioners interested in knowledge science, including those working with semantic technologies and other forms of digital objects.

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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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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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DOI: 10.3897/arphapreprints.e116230

Authors: Marco Visani

Abstract: This study is centered on Natural Products (NPs) - specific chemicals synthesized by living organisms. These NPs hold significant importance in various domains, notably medicine, agriculture, and ecology. A primary resource for our research is the LOTUS database, which catalogues a vast array of NPs and their occurrence. Yet, a gap exists: there are no existing model to predict the occurrence of these NPs across different species.In our initial strategy, the occurrence of natural products was viewed as a collection of observations and their associated variables. Although simple, this strategy immediately showed its limits when dealing with the complex nature of NPs. We switched to an advanced graph-based method after seeing the necessity for a more thorough strategy to accurately represent the intricate interactions governing NPs expression. When considering species in a phylogeny or molecular pathways, the graph-based method perceives data as a network of connected entities, offering a far more logical and natural way of thinking. By employing this better methodology, we have developed a more effective approach for investigating the intricate world of Natural Products. We hope that this strategy will open up new research directions and possibly result in ground-breaking NP-related findings.

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DOI: 10.3897/rio.9.e106849

Authors: Raphael Abban, Sarpong Kwabena, Samuel Duodu, Lydia Mosi, Isawumi Abiola

Abstract: Urinary tract infections (UTIs) are frequent hospital-acquired infection, with Escherichia coli and Proteus mirabilis accounting for 90% of complicated UTIs. Emergence of multidrug-resistant (MDR) bacteria have complicated the treatment UTIs. P. mirabilis related UTIs has been associated with the production of urinary stones and long-term infections in patients with catheters. P. mirabilis and other uropathogens constitute a largely unexplored pathogen group. The pathogen is resistant to most antibiotics as a result of its impermeable outer membrane (OM). The β-barrel assemble machinery folds and inserts outer membrane proteins; however, there are no antibiotics targeting the OM assemble in clinical use currently. Therefore, this study seeks to identify drugs that will inhibit the activity of P. mirabilis B complex proteins and also determine their effects on P. mirabilis OM biogenesis. This would be achieved by screening approved drugs against the P. mirabilis Bam complex using computer-based in silico screening and cellular-based assays. First, the binding effects of drugs on P. mirabilis B complex proteins will be determined using docking algorithms. The antimicrobial and antivirulence activity of selected drugs from in silico analysis will be screened against MDR P. mirabilis. Finally, the effect of active drug(s) on the OM biogenesis of wild-type P. mirabilis and mutant P. mirabilis will be determined using peptide nucleic acids (PNA). Western lot analysis will be used to determine the abundance of proteins involved in OM biogenesis. Successful completion of this study will lead to the identification of novel antibiotics against MDR P. mirabilis and associated mechanisms while providing the foundation for future research endeavours on other uropathogens.

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DOI: 10.3897/rio.9.e107227

Authors: Georgios Dougas

Abstract: Shortwave and microwave diathermy devices are commonly used in physical therapy as heating treatment. The rise in temperature occurs due to the flow of electric current in the treated area. Ions are evenly distributed in a predicted pattern from skin to deeper tissues. We hypothesise that the diathermy physiotherapy devices (DPDs) can be repurposed as a means of neutralisation of the Rabies virus (RABV) by exploiting the generated electric charges. In order to minimise the ohmic heating of the tissue, the pulsed output of the diathermy devices is preferred where the ‘on’ time of active energy emission is considerably shorter than the ‘off’ time. RABV proteins mediating cell invasion, cytoplasmic replication and budding, contain polar components that can be adversely affected by non-thermal electric phenomena. Repurposed DPDs can replace the Rabies immunoglobulin (RIG) by targeting the site of inoculation i.e. the area of the animal bite, provided that the delivered electric charges can reduce pathogenicity by altering key viral proteins. The modality is advantageous compared to conventional RIG since it can theoretically neutralise all Lyssavirus species, is not limited by the compartment syndrome, can intercept RABV even after it gains access to the peripheral neural network where conventional post-exposure prophylaxis is ineffective and is cost-effective in the long term. The principle of physical alteration of vulnerable proteins by electricity delivered by electromagnetic radiation is not limited to RABV, but may be applied to a spectrum of viral pathogens.

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DOI: 10.3897/rio.9.e113378

Authors: Helen Hardy, Laurence Livermore, Paul Kersey, Ken Norris, Vincent Smith

Abstract: UK natural science collections hold over 137 million items, an unrivalled source of data about 4.56 billion years of planetary development and hundreds of years of biological change, including the differences made by humans — but the scientific, commercial, and societal benefits of these collections are constrained by the limits of physical access, and by highly fragmented digitisation efforts with less than 10% digitally available. Following work with Frontier Economics in 2021, which showed potential for £2 billion in benefits to the UK economy from digitising all UK natural science collections, in 2022–23 the Natural History Museum London worked, with analytical support from McKinsey and Company, to understand the impact of what has already been digitised and shared by UK natural science collections — what is the demand for these data, what are they used for, and how does this deliver efficient, effective and impactful research?This study focuses on usage via the Global Biodiversity Information Facility, the largest source of relevant usage data, examining 7.6 million records from twelve UK institutions. While these UK collections data are just 0.3% of total GBIF occurrences, they are cited in 12% of peer reviewed publications citing GBIF data, showing the disproportionate impact of UK collections data and the historical, geographical, and taxonomic richness that they bring. Researchers have already benefited from more than £18 million of efficiency savings from digital UK specimen data. Data from natural science collections held in the UK are uniquely impactful resources, vital to a future in which people and planet thrive, and a step change in the pace of digitisation is needed to unlock their potential for researchers, policymakers, and society.

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DOI: 10.3897/rio.9.e105198

Authors: Monique Janssens, Stefan Gaillard, Judith de Haan, Wim de Leeuw, Matthew Brooke, Maura Burke, Jacques Flores, Iris Kruijen, Julia Menon, Adrian Smith, Ivo Tiebosch, Felix Weijdema

Abstract: Open science in its broadest sense can make better science and provide benefits to researchers. When applied to animal experimentation, it can prevent unnecessary use of animals, because knowledge and experiences about past animal experimentation are shared openly to be consulted and used by other researchers. By extension, open science can accelerate the much anticipated transition towards animal-free innovations or New Approach Methodologies (NAMs). The purpose of this paper is to bring together and further share the preparations and findings of a symposium held at Utrecht University on aspects of open science that researchers doing animal experiments can and should take into account to improve their research and benefit themselves. The paper offers a one-figure guideline for that purpose.

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DOI: 10.3897/rio.9.e110501

Authors: Konrad U. Förstner, Anke Becker, Jochen Blom, Peer Bork, Thomas Clavel, Marius Dieckmann, Alexander Goesmann, Barbara Götz, Thomas Gübitz, Franziska Hufsky, Sebastian Jünemann, Marie-Louise Körner, Manja Marz, Ulisses Nunes Da Rocha, Jörg Overmann, Alfred Pühler, Dietrich Rebholz-Schuhmann, Alexander Sczyrba, Jens Stoye, Justine Vandendorpe, Thea Van Rossum, Alice McHardy

Abstract: Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide non-microbial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany.

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DOI: 10.3897/rio.9.e107939

Authors: Daniel Neidigk, Allie Linkous, Rodney Guttmann

Abstract: Studies have demonstrated that some individuals display pathological hallmarks of Alzheimer's disease (AD) but are not afflicted with cognitive decline. The ability to maintain cognitive function despite the presence of pathology is referred to as cognitive reserve. This project aims to identify the molecular pathways involved in cognitive reserve using Drosophila melanogaster (Drosophila) models of AD. Specifically, a theoretical approach using experimental evolution to drive a population of AD-like Drosophila carrying a tau mutation to develop cognitive reserve is proposed. To accomplish this, a population of AD-like Drosophila will be placed in a single population cage along with wild-type flies and forced to compete for food and water. The first generation of AD-like Drosophila will be generated using random mutagenesis of the initially isogenic AD-like fly. The selected tau mutant displays a rough eye condition which allows for easy distinction between tau mutant and wild-type flies. It is hypothesised that AD-like flies with cognitive decline will be unable to survive because their limited cognitive abilities will prevent them from effectively competing for food and water. In contrast, AD-like flies with mutations that promote cognitive reserve will be better capable of survival. After 90-99% of mutant flies have died, the surviving mutant flies will be back-crossed to the P1 mutant to maintain tau mutation stability. It is expected that artificial selection will result in the creation of a generation of tau mutant flies that demonstrate cognitive abilities comparable to those of wild-type flies despite maintaining an AD-like tau mutation. This approach will monitor the successful trajectory of the evolution of increased cognitive reserve through survival curve analysis and measures of cognition. A limitation of the method is that only a dominant mutation or series of dominant mutations would be identified using this approach.

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DOI: 10.3897/rio.9.e108748

Authors: Hangxing Jia

Abstract: Obesity has been a global health problem since the twentieth century. Despite the intensive research, there is no scientific consensus on the onset of obesity. The energy balance model (EBM) and the carbohydrate-insulin model (CIM) are two competing obesity theories, each with supporting and conflicting evidence. In this essay, I propose a new model, the energy-rush and insulin model (ERIM) which integrates not only the energy intake and expenditure, but also the food composition and digestibility, to explain how the high energy-rush and insulin secretion contribute to the development of obesity. The ERIM offers a novel framework to explain how obesity occurs and proposes new recommendations which may reverse the obesity epidemic in the future.

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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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DOI: 10.3897/rio.9.e105155

Authors: Mathilde Bessert-Nettelbeck, Andreas Bischof, Ulrike Sturm, Emilia Nagy, Martina Schraudner, Julia Backhaus, Till Bruckermann, Susanne Hecker, Justus Henke, Karola Köpferl, Sabrina Kirschke, Christin Liedtke, Felix Mahr, Arne Maibaum, Audrey Podann, Wiebke Rössig, Martina Schäfer, Carolin Schröder, Philipp Schrögel, Victoria Shennan, Norbert Steinhaus, Mhairi Stewart, Vanessa van den Bogaert, Silke Voigt-Heucke

Abstract: Citizen science, transdisciplinary research, dialogic forms of science communication or public engagement: these and other research approaches and fields, often subsumed under participatory research, have in common that they enable people outside of academia to actively engage in the production of scientific knowledge. However, each of these fields sets its own goals, uses different formats and has a different scope and impact. The conference 'Opportunities and Limitations of Participation in Academia' held in September 2022 as part of the German Science Year 'Participate!' aimed to connect the various participation communities in Germany and to explore commonalities and success factors. Through intensive discussions in four working groups, a keynote speech and a panel discussion, the conference initiated an exchange of ideas and experiences amongst researchers in a converging field. This report is a summary of the key questions and outcomes of the conference.

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DOI: 10.3897/rio.9.e99607

Authors: Michael Boehmler, David DeMay, Adriane Rogers, Heidi Murray, Lawrence Hribar

Abstract: The Florida Keys Mosquito Control District utilises dry ice-baited light traps to monitor mosquito populations on Key Largo, Florida. This paper describes the methodology of trapping, habitat description and dataset of adult mosquito populations from 18 years of weekly monitoring from a single site on Key Largo, Monroe County, Florida, USA.This paper details a previously unreported dataset derived from trap collections made on Key Largo, Florida at a site designated as “Gun Club Road.”

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DOI: 10.3897/rio.9.e96576

Authors: Osamudiamen Obasuyi

Abstract: The sustainable development goals (SDGs) of providing universal health coverage for all and ending poverty by 2030 aim to make healthcare accessible and available for all, irrespective of status, gender or race. Unfortunately, access to universal healthcare is still hampered by preventable inequalities, especially amongst the Low-Middle income countries (LMICs).Cataracts are the leading cause of preventable blindness globally, affecting over 17 million people; 80% of these people reside in the LMICs and cost-effective cataract surgery is the only way to treat it. However, barriers exist that prevent access to cataract surgery amongst these people. Despite widespread reports of these barriers to cataract surgical access, the complex relationships between the barriers and cataract surgical access have yet to be fully explored by researchers or policy-makers.A randomised control trial involving three groups is proposed and presented in this paper to test the relationship between well-known barriers to cataract surgical access in resource-poor communities and programmes designed to overcome them.

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DOI: 10.3897/rio.8.e98874

Authors: Audrey Darnaude, Sophie Arnaud-Haond, Ewan Hunter, Oscar Gaggiotti, Anna Sturrock, Maria Beger, Filip Volckaert, Angel Pérez-Ruzafa, Lucía López-López, Susanne E. Tanner, Cemal Turan, Servet Ahmet Doğdu, Stelios Katsanevakis, Federica Costantini

Abstract: Truly sustainable development in a human-altered, fragmented marine environment subject to unprecedented climate change, demands informed planning strategies in order to be successful. Beyond a simple understanding of the distribution of marine species, data describing how variations in spatio-temporal dynamics impact ecosystem functioning and the evolution of species are required. Marine Functional Connectivity (MFC) characterizes the flows of matter, genes and energy produced by organism movements and migrations across the seascape. As such, MFC determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective MFC knowledge can therefore improve predictions of the impacts of environmental change and help to refine management and conservation strategies for the seas and oceans. Gathering these data are challenging however, as access to, and survey of marine ecosystems still presents significant challenge. Over 50 European institutions currently investigate aspects of MFC using complementary methods across multiple research fields, to understand the ecology and evolution of marine species. The aim of SEA-UNICORN, a COST Action supported by COST (European Cooperation in Science and Technology), is to bring together this research effort, unite the multiple approaches to MFC, and to integrate these under a common conceptual and analytical framework. The consortium brings together a diverse group of scientists to collate existing MFC data, to identify knowledge gaps, to enhance complementarity among disciplines, and to devise common approaches to MFC. SEA-UNICORN will promote co-working between connectivity practitioners and ecosystem modelers to facilitate the incorporation of MFC data into the predictive models used to identify marine conservation priorities. Ultimately, SEA-UNICORN will forge strong forward-working links between scientists, policy-makers and stakeholders to facilitate the integration of MFC knowledge into decision support tools for marine management and environmental policies.

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DOI: 10.3897/rio.8.e91179

Authors: Kenneth Alibek, Luiza Niyazmetova, Sean Farmer, Terence Isakov

Abstract: Autism spectrum disorders (ASD) are a range of neurodevelopmental conditions that are clinically present early in childhood with the symptoms of social withdrawal and repetitive behavior. Despite an extensive research on ASD, no commonly accepted theory on the disease etiology exists. Hence, we reviewed several scientific publications, including reviews, preclinical and clinical investigations, and published hypotheses to analyze various opinions on the nature and cause of the disorder. Many studies suggest that infections and inflammation during pregnancy play a significant role in genetic and epigenetic changes in the developing fetus, resulting in an autistic phenotype in a child. Still, there is a lack of comprehensive literature about the multitude of autism inducing factors. Therefore, this article reviews and discusses available scientific evidence on the roles of viral, bacterial, fungal, and parasitic infections, overactivation of the immune system, and intestinal microflora in the pathogenesis and clinical manifestation of ASD. The overview of the scientific publications, including our own studies, suggests that TORCH infections, imbalanced microbiome, and persistent inflammation are significantly associated with the disruption of the social domain in ASD children. The ASD-related changes begin prenatally as maternal-to-fetal immune activation triggered by infection. It results in continuous low-grade inflammation and oxidative stress in a fetus, causing germline and somatic genetic changes in the developing brain and the establishment of the dysregulated immune system. These changes and dysregulations result in central and peripheral nervous systems dysfunctions as well as other comorbid conditions found in autistic children.

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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/rio.8.e81568

Authors: Pia Hollenbach, Monika Goetzoe, Malith de Silva

Abstract: The SARS-COV-2 pandemic created a serious shock and surprise to the disaster governance mechanisms in existence. Even the most advanced disaster governance systems in the world struggled to govern, respond, communicate risk and build resilience against the pandemic. The overall management – locally and globally- showed that relevant stakeholders such as social workers that work frontline but also within disaster management relevant fields, were not heart nor taken their potentials and knowledge into consideration to sustainably set up a disaster management and responds strategy. Applying a comparative multi-sited ethnographic approach, the study aims to highlight the potential agency of social work as a bridging agent to enhance the efficiency and effectiveness of existing disaster governance and communication architecture and improve the resilience of communities to cope with the socio-ecological complexity of future disasters, similar to SARS-COV-2. Impact will be created in four main areas: (1) Actors in disaster governance will be educated using the new knowledge produced on contextualized disaster governance and communication strategies and impacts on community resilience; (2) Enhanced capacity and awareness of professional social work practitioners on their role/s as bridging agents within the disaster governance architecture to enhance disaster risk communication and community resilience; (3) Improved capacity for decision and policy-making and strengthened agency of social work in the field of disaster governance through the introduction of professional development training and the ToolKit SW2BRIDGE; and (4) Improved social work education at the university level through the introduction of a post-graduate programme on the application of social work in disasters.

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DOI: 10.3897/rio.8.e80223

Authors: Audrey Darnaude, Sophie Arnaud-Haond, Ewan Hunter, Oscar Gaggiotti, Anna Sturrock, Maria Beger, Filip Volckaert, Angel Pérez-Ruzafa, Lucía López-López, Susanne E. Tanner, Cemal Turan, Servet Ahmet Doğdu, Stelios Katsanevakis, Federica Costantini

Abstract: Truly sustainable development in a human-altered, fragmented marine environment subject to unprecedented climate change, demands informed planning strategies in order to be successful. Beyond a simple understanding of the distribution of marine species, data describing how variations in spatio-temporal dynamics impact ecosystem functioning and the evolution of species are required. Marine Functional Connectivity (MFC) characterizes the flows of matter, genes and energy produced by organism movements and migrations across the seascape. As such, MFC determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective MFC knowledge can therefore improve predictions of the impacts of environmental change and help to refine management and conservation strategies for the seas and oceans. Gathering these data are challenging however, as access to, and survey of marine ecosystems still presents significant challenge. Over 50 European institutions currently investigate aspects of MFC using complementary methods across multiple research fields, to understand the ecology and evolution of marine species. The aim of SEA-UNICORN, a COST Action within the European Union Horizon 2020 framework programme, is to bring together this research effort, unite the multiple approaches to MFC, and to integrate these under a common conceptual and analytical framework. The consortium brings together a diverse group of scientists to collate existing MFC data, to identify knowledge gaps, to enhance complementarity among disciplines, and to devise common approaches to MFC. SEA-UNICORN will promote co-working between connectivity practitioners and ecosystem modelers to facilitate the incorporation of MFC data into the predictive models used to identify marine conservation priorities. Ultimately, SEA-UNICORN will forge strong forward-working links between scientists, policy-makers and stakeholders to facilitate the integration of MFC knowledge into decision support tools for marine management and environmental policies.

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DOI: 10.3897/rio.7.e78844

Authors: Danail Popov, Priyanka Roychoudhury, Helen Hardy, Laurence Livermore, Ken Norris

Abstract: The Natural History Museum, London has been creating digital data about collections for many years, with a formal Digital Collections Programme since 2014. Efforts to monitor the outcomes and impact of this work have focused on metrics of digital access, such as download events, and on citations of digital specimens as a measure of use. Digitisation projects and resulting research have also been used as impact case studies, highlighting areas such as human health and conservation. In 2021, the Museum decided to explore the economic impacts of collections data in more depth, and commissioned Frontier Economics to undertake modelling, resulting in this report. While the methods in this report are relevant to collections globally, this modelling focuses on benefits to the UK, and is intended to support the Museum’s own digitisation work, as well as a current scoping study funded by the Arts & Humanities Research Council about the case for digitising all UK natural science collections as a research infrastructure. This study focuses on digitisation in the round, not distinguishing between different collection types or levels of data creation at this stage. Three methods have been used: first, analysing five key thematic areas or sectors where data from natural science collections are likely to lead to benefits; secondly, analysing typical returns on investment in scientific research; and thirdly, examining the efficiency savings that can be reinvested in research if data are available freely and openly. Together, these methods confirm benefits in excess of £2 billion over 30 years, representing a seven to ten times return on investment.

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DOI: 10.3897/rio.7.e77736

Authors: Ibraheem Alimi, Emmanuel Keku

Abstract: Cryptococcosis is a fungal disease that is characterized by inflammation of the lungs and central nervous system, and it is commonly associated with HIV/AIDS. Even though the disease accounts for roughly 15% of all AIDS-related deaths, it is relatively neglected. This is most especially true in Southern Africa which has the highest HIV/AIDS cases in the world and accounts for more than 10% of all HIV/AIDS cases worldwide most especially in Southern African countries such as Swaziland (Eswatini) which has the highest HIV/AIDS adult prevalence rate in the world. Despite this, there are little or no previous studies with regards to the epidemiological trends for cryptococcosis in Swaziland (Eswatini) which further suggests that it is relatively neglected. With the increasing spread of virulent strains of the fungus such as Cryptococcus gattii causing outbreaks in several countries around the world, it is important to have a concrete understanding of the epidemiological trends for cryptococcosis in Swaziland (Eswatini). This is also important during the current coronavirus outbreak as previous studies have reported higher morbidity and mortality rates among COVID-19 patients that are also co-infected with HIV/AIDS, cryptococcus as well as other secondary infections. This is further supported by the fact that Southern Africa has the highest number of COVID-19 cases in Africa as well as one of the highest in the world. As a result, the purpose of this study is to determine the epidemiological trends for cryptococcosis in Swaziland (Eswatini) as this will enable adequate control, management, assessment, policies, and regulations that will be useful during outbreaks. This will be achieved by performing a repeated cross-sectional study to determine the epidemiological changes and trends for cryptococcosis in Swaziland (Eswatini) over a 5-year period from 2023 to 2028.

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DOI: 10.3897/rio.7.e77666

Authors: Judita Tomaskinova, Davide Geneletti, Lynn Dicks, Miriam Grace, Marcus Collier, Davide Longato, Pavel Stoev, Anna Sapundzhieva, Mario Balzan

Abstract: This article presents teaching and learning material from three strategically designed ReNature Horizon 2020 project training activities. A total of twelve presentations covering different aspects of NbS implementation are presented with this article. Additionally, this article also includes materials produced by learners, throughout their work within self-organised groups carried out during the Second ReNature Training School. This is the second article publishing teaching and learning material arising from the ReNature project.

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DOI: 10.3897/rio.7.e71271

Authors: Marco Cirillo

Abstract: Chemotherapy and other invasive therapies are often limited by side effects, pain and negative experiences that can limit adherence to the therapy itself. Such negative components add to the patient's depressive state due to the disease. This research project proposes the use of deep sedation during chemotherapy sessions or other disabling therapies in the treatment of tumors or other severe diseases. The proposed protocol provides for an ad hoc hospitalization which could be during the night, during the day or limited to a few hours. Administration during sleep eliminates the memory and the negative impact the treatment has on the rest of the patient's daily life. This approach also agrees with the evidence of the circadian rhythm of cellular repair processes, which is greater at sunrise and sunset and linked to a good quantity and quality of sleep. In conclusion, this project aims to reduce the negative impact and increase the adherence to and efficacy of the therapy itself.

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DOI: 10.3897/rio.7.e70642

Authors: Adam Bernstein, Randall Moore, Lauren Rhee, Dina Aronson, David Katz

Abstract: Malnutrition is common among hospitalized patients and associated with longer hospital stays, higher rates of rehospitalization, and increased mortality. Validated questionnaires of varying sensitivity and specificity to help identify patients at risk of malnutrition have been developed, but none has been broadly adopted. Tools to identify patients at risk for malnutrition should be quick, inexpensive, easy to administer and use, not require specialized nutrition knowledge, and provide results which can be entered into an electronic medical record; ideally, the tool should be deployed within 24 hours of admission and repeated if warranted. We hypothesize that a novel digital nutrition assessment tool which uses the Diet Quality Photo Navigation (DQPN) method, can help triage hospitalized patients toward further evaluation of nutritional status. We further propose that micronutrient deficiencies may be identified at the same time as malnutrition and that the reimbursement and cost savings from DQPN will prove substantially greater than the combined costs of its use and triggered dietitian consult. Deploying DQPN upon admission will represent an addition to standard hospital intake procedure that is frictionless for patients and health professionals, and one which may be overseen by clerical rather than clinical staff. The digital format of DQPN, which can be integrated into electronic medical records, will facilitate easier tracking and management of nutritional status over the course of hospitalization and post-discharge. To evaluate the hypotheses, DQPN will be deployed in a hospital setting to a group of patients who will also be seen by a registered dietitian to assess the nutritional status of each patient. Receiver operating characteristic curves will determine the point, or criterion, at which maximal true positivity rate and least false positivity rate for a diagnosis of malnutrition and specific nutrient deficiencies align. The study cohort will also be compared to a matched historical cohort to compare total medical spend and reimbursement between the intervention cohort and matched control. Testing of these hypotheses will thus allow for insight into whether DQPN may be used to identify malnutrition and nutrient deficiencies in hospitalized patients and, in so doing, improve patient outcomes, reduce healthcare utilization, and bring financial benefit to hospitals.

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DOI: 10.3897/rio.7.e70183

Authors: Nazareno Scaccia, Taras Günther, Estibaliz Lopez de Abechuco, Matthias Filter

Abstract: In many interdisciplinary research domains, the creation of a shared understanding of relevant terms is considered the foundation for efficient cross-sector communication and interpretation of data and information. This is also true for the domain of One Health (OH) where many One Health Surveillance (OHS) documents rarely contain glossaries with a list of terms for which their specific meaning in the context of the given document is defined (Cornelia et al. 2018, Buschhardt et al. 2021). The absence of glossaries within these documents may lead to misinterpretation of surveillance results due to the wrong interpretation of terminology specifically when term definitions differ across OH sectors. Under the One Health EJP project ORION, the OHEJP Glossary was recently created. The OHEJP Glossary is a tool to improve communication and collaboration amongst OH sectors by providing an easy-to-use online resource that lists relevant OH terms and sector-specific definitions. To improve the accessibility of content from the OHEJP Glossary and support the creation of integrative glossaries in future OHS-related documents, the OHEJP Glossaryfication Web Service was created. This service can support the practical use of the OHEJP Glossary and other relevant online glossaries by OH professionals.The Glossaryfication Web Service (GWS) is an application that automatically identifies terms in any uploaded text-based document and creates a document-specific list of matching definitions in selected online glossaries. This auto-generated document-specific glossary can easily be adjusted by the user, for example, by selecting the desired definition in case multiple definitions were found for a specific term. The document-specific glossary could then be downloaded, manually adjusted and finally included into the original document where it supports the correct interpretation of terminology used. Especially in sector-specific reports, such as from animal health or public health authorities, this can be beneficial to ensure the correct interpretation by other OH sectors in the future. The GWS was developed with the open-source desktop software KNIME Analytics Platform and runs as a web service on a KNIME Web Server infrastructure. The core data processing functionality in the GWS is based on KNIME’s Text Processing extension. KNIME's JavaScript nodes provided the basis for an interactive user interface where users can easily upload their files and select between different reference glossaries, such as the OHEJP Glossary, the CDC Glossary, the WHO Glossary or the EFSA Glossary. After retrieval of the user input settings, the GWS tags words within the provided document and maps these tagged words with matching entries in the selected glossaries. As the main output, the user receives a downloadable list of matching terms with their corresponding definitions, sectorial assignments and references, which can then be added by the user to the original document. The GWS is freely accessible via this link as well as the underlying KNIME workflow.

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DOI: 10.3897/rio.7.e70042

Authors: Lane Rasberry, Daniel Mietchen

Abstract: We present the design of a project to develop Wikipedia content on general vaccine safety and the COVID-19 vaccines, specifically. This proposal describes what a team would need to distribute public health information in Wikipedia in multiple languages in response to a disaster or crisis, and to measure and report the communication impact of the same. Researchers at the School of Data Science at the University of Virginia made this proposal in response to a February 2021 call from a sponsor which was seeking to share public health information to respond globally to vaccine hesitancy related to the COVID-19 vaccines. This proposal was not selected for funding, and now the research team is sharing the proposal here with an open copyright license for anyone to reuse and remix. Most of the text here is from the original proposal, but there are modifications to remove the names of the funder, named partners, and for other details to make this text more reusable. The budget in this proposal has been converted from a dollar amount to equivalent descriptions in terms of labor hours, and the timeline was adapted from absolute to relative months.

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DOI: 10.3897/rio.7.e68121

Authors: Daniel Mietchen, Lane Rasberry, Thais Morata, John Sadowski, Jeanette Novakovich, James Heilman

Abstract: In this era of information overload and misinformation, it is a challenge to rapidly translate evidence-based health information to the public. Wikipedia is a prominent global source of health information with high traffic, multilingual coverage, and acceptable quality control practices. Viewership data following the Ebola crisis and during the COVID-19 pandemic reveals that a significant number of web users located health guidance through Wikipedia and related projects, including its media repository Wikimedia Commons and structured data complement, Wikidata.The basic idea discussed in this paper is to increase and expedite health institutions' global reach to the general public, by developing a specific strategy to maximize the availability of focused content into Wikimedia’s public digital knowledge archives. It was conceptualized from the experiences of leading health organizations such as Cochrane, the World Health Organization (WHO) and other United Nations Organizations, Cancer Research UK, National Network of Libraries of Medicine, and Centers for Disease Control and Prevention (CDC)'s National Institute for Occupational Safety and Health (NIOSH). Each has customized strategies to integrate content in Wikipedia and evaluate responses.We propose the development of an interactive guide on the Wikipedia and Wikidata platforms to support health agencies, health professionals and communicators in quickly distributing key messages during crisis situations. The guide aims to cover basic features of Wikipedia, including adding key health messages to Wikipedia articles, citing expert sources to facilitate fact-checking, staging text for translation into multiple languages; automating metrics reporting; sharing non-text media; anticipating offline reuse of Wikipedia content in apps or virtual assistants; structuring data for querying and reuse through Wikidata, and profiling other flagship projects from major health organizations.In the first phase, we propose the development of a curriculum for the guide using information from prior case studies. In the second phase, the guide would be tested on select health-related topics as new case studies. In its third phase, the guide would be finalized and disseminated.

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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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DOI: 10.3897/rio.7.e66132

Authors: Patrik Lindenfors, Jonas Svensson

Abstract: Some form of religion exists in every documented society on earth. However, ‘religion’ is a multifaceted phenomenon commonly including aspects, such as rituals, myths, rules and regulations concerning ethical behaviour, social practices and some form of belief in the supernatural (e.g. gods, spirits or souls). Due to its pervasiveness, many researchers of biological and cultural evolution have suggested that religion needs a universal evolutionary explanation. However, most proposed explanations have either treated religion as a single all-encompassing entity or only focused on a single or a few aspects of religion. We propose, instead, to carry out an extensive review of such suggested evolutionary explanations with the express aim of pairing up proposed explanations with religious components in order to form a more comprehensive depiction of causation and how religion and human cognition both have evolved, each influenced by the other. We also propose to summarise predictions and hypotheses that spring from each explanation, with the express aim of stating how each may be evaluated and tested. Crucially, different aspects of religion may have different explanations and different explanations may apply to several aspects of religion. Proposed explanations will be summarised in a series of thematically oriented scientific articles, as well as in a summary monograph. Our dual competencies, in evolutionary theory and religious studies, provide us with a unique opportunity to evaluate these issues from both a natural and a humanistic point of view.

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DOI: 10.3897/rio.7.e66490

Authors: Lane Rasberry, Daniel Mietchen

Abstract: This project seeks to conduct language translation on metadata labels for research publications, attribution data, and clinical trials information to make data about medical research queriable in underserved languages through Wikidata and the Linked Open Web. This project has the benefit of distributing content through Wikipedia and Wikidata, which already have an annual userbase of a billion users and which already have established actionable standards to practice diversity, inclusion, openness, FAIRness, and transparency about program development. The impact will be localized access to basic research information in various Global South languages to integrate with existing community efforts for establishing the same. Although Wikidata development in this direction seems inevitable, the cultural and social exchange required to establish global multilingual research partnerships could begin now with support rather than later as a second phase effort for including the developing world. Wikipedia and Wikidata are established forums with an existing active userbase for multilingual research collaboration, but the research practices there still are immature. By applying metadata expertise through this project, we will elevate the current amateur development with more stable Linked Open Data compatibility to English language databases. Using the wiki distribution and discussion platform to develop the global conversation about data sharing will set good precedents for the trend of global research collaboration.

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DOI: 10.3897/rio.7.e66204

Authors: Dawid Gondek, Bettina Moltrecht, George Ploubidis

Abstract: There is a growing amount of evidence indicating increased levels of psychological distress, suicide rates and decreased well-being in midlife (age 45-55). We refer to this phenomenon as the ‘midlife mental health crisis’. As there is little empirical evidence or theoretical grounds to explain the midlife mental health crisis, we propose a research agenda.In order to facilitate further research, we consulted members of public, mental health professionals and researchers on potential reasons for the midlife mental health crisis. Subsequently, we translated those into research questions testable with the British birth cohorts. We propose a series of studies using three statistical modelling approaches: descriptive (what is the midlife mental health crisis?), predictive (who is at increased risk of experiencing the midlife mental health crisis?) and explanatory (what are the processes leading to the midlife mental health crisis?).

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DOI: 10.3897/rio.7.e62024

Authors: Dawid Gondek, Bettina Moltrecht, George Ploubidis

Abstract: There is a growing amount of evidence indicating increased levels of psychological distress, suicide rates and decreased well-being in midlife (age 45-55). We refer to this phenomenon as the ‘midlife mental health crisis’. As there is little empirical evidence or theoretical grounds to explain the midlife mental health crisis, we propose a research agenda.In order to facilitate further research, we consulted members of public, mental health professionals and researchers on potential reasons for the midlife mental health crisis. Subsequently, we translated those into research questions testable with the British birth cohorts. We propose a series of studies using three statistical modelling approaches: descriptive (what is the midlife mental health crisis?), predictive (who is at increased risk of experiencing the midlife mental health crisis?) and explanatory (what are the processes leading to the midlife mental health crisis?).

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DOI: 10.3897/rio.7.e64121

Authors: Vincent Weidlich

Abstract: Prejudice against citizens with right-aligned political views in western cosmopolitan cities was explored, and possible interventions proposed. Literature and theories were reviewed, with social psychological and sociological theories compiled that explain the reasons for this prejudice and an intervention to solve this problem. Scientific research in social sciences is dominated by bias from left-aligned researchers in social psychology and psychology. Dysfunctional scientific processes prominent in this area of sciences are due to the sacralization of social science. A significantly small percent of social and personality psychologists identify as politically conservative. A significant amount of errors and distortions were found in sociology textbooks. Media and corporation biases toward left-aligned political views were found, and right-aligned individuals are out-group members in cosmopolitan cities. Inoculation by media assignments and critical literacy education is proposed, that could prevent school students from being influenced by stealth messages and propaganda. Media campaigns targeting the full spectrum of political views is proposed, that could help reduce biases of citizens. A family and community health class is proposed, that could improve student’s psychological, family, and social health. Youth and adult clubs are proposed, that could help reduce animosity between social groups, and promote solidarity and community health.

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DOI: 10.3897/rio.7.e62936

Authors: Victor Padilla-Sanchez

Abstract: SARS-CoV-2 has caused more than 80 million infections and close to 2 million deaths worldwide as of January 2021. This pandemic has caused an incredible damage to humanity being it medically and/or financially halting life as we know it. If it were not enough, the current virus is changing to a more deadly form because of the mutations that are arising on its genome. Importantly, two variants have emerged in recent months, one in United Kingdom and the other in South Africa that are more infectious and escape antibody binding. These two variants have mutations in the receptor binding domain of the spike glycoprotein namely N501Y (UK, SA), K417N (SA) and E484K (SA). Here, I present a structural analysis of spike glycoprotein bound to ACE2 (angiotensin converting enzyme 2) where the mutations have been introduced in silico showing the reason why these variants bind better to ACE2 receptors.

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DOI: 10.3897/rio.6.e62369

Authors: Marco Cirillo

Abstract: Mitral valve repair is one of the most frequent interventions in cardiac surgery. It involves eliminating the dysfunctional part(s) of the mitral valve and reconstructing, using the residual tissue or with the addition of prosthetic components, a properly functioning valve, without residual stenosis or regurgitation. A fundamental component of mitral repair is the implantation of a ring (annuloplasty) which reconstitutes the normal, saddle-shaped geometry of the valve. Such ring is usually implanted at the end of the surgical reconstruction regardless of the repair techniques. The implantation of the ring can however change the final anatomy of the valve in an unexpected way and therefore force new corrective surgical actions. We therefore propose a research project that plans the execution of annuloplasty as the first surgical step and then the correction of the valvular disease affecting the leaflets and chordae. The sizing of the ring is always performed on parts of the valve that are usually not changed during the reconstructive surgery, therefore it is possible to decide its size before surgically correcting the valve. In this way we could act on the leaflets and chordae in the definitive geometrical arrangement of the mitral valve.

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DOI: 10.3897/rio.6.e61662

Authors: Luca Cassetta, Pedro Rodrigues, Toni Andreu, Bruno Botta, Sven Brandau, Chrissie Brierley, Clive Wilson, Inga Dadeshidze, Lucia Forzi, Federica Ortelli, Mafalda Quintas

Abstract: Cancer has been for many years the second leading cause of mortality right after cardiovascular diseases, representing 25% of all the deaths reported yearly and this tendency is expected to increase. Although the recent public health emergency caused by COVID-19 pandemic diverted much of the attention of policy makers, the public opinion and even researchers from other important, economical relevant and deadly diseases, cancer still remains as one of the major healthcare issues. Moreover, recent studies revealed the negative effects of COVID-19 pandemic on the increase of avoidable cancer-related deaths. It is then the perfect time to bring back the spotlight onto the topic of cancer.The aim of this paper is to share the outcomes of the workshop organized by the COST (European Cooperation in Science and Technology) Association, bringing together sixty participants representing a broad variety of stakeholders, to discuss a holistic approach on how to beat cancer by 2030.The conclusions of this workshop are highly relevant for the community and are supporting the work being undertaken by the EU Mission Board on Cancer. This report lays down the main conclusions and recommendations agreed by the workshop participants, focusing on different aspects such as better stakeholder collaboration, citizen education, innovative therapies, and patient-centric care.

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DOI: 10.3897/rio.6.e61709

Authors: Kenneth Alibek, Albina Tskhay

Abstract: In the case of current COVID-19, successful prophylactic approaches are likely to have a greater impact than successful treatment approaches. In this article, we discuss the challenges before the creation of anti-SARS-CoV-2 vaccines and opportunities of other means that can enhance non-specific immunity focusing on interferon in particular. Since efficacy of intranasal interferons against a number of pathogens throughout a period of 37 years and against COVID-19 as well as safety have been shown, this method of protection can be introduced in a short period while using a permitted off-label application approach.

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DOI: 10.3897/rio.6.e60893

Authors: Judita Tomaskinova, Lynn Dicks, Marcus Collier, Davide Geneletti, Miriam Grace, Davide Longato, Renata Sadula, Pavel Stoev, Anna Sapundzhieva, Mario V Balzan

Abstract: Nature-based solutions (NbS) have the potential to build climate resilience and tackle key societal challenges while also providing multiple co-benefits to biodiversity and human well-being. The demand for nature-based innovation is strongly felt in Malta – a small island state, with the highest population density in the European Union. Against this background, the Horizon 2020 project ReNature (Promoting research excellence in nature-based solutions for innovation, economic growth and human well-being in Malta) has the goal to enhance research excellence of the Malta College of Arts, Science and Technology (MCAST), as well as the national research, policy, business and stakeholder community. The six strategically designed training activities fostering capacity-building and research excellence, delivered during the first half of the project, resulted in useful learning outputs. These are twelve presentations, available as attachments to this article, which cover a large scope of topics related to the implementation of NbS. At a later stage, ReNature will publish another round of learning outputs, resulting from the rest of the training activities planned within the scope of the project.

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DOI: 10.3897/rio.6.e59646

Authors: Anna Sapundzhieva, Mario V Balzan, Judita Tomaskinova, Leticia De Santis, Marcus Collier, Jean Williams, Lynn Dicks, Miriam Grace, Davide Geneletti, Iliyana Demirova

Abstract: The ReNature nature-based solutions compendium (http://renature-project.eu/compendium) is an open-source collection, which contains data on nature-based solutions in Malta. Initially collecting information only about Malta, the compendium is growing to include submissions from across the whole Mediterranean region. The development of an open-source compendium plays an essential role in the co-creation of knowledge, and fostering capacity-building at a national and international level, which are some of the key objectives of ReNature. By sharing existing and successful implementation of nature-based solutions, the platform is giving examples of good practices for practitioners and the research community. This paper reviews the process of the development of the ReNature open-source compendium.

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DOI: 10.3897/rio.6.e58970

Authors: Mario V Balzan, Judita Tomaskinova, Marcus Collier, Lynn Dicks, Davide Geneletti, Miriam Grace, Davide Longato, Renata Sadula, Pavel Stoev, Anna Sapundzhieva

Abstract: Nature-based solutions (NBS) is a term often used to refer to adequate green infrastructure that provides multiple benefits to society whilst addressing societal challenges. They are defined as actions to protect, sustainably manage and restore natural or modified ecosystems that address societal challenges effectively and adaptively, simultaneously providing human well-being and biodiversity benefits. Malta, the smallest member state of the EU, has been characterised by rapid economic growth and urbanisation and Maltese citizens had the highest rate of exposure to pollution, grime or other environmental problems, in the EU. The project ReNature aims to establish and implement a nature-based solutions research strategy for Malta with a vision to promote research and innovation and develop sustainable solutions whilst improving human well-being and tackling environmental challenges. Here, we introduce the opening of ReNature collection of research articles in the Open Access Research Ideas and Outcomes (RIO) journal to publish unconventional research outputs and training materials. It will host key outputs relating to the sustainable use of biodiversity, biodiversity – ecosystem functioning, green infrastructure and ecosystem service assessments across rural-urban gradients, equitable access to the benefits derived from nature in cities and socio-environmental justice, payments for ecosystem services, and designing nature-based solutions.

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DOI: 10.3897/rio.6.e55281

Authors: Victor Padilla-Sanchez

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China in December 2019. Since then, COVID-19, the disease caused by SARS-CoV-2, has become a rapidly spreading pandemic that has reached most countries in the world. So far, there are no vaccines or therapeutics to fight this virus. Here, I present an in silico analysis of the virus spike glycoprotein (recently determined at atomic resolution) and provide insights into how antibodies against the 2002 virus SARS-CoV might be modified to neutralize SARS-CoV-2. I ran docking experiments with Rosetta Dock to determine which substitutions in the 80R and m396 antibodies might improve the binding of these to SARS-CoV-2 and used molecular visualization and analysis software, including UCSF Chimera and Rosetta Dock, as well as other bioinformatics tools, including SWISS-MODEL. Supercomputers, including Bridges Large, Stampede and Frontera, were used for macromolecular assemblies and large scale analysis and visualization.

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DOI: 10.3897/rio.6.e54802

Authors: Shantibhusan Senapati, Jayalaxmi Dash, Manisha Sethi, Subhankar Chakraborty

Abstract: The outbreak of 2019 novel corona virus disease (COVID-19) is now a global public health crisis and declared as a pandemic. Several recent studies suggest that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein binds to human angiotensin-converting enzyme 2 (ACE2). The information obtained from these structural and biochemical studies provides a strong rationale to target SARS-CoV-2 spike protein and ACE2 interaction for developing therapeutics against this viral infection. Here, we propose to discuss the scope of bioengineered probiotics expressing human ACE2 as a novel therapeutic to control the viral outbreak.

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DOI: 10.3897/rio.6.e54770

Authors: Daniel Mietchen, Jundong Li

Abstract: In this project, we will explore the range of data-related decisions made during public health emergencies like the ongoing COVID-19 pandemic and analyze the flow of information, data, and metadata within networks of such decisions.Data sharing is now considered a key component of addressing present, future, and even past public health emergencies, from local to global levels. Researchers, research institutions, journals and others have taken steps towards increasing the sharing of data around the ongoing COVID-19 pandemic and in preparation for future pandemics.We will quantify the effects of data flow modifications to identify parameter sets under which specific modes of sharing or withholding information have the largest effects on outbreak dynamics. For these high-impact parameter sets, we will then assess the current and past availability of corresponding data, metadata, and misinformation, and estimate the effects on outbreak mitigation and preparedness efforts.

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DOI: 10.3897/rio.6.e53767

Authors: Madhusudana Girija Sanal, Ravi Chandra Dubey

Abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2/2019-nCoV) infection has become a pandemic called COVID-19. The virus binds to angiotensin converting enzyme 2 (ACE2) and TMPRSS2 which are abundantly expressed on various human cells including lung epithelial cells and intestinal cells and the virus can infect these cells. Currently no specific treatments or vaccines are available for this disease. A per oral live attenuated vaccine can be a good strategy in SARS-CoV-2 infection because the attenuated virus initially infects the gut, stimulates the mucosa associated immune system sparing the respiratory system during the initial immune response. The live virus can also spread in the community boosting herd immunity.

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DOI: 10.3897/rio.6.e53608

Authors: Brady Mattsson, Werner Toth, Marianne Penker, Pia Kieninger, Harald Vacik

Abstract: Coupled human and natural systems exhibit complex interactions (e.g. feedback-loops) that are often poorly understood. Decision-makers from regional (e.g., state or provincial) scale environmental stewardship programs to international policy makers are often faced with uncertainties about future climatic and sociopolitical conditions (henceforth, system change) when supporting livelihoods and ecosystem services derived from lands and waters they oversee. Understanding how these system changes interact with adaptive decision-making processes toward stewardship of ecosystem services represents a considerable gap in knowledge. Adaptation, or iterative adjustment of management practices in response to or anticipation of system change, has been forwarded as a means of effective ecosystem stewardship. Furthermore, lack of clarity about value tradeoffs among competing program objectives (e.g., economics and aesthetics) often precludes development and implementation of adaptation. Although there have been several qualitative studies on regional to national adaptation, lacking is an empirical understanding of how the drivers and value tradeoffs associated with adaptation differ among regions and between related sectors spanning multiple countries. Diverse cultural heritages and political structures among regions of central Europe offer great opportunities for examining spatial patterns of limitations to regional-scale adaptation in forest and agricultural sectors. This project will develop a quantitative index of adaptation for examining hypotheses about patterns of rural adaptation within regions of nine countries in central Europe. Alternative hypotheses describe contrasting assumptions regarding geographic variation in the relative importance among drivers and objectives associated with adaptation. Predictions derived from these hypotheses will be examined through a survey instrument that gathers information from programs focused on rural stewardship. Survey data will be analyzed using a hierarchical Bayesian approach that accounts for biases and missing information often resulting from surveys. Interviews will be used to validate survey responses and receive feedback on inferences made from the analysis of the survey data. Placing findings within the context of existing adaptation literature and evaluating subtler patterns that emerge from the survey data will generate new hypotheses to be examined through future research. The research will be conducted at University of Natural Resources and Life Sciences (BOKU) in Vienna. The applicant Harald Vacik from the Institute of Silviculture at the Department of Forest and Soil Sciences has proven his expertise on the evaluation of natural resource management in the context of sustainability, biodiversity and climate change. The post docs Brady Mattsson, Pia Kieninger and the PhD student Werner Toth contribute with their experience in developing climate adaptation decision support systems and providing uncertainty analysis in environmental decision-making. The proposed study will be an important step in advancing knowledge about adaptation and the interplay between humans and nature in maintaining a sustainable supply of ecosystem goods and services. This novel research integrates multiple scientific disciplines (e.g., ecology, sociology, decision theory, statistics) and to generate an integrated index of adaptation.

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DOI: 10.3897/rio.6.e53542

Authors: Roger Hyam

Abstract: BACKGROUND: Recent studies have shown an association between vegetation around dwellings and mortality, with mental health as a possible mediator.OBJECTIVES: Examine whether there is an association between greenness and mortality or greenness and the proportion of the population being prescribed drugs for anxiety, depression or psychosis in urban areas of Scotland.METHODS: Two greenness maps were prepared based on Landsat 8 Normalised Difference Vegetation Index data from 2013 to 2016, one for summer and one for winter. Greenness was sampled from these maps around each of 91,357 urban postcodes. The greenness data was averaged by 4,883 urban Data Zones covering 71% of the Scottish population and compared with mortality and prescription rate data from the Scottish Index of Multiple Deprivation.RESULTS: The areas least green in the summer were found to have higher mortality rates but no association was found between mortality and winter-greenness. The largest relative differences of mortality were around 9%. High levels of summer-greenness were associated with an increase in mental health prescription rates but areas with the highest differences between summer and winter-greenness had lower prescription rates than other areas. The largest relative difference in prescription rate was 17%. All models controlled for overall deprivation. It is hypothesised that the year round greenness of mown grass is associated with increased mental health prescriptions and obscures the benefits of other kinds of vegetation on both mortality and mental health.DISCUSSION: There is an association between greenness and mortality and greenness and mental health. The association is both statistically significant and large enough to be of importance for policy making. Higher levels of non mown grass vegetation may be preferable for human wellbeing but more detailed understanding of the diversity of plant life in urban areas and how people related to it is required to make more specific recommendations.

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DOI: 10.3897/rio.6.e52052

Authors: Guy Ziv, Michael Beckmann, James Bullock, Anna Cord, Ruth Delzeit, Cristina Domingo, Gunnar Dreßler, Nina Hagemann, Joan Masó, Birgit Müller, Markus Neteler, Anna Sapundzhieva, Pavel Stoev, Jon Stenning, Milica Trajković, Tomáš Václavík

Abstract: Half of the European Union (EU) land and the livelihood of 10 million farmers is threatened by unsustainable land-use intensification, land abandonment and climate change. Policy instruments, including the EU Common Agricultural Policy (CAP) have so far failed to stop this environmental degradation. BESTMAP will: 1) Develop a behavioural theoretical modelling framework to take into account complexity of farmers’ decision-making; 2) Develop, adapt and customize a suite of opensource, flexible, interoperable and customisable computer models linked to existing data e.g. LPIS/IACS and remote sensing e.g. Sentinel-2; 3) Link economic, individual-farm agent-based, biophysical ecosystem services and biodiversity and geostatistical socio-economic models; 4) Produce a simple-to-use dashboard to compare scenarios of Agri-Environmental Schemes adoption; 5) Improve the effectiveness of future EU rural policies’ design, monitoring and implementation.

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DOI: 10.3897/rio.6.e48887

Authors: Helen Minnis, Maj-Britt Posserud, Lucy Thompson, Christopher Gillberg

Abstract: We integrate recent findings from neuro-anatomy, electroencephalography, quantum biology and social/neurodevelopment to propose that the brain surface might be specialised for communication with other brains.Ground breaking, but still small-scale, research has demonstrated that human brains can act in synchrony and detect the brain activity of other human brains. Group aggregation, in all species, maximises community support and safety but does not depend on verbal or visual interaction. The morphology of the brain’s outermost layers, across a wide range of species, exhibits a highly folded fractal structure that is likely to maximise exchange at the surface: in humans, a reduced brain surface area is associated with disorders of social communication. The brain sits in a vulnerable exposed location where it is prone to damage, rather than being housed in a central location such as within the ribcage.These observations have led us to the hypothesis that the brain surface might be specialised for interacting with other brains at its surface, allowing synchronous non-verbal interaction. To our knowledge, this has not previously been proposed or investigated.

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DOI: 10.3897/rio.6.e49942

Authors: Tomas Johannisson

Abstract: Background The cerebral cortex is composed of functional units known as columns. The “two levels” hypothesis states that the activity in a column is either at a high level or at a normal, relatively low level. Measurements indicate that the duration of the high activity in a column is around 450 ms. The number of highly active columns is often 4–5. These data are from previous studies on alpha waves in electroencephalograms. The idea is that alpha waves are created when a regulating system keeps the number of highly active columns within proper limits. If this is true, then regulating signals determines the length of the alpha waves, which opens up for a possibility to test the hypothesis.Methods and results Wavelengths were measured in sequences of alpha waves, and distinctive patterns in the wavelength variation were found. The elements of these patterns were repeated at intervals that exactly matched the predicted duration of high activity in individual columns.Conclusions The discovery of patterns in the wavelength variation confirms the central part of the two levels hypothesis. The patterns reveal the actual number of highly active columns. Moreover, the duration of high activity in a column can be measured. Number and duration outside the optimal ranges may lead to a variety of symptoms.

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DOI: 10.3897/rio.5.e37478

Authors: Sven Schade, Wiebke Herding, Arne Fellermann, Alexander Kotsev, Michel Gerboles, Annette Borowiak

Abstract: Low-cost air quality sensors continue to spread. While their measurement quality does not compete with high-end instrumentation deployed in official air quality monitoring stations, they have a great potential to complement existing air quality assessments. However, we still see challenges related to data quality, data interoperability, and for collaborating on data assimilation and calibration. In order to move ahead we gathered as a group of 38 organisations from 14 different countries, including governmental authorities, network operators, citizen science initiatives, environmental Non-Governmental Organisations (NGOs), and academic researchers to explore how we can collaborate and better leverage each other’s work. This statement captures our joint findings and recommendations. Our key observations include: Co-operation between official monitoring networks (reference quality data) and lower-cost sensor operators is a key to make air quality data more usable. To be able to combine forces and benefit from each other’s expertise, the different perspectives of all stakeholders should be taken into account. There is a need to ensure that all users understand the possibilities and the limitations of making sense out of observations from different sensors. It is not realistic to expect that in the near future the data quality of lower-cost sensors will be as good as that of the official data. A way to make use of data that is of lower accuracy is by employing them in air quality modelling. Transparency about data quality is important to build more trust in the data, and to avoid unrealistic expectations. The need for interoperability should be clearly articulated and promoted by potential data users. There a need (and an opportunity) to provide guidance and standard operating procedures for the deployment and calibration of lower-cost sensors in order to increase the data quality delivered by participants of citizen science projects. Presently, we prefer to consider fixed-stationary sensors in a network instead of mobile sensor data. Furthermore, stationary data should not be aggregated with data from mobile sensors. Publishing and sharing this statement is only small step in the right direction and further actions have to be taken, inlcuding more in-depth discussions of the recommendations in smaller groups and follow-up meetings on dedicated topics.

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DOI: 10.3897/rio.5.e34059

Authors: Sven Schade, Wiebke Herding, Arne Fellermann, Alexander Kotsev

Abstract: Low-cost air quality sensors continue to spread. While their measurement quality does not compete with high-end instrumentation deployed in official air quality monitoring stations, they have a great potential to complement existing air quality assessments. However, we still see challenges related to data quality, data interoperability, and for collaborating on data assimilation and calibration. In order to move ahead we gathered as a group of 38 organisations from 14 different countries, including governmental authorities, network operators, citizen science initiatives, environmental Non-Governmental Organisations (NGOs), and academic researchers to explore how we can collaborate and better leverage each other’s work. This statement captures our joint findings and recommendations. Our key observations include: Co-operation between official monitoring networks (reference quality data) and lower-cost sensor operators is a key to make air quality data more usable. To be able to combine forces and benefit from each other’s expertise, the different perspectives of all stakeholders should be taken into account. There is a need to ensure that all users understand the possibilities and the limitations of making sense out of observations from different sensors. It is not realistic to expect that in the near future the data quality of lower-cost sensors will be as good as that of the official data. A way to make use of data that is of lower accuracy is by employing them in air quality modelling. Transparency about data quality is important to build more trust in the data, and to avoid unrealistic expectations. The need for interoperability should be clearly articulated and promoted by potential data users. There a need (and an opportunity) to provide guidance and standard operating procedures for the deployment and calibration of lower-cost sensors in order to increase the data quality delivered by participants of citizen science projects. Presently, we prefer to consider fixed-stationary sensors in a network instead of mobile sensor data. Furthermore, stationary data should not be aggregated with data from mobile sensors. Publishing and sharing this statement is only small step in the right direction and further actions have to be taken, inlcuding more in-depth discussions of the recommendations in smaller groups and follow-up meetings on dedicated topics.

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DOI: 10.3897/rio.5.e33400

Authors: Mary Kelly-Quinn, Michael Bruen, Jens Carlsson, Angela Gurnell, Helen Jarvie, Jeremy Piggott

Abstract: This paper outlines the research being undertaken by the recently-initiated four-year (to March 2022) project on the small stream network in Ireland (SSNet) funded by the Irish Environmental Protection Agency (EPA). The overarching objective of SSNet is to advance knowledge on the role of small streams in water quality, biodiversity and ecosystem services protection that will inform policy, measures and management options to meet water quality and other resources protection targets. The project will start with a synthesis of available information on the importance of small streams to initiate communication with stakeholders and introduce the project. This will be followed by a compilation and analysis of existing data on small streams in Ireland to inform the selection of sites for the proposed research. Three work packages will collect new data on hydrochemistry with a focus on the nutrient retention potential of headwater streams, hydromorphology and biodiversity. All three investigations will share common sites to enable interconnections between the three elements to be explored and provide an integrated approach to the research. Modelling based on the results from each of the aforementioned tasks will be used to estimate the level of intervention in the small stream network required to have measurable effects throughout a catchment on both water quality (N, P & sediment) and flows, and overall delivery/maintenance of ecosystem services. We will also engage volunteers in both biological water quality and hydromorphological assessments and evaluate the potential of citizen science in facilitating greater monitoring coverage of the small stream network.

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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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DOI: 10.3897/rio.4.e30729

Authors: Solveig Hausken, Natalie Barker-Ruchti, Astrid Schubring, Stefan Grau

Abstract: This interdisciplinary research project will produce evidence-based recommendations on how injuries in Swedish youth football (soccer) can be prevented. Fewer injuries will positively impact athlete health, performance and career longevity and have the potential to promote life-long physical activity and wellbeing.Injury pattern research demonstrates that injuries are a significant problem in (Swedish) youth sport. Football has a higher traumatic and overuse injury rate than many contact/collision sports (e.g., field hockey, basketball). In research on youth football, the incidence of overuse training injuries was measured as high as 15.4 injuries per 1000 training hours, and the incidence of traumatic and overuse match injuries was 47.5 injuries per 1000 match hours. The injury frequency is alarming and applies to the 54% of children aged 7-14 and the 39% of youths aged 15-19 years who participate in Swedish organised sports. A large body of research identifies injury risk factors and preventative strategies; however, as the recent IOC consensus statement on youth athletic development points out, the existing, mostly bio-medical knowledge does not provide effective evidence-based injury prevention strategies. To address this deficit, interdisciplinary and context-driven knowledge on injury development in youth sport is needed.The proposed project will produce scientific evidence through four consecutive studies: a) Questionnaire to register the types, frequency and management of injuries; b) Laboratory testing of biomechanical, clinical and training-specific parameters to establish individual physical and sport-specific dispositions; c) Observation of sporting contexts to understand sporting cultures, coaching methods and coach-athlete relationships; and d) Interviews with coaches and players to recognize knowledge that shapes coaching and training. The sample of youth players will be recruited from Sweden’s most popular and injury-prone sport: football. Each of the four studies will conduct its own data production and analyses, and a collective analysis will produce integrated evidence. Concrete recommendations for best sporting practice will be developed, which will serve sporting federations, sport education institutions, coaches, sport support staff and players.

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DOI: 10.3897/rio.4.e29438

Authors: Carlos Mingorance Gámez

Abstract: Granulocytes share the common feature of having a lobulated nucleus, a fact whose function has yet to be discussed in depth. This hypothesis suggests that the division of the nuclei follows an epigenetic purpose, separating genes into compartments with different regulatory mechanisms, which may be due to intrinsic factors like regulatory RNA or extrinsic factors like proteins. This paper describes the outlines of a line of research for both the initial testing to test the hypothesis and the following descriptive studies, including potential clinical uses in the prognosis or diagnosis of diseases that present dysregulation of the number of lobes. The chosen approach is to study the pattern of distribution (random or otherwise) of genes amongst the lobes.

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DOI: 10.3897/rio.4.e28578

Authors: Josephine Warren, Brian Martin

Abstract: New diseases in humans and animals have been the subject of considerable research as well as policy development and popular attention. Researchers commonly proceed on the basis of plausible assumptions about mechanisms, pathways, and dangers but seldom question the assumptions themselves. Studies in the history and sociology of science show that research trajectories are conditioned by social, political, and economic arrangements. The assumptions underlying research into three new diseases—devil facial tumor disease in Tasmanian devils, AIDS in humans, and leukemia in soft-shell clams—are examined, and dominant and alternative research programs compared. In each case, most research has assumed the disease is spread through “natural processes”, while research about possible human influences has been left undone.

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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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DOI: 10.3897/rio.4.e28069

Authors: Jason Friesen, Brendon Friesen, Ee Syn Tan

Abstract:

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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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DOI: 10.3897/rio.4.e26370

Authors: Pradeep Joseph

Abstract: The state of health disparities in the United States has remained relatively stable over a number of years. Although overall outcomes for all patients have improved, a difference persists in how different racial, ethnic, and gender groups have fared in our health care system. Many programs that have sought to combat this problem have been predicated on the belief that only a small number of providers in the medical community are aware of their own biases. Accordingly, it was believed that bias awareness is the direct conduit for this particular change in the health system. However, the results of such programs have been unsatisfactory. The reason for such ineffectiveness is that many programs have not taken into account the presence of implicit bias within the patient-provider relationship. This complex form of bias operates in specific ways, and must be dealt with appropriately. The use of digital checklists to aid in clinical decision making has proved to be both a way that patients can receive equitable care, and a way to improve overall patient outcomes. Secondly, in order to reach the most at-risk populations, health care must expand beyond the hospital walls, and out into the community. Nurse navigator programs have been shown to accomplish this with great success. Together, checklists and nurse navigators are the necessary next-step in the battle against health care disparities. What’s more, this two-pronged approach is relatively simple to implement. By making use of current electronic medical records, digital checklists can be quickly installed. Likewise, nurse navigator programs, a comparatively inexpensive option, can be rolled out quickly because of their simple design. A focus on the patient-provider relationship and community outreach is critical for progress in eliminating health care disparities.

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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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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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DOI: 10.3897/rio.3.e21700

Authors: Cameron Neylon

Abstract: The project “Problemes négligés du système de santé au Niger” focusses on a core set of often-neglected issues that nevertheless have an overall negative impact on health system effectiveness in Niger. For example, poor quality maternal health services result from challenges related to the midwifery profession and from pressures from addressing the effects of illegal termination of pregnancy. Overall health system governance is undermined by weak management of human resources and health information systems as well as problems related to decentralisation of health care provision and dependence on external funding for health projects. LASDEL applies a rapid assessment and qualitative research approach to working with patients and health care professionals to identify the scale and characteristics of these problems. The project goal is to develop an evidence base to support tackling these neglected issues. Développer des recherches sur les « problèmes négligés » dans la gouvernance de la santé, et sur cette base contribuer à des réformes des systèmes de santé permettant une meilleure qualité des soins pour les populations vulnérables. "Develop research on "neglected problems" in the provision of health systems, and through this work, contribute to health system reforms, that provide better quality of care for vulnerable populations." As can be seen above, many of these issues relate to reproductive health and more generally to health issues of disadvantaged groups. Some issues are neglected for political or social reasons meaning that they are not recognised or acknowledged and in some cases are criminalised. Therefore there are profound issues of participant privacy, protection and even safety for this project. Data sharing therefore requires thoughtful anonymisation and selection. The project group is Francophone with limited English language knowledge and the researchers and the context is largely in French. In common with much of Francophone Africa there has been limited development of Open Access to research outputs or Open Research Data agendas at governmental or funder levels. Outside of Canada and France there has been limited development of infrastructure, systems or policy relating to data sharing in the global francophonie specifically.

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DOI: 10.3897/rio.3.e21703

Authors: Cameron Neylon

Abstract: The Tobacco Control Economics Project is a project that seeks to gather evidence on tobacco use and economics in southern Africa. It is a project of the University of Cape Town with support from the DataFirst repository based at the University of Cape Town. Its aim is to gather data that already exists, sometimes in digital form, frequently in offline records or in some cases paper records, and bring them together as an open resource. The project faces challenges of data gathering as well as permissions. Frequently data is or should be “available” in some form but control over the data is relinquished only unreluctantly. In many cases the legal standing of data is unclear. Many of the challenges relating to the bringing together of the data involve ascertaining what the legal standing of a dataset is or gaining permissions for its re-use. DataFirst is a longstanding data sharing infrastructure with professional and experienced data management staff. Challenges of ensuring continued funding and maintenance are similar to those of data infrastructures globally. The infrastructure meets international standards and provides leadership to other services and platforms in this space.

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DOI: 10.3897/rio.3.e21705

Authors: Cameron Neylon

Abstract: There is a wide and growing interest in promoting Research Data Management (RDM) and Research Data Sharing (RDS) from many stakeholders in the research enterprise. Funders are under pressure from activists, from government, and from the wider public agenda towards greater transparency and access to encourage, require, and deliver improved data practices from the researchers they fund. Funders are responding to this, and to their own interest in improved practice, by developing and implementing policies on RDM and RDS. In this review we examine the state of funder policies, the process of implementation and available guidance to identify the challenges and opportunities for funders in developing policy and delivering on the aspirations for improved community practice, greater transparency and engagement, and enhanced impact. The review is divided into three parts. The first two components are based on desk research: a survey of existing policy statements drawing in part on existing surveys and a brief review of available guidance on policy development for funders. The third part addresses the experience of policy implementation through interviews with funders, policy developers, and infrastructure providers. In our review we identify, in common with other surveys, that RDM and RDS policies are increasingly common. The most developed are found amongst funders in the United States, United Kingdom, Australia, and European Union. However many other funders and nations have aspirational statements or are developing policy. There is a broad pattern of policy development moving from aspiration, to recommendations, to requirements, and finally reporting and auditing of data management practice. There are strong similarities across policies: a requirement for data management planning, often in grant submissions, expectations that data supporting published articles will be made available, and in many cases requirements for data archiving and availability over extended periods beyond grants. However there are also important differences in implementation. There is essentially no information available on the uptake and success of different policies in terms of compliance rates, or degrees of data availability. Many policies require a Data Management Plan as part of grant submission. This requirement can be enforced but there is disagreement on the value of this. One view is that requirements such as DMPs are the only way to force researchers to pay attention to these issues. The other is that such requirements lead to a culture of compliance in which the minimal effort is made and planning is seen as a “tick-box” exercise that has no further value. In this view requirements such as DMPs may actually be damaging the effort to effect culture change towards improved community practice. One way to bring these two views together is to see DMPs as living documents that form the basis of collaboration between researchers, funders, and data managers throughout the life of a research project. This approach is reflected in guidance on policy development that emphasises the importance of clarifying responsibilities of various stakeholders and ensuring that researchers are both recognised for good practice and see tangible benefits. More broadly this points to the need for the program of improving RDM and RDS to be shared project with the incentives for funders and researchers aligned as far as is possible. In the interviews successful policy implementation was often seen to be dependent on funders providing the required support, both in the form of infrastructure and resourcing, and via the provision of internal expertise amongst program managers. Where resources are limited, leveraging other support, especially from institutional sources, was seen as important as was ensuring the scope of policy requirements were commensurate with the support available and readiness of research communities. Throughout the desk research and the interviews a consistent theme is the desire for cultural change, where data management and sharing practices are embedded within the norms of behaviour for research communities. There is general agreement that progress from aspirational policies to achieving compliance is challenging and that broad cultural change, with the exception of specific communities, is a long way off. It is interesting to note that discussion of cultural change is largely externalised. There is little engagement with the concept of culture as an issue to consider or work with and very little engagement with models of how cultural change could be enabled. The disagreement over the value of DMPs is one example of how a lack of active engagement with culture and how it changes is leading to problems. Key Findings Policies on RDM and RDS are being developed by a number of agencies, primarily in the Global North. These policies are broadly consistent in aspiration and outlines but differ significantly in details of implementation. Policies generally develop along a path starting with aspirational statements, followed by recommendations, then requirements, and finally auditing and compliance measures. Measurement of policy adoption and compliance in terms of the over goals of increased availability and re-use of data is not tracked and is likely unmeasurable currently. Data Management Plans are a central requirement for many policies, in part because they can be made compulsory and act as a general focus for raising awareness. There are significant differences in the views of stakeholders on the value of Data Management Planning in its current form. Some stakeholders regard them as successful in raising awareness albeit with some limitations. Some regard them as actively damaging progress towards real change in practice by making RDM appear as one administrative activity among the many required for grant submission Successful policy implementation is coupled with funder support for infrastructure and training. Seeing RDM as an area for collaboration between funders and researchers may be valuable Internal expertise and support within a funder is often a gap which becomes a problem with monitoring and implementation DMPs can be a helpful part of process but it will be important to make them useful documents throughout and beyond the project If the object of RDM and RDS policy is cultural change in research communities then direct engagement with understanding the various cultures of researcher and other stakeholder communities, alongside frameworks of how they change is an important area for future focus.

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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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DOI: 10.3897/rio.3.e20695

Authors: Jennifer Wessel, David Marrero

Abstract: Extensive research now demonstrates that lifestyle modification can significantly lower risk of developing type 2 diabetes (T2D) in high-risk adults. In children, the evidence for lifestyle modification is not as robust, but the rapidly rising rate of obesity in children coupled with the substantial difficulty in changing behaviors later in life illuminates the need to implement prevention efforts early in the life course of children. Genetic data can now be used early in the life course to identify children at high-risk of developing T2D before traditional clinical measures can detect the presence of prediabetes; a metabolic condition associated with obesity that significantly increases risk for developing T2D.  Such early detection of risk may enable the promotion of “primordial prevention” in which parents implement behavior change for their at risk children.  Young children with genetic risk are a novel target population.  Here we review the literature on genetic testing for prevention as it relates to chronic diseases and specifically use T2D as a model. We discuss the history of primordial prevention, the need for primordial prevention of T2D and the role genetic testing has in primordial prevention of high-risk families.

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DOI: 10.3897/rio.3.e20696

Authors: Andrey Vyshedskiy, Shreyas Mahapatra, Rita Dunn

Abstract: We analyzed all published reports of individuals not exposed to syntactic language until puberty: two feral children, who grew up without hearing any language, and eight deaf linguistic isolates, who grew up communicating to their families using homesign or kitchensign, a system of gestures which allows them to communicate simple commands but lacks much in the way of syntax. A common observation in these individuals is the lifelong difficulty understanding syntax and spatial prepositions, even after many years of rehabilitation. This debilitating condition stands in stark contrast to linguistic isolates’ performance on memory as well as semantic tests: they could easily remember hundreds of newly learned words and identify previously seen objects by name. The lack of syntactic language comprehension in linguistic isolates may stem from inability to understand words and/or grammar or inability to mentally synthesize known objects into novel configurations. We have previously shown that purposeful construction of novel mental images is the function of the lateral prefrontal cortex (LPFC) ability to dynamically control posterior cortex neurons (Vyshedskiy et al. 2017). Here we have ranked all tests performed on linguistic isolates by their reliance on the LPFC control of the posterior cortex: a) the amount of posterior cortex territory that needs to be recruited by the LPFC and b) the number of disparate objects that have to be combined together by the LPFC in order to answer the test question. According to our analysis, linguistic isolates performed well in all tests that did not involve the LPFC control of the posterior cortex, showed decreasing scores in tests that involved greater recruitment of the posterior cortex by the LPFC, and failed in tests that involved greatest recruitment of posterior cortex necessary for mental synthesis of multiple objects. This pattern is consistent with inadequate frontoposterior connections in linguistic isolates. We discuss implications of these findings for the importance of early syntactic language exposure in formation of frontoposterior connections.

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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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