1
|
Groenewold M, Bleeker EAJ, Noorlander CW, Sips AJAM, van der Zee M, Aitken RJ, Baker JH, Bakker MI, Bouman EA, Doak SH, Drobne D, Dumit VI, Florin MV, Fransman W, Gonzalez MM, Heunisch E, Isigonis P, Jeliazkova N, Jensen KA, Kuhlbusch T, Lynch I, Morrison M, Porcari A, Rodríguez-Llopis I, Pozuelo BM, Resch S, Säämänen AJ, Serchi T, Soeteman-Hernandez LG, Willighagen E, Dusinska M, Scott-Fordsmand JJ. Governance of advanced materials: Shaping a safe and sustainable future. NANOIMPACT 2024; 35:100513. [PMID: 38821170 DOI: 10.1016/j.impact.2024.100513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/30/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
The past few decades of managing the uncertain risks associated with nanomaterials have provided valuable insights (knowledge gaps, tools, methods, etc.) that are equally important to promote safe and sustainable development and use of advanced materials. Based on these insights, the current paper proposes several actions to optimize the risk and sustainability governance of advanced materials. We emphasise the importance of establishing a European approach for risk and sustainability governance of advanced materials as soon as possible to keep up with the pace of innovation and to manage uncertainty among regulators, industry, SMEs and the public, regarding potential risks and impacts of advanced materials. Coordination of safe and sustainable advanced material research efforts, and data management according to the Findable, Accessible, Interoperable and Reusable (FAIR) principles will enhance the generation of regulatory-relevant knowledge. This knowledge is crucial to identify whether current regulatory standardised and harmonised test methods are adequate to assess advanced materials. At the same time, there is urgent need for responsible innovation beyond regulatory compliance which can be promoted through the Safe and Sustainable Innovation Approach. that combines the Safe and Sustainable by Design concept with Regulatory Preparedness, supported by a trusted environment. We further recommend consolidating all efforts and networks related to the risk and sustainability governance of advanced materials in a single, easy-to-use digital portal. Given the anticipated complexity and tremendous efforts required, we identified the need of establishing an organisational structure dedicated to aligning the fast technological developments in advanced materials with proper risk and sustainability governance. Involvement of multiple stakeholders in a trusted environment ensures a coordinated effort towards the safe and sustainable development, production, and use of advanced materials. The existing infrastructures and network of experts involved in the governance of nanomaterials would form a solid foundation for such an organisational structure.
Collapse
Affiliation(s)
- Monique Groenewold
- National Institute for Public Health and the Environment (RIVM), Centre for Safety of Substances and Products, Bilthoven, the Netherlands.
| | - Eric A J Bleeker
- National Institute for Public Health and the Environment (RIVM), Centre for Safety of Substances and Products, Bilthoven, the Netherlands
| | - Cornelle W Noorlander
- National Institute for Public Health and the Environment (RIVM), Centre for Safety of Substances and Products, Bilthoven, the Netherlands
| | - Adriënne J A M Sips
- National Institute for Public Health and the Environment (RIVM), Centre for Safety of Substances and Products, Bilthoven, the Netherlands
| | | | - Robert J Aitken
- Institute of Occupational Medicine (IOM), Edinburgh, United Kingdom
| | - James H Baker
- Nanotechnology Industries Association (NIA), Brussels, Belgium
| | - Martine I Bakker
- National Institute for Public Health and the Environment (RIVM), Centre for Safety of Substances and Products, Bilthoven, the Netherlands
| | - Evert A Bouman
- The Climate and Environmental Research Institute (NILU), Department of Environmental Chemistry and Health, Kjeller, Norway
| | - Shareen H Doak
- Swansea University, Medical School, Faculty of Medicine, Health & Life Sciences, SA2 8PP, Wales, United Kingdom
| | - Damjana Drobne
- University of Ljubljana, Department of Biology, Biotechnical Faculty, Ljubljana, Slovenia
| | - Verónica I Dumit
- German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Berlin, Germany
| | | | | | - Mar M Gonzalez
- Organisation for Economic Co-operation and Development (OECD), Paris, France
| | - Elisabeth Heunisch
- Federal Institute for Occupational Safety and Health (BAUA), Dortmund/ Berlin, Germany
| | | | | | - Keld Alstrup Jensen
- National Research Centre for the Working Environment (NFA), Copenhagen, Denmark
| | - Thomas Kuhlbusch
- Federal Institute for Occupational Safety and Health (BAUA), Dortmund/ Berlin, Germany
| | - Iseult Lynch
- University of Birmingham, School of Geography, Earth and Environmental Sciences, Edgbaston, Birmingham, United Kingdom
| | | | - Andrea Porcari
- Italian Association for Industrial Research (AIRI), Roma, Italy
| | | | | | - Susanne Resch
- BioNanoNet Forschungsgesellschaft mbH, Graz, Austria
| | | | - Tommaso Serchi
- Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
| | - Lya G Soeteman-Hernandez
- National Institute for Public Health and the Environment (RIVM), Centre for Safety of Substances and Products, Bilthoven, the Netherlands
| | - Egon Willighagen
- Maastricht University, Dept of Bioinformatics - BiGCaT, NUTRIM, Maastricht, the Netherlands
| | - Maria Dusinska
- The Climate and Environmental Research Institute (NILU), Department of Environmental Chemistry and Health, Kjeller, Norway
| | | |
Collapse
|
2
|
Balraadjsing S, J G M Peijnenburg W, Vijver MG. Building species trait-specific nano-QSARs: Model stacking, navigating model uncertainties and limitations, and the effect of dataset size. ENVIRONMENT INTERNATIONAL 2024; 188:108764. [PMID: 38788418 DOI: 10.1016/j.envint.2024.108764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
A strong need exists for broadly applicable nano-QSARs, capable of predicting toxicological outcomes towards untested species and nanomaterials, under different environmental conditions. Existing nano-QSARs are generally limited to only a few species but the inclusion of species characteristics into models can aid in making them applicable to multiple species, even when toxicity data is not available for biological species. Species traits were used to create classification- and regression machine learning models to predict acute toxicity towards aquatic species for metallic nanomaterials. Afterwards, the individual classification- and regression models were stacked into a meta-model to improve performance. Additionally, the uncertainty and limitations of the models were assessed in detail (beyond the OECD principles) and it was investigated whether models would benefit from the addition of more data. Results showed a significant improvement in model performance following model stacking. Investigation of model uncertainties and limitations highlighted the discrepancy between the applicability domain and accuracy of predictions. Data points outside of the assessed chemical space did not have higher likelihoods of generating inadequate predictions or vice versa. It is therefore concluded that the applicability domain does not give complete insight into the uncertainty of predictions and instead the generation of prediction intervals can help in this regard. Furthermore, results indicated that an increase of the dataset size did not improve model performance. This implies that larger dataset sizes may not necessarily improve model performance while in turn also meaning that large datasets are not necessarily required for prediction of acute toxicity with nano-QSARs.
Collapse
Affiliation(s)
- Surendra Balraadjsing
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA Leiden, the Netherlands.
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA Leiden, the Netherlands; Centre for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, the Netherlands
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA Leiden, the Netherlands
| |
Collapse
|
3
|
Jeliazkova N, Longhin E, El Yamani N, Rundén-Pran E, Moschini E, Serchi T, Vrček IV, Burgum MJ, Doak SH, Cimpan MR, Rios-Mondragon I, Cimpan E, Battistelli CL, Bossa C, Tsekovska R, Drobne D, Novak S, Repar N, Ammar A, Nymark P, Di Battista V, Sosnowska A, Puzyn T, Kochev N, Iliev L, Jeliazkov V, Reilly K, Lynch I, Bakker M, Delpivo C, Sánchez Jiménez A, Fonseca AS, Manier N, Fernandez-Cruz ML, Rashid S, Willighagen E, D Apostolova M, Dusinska M. A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials. Nat Protoc 2024:10.1038/s41596-024-00993-1. [PMID: 38755447 DOI: 10.1038/s41596-024-00993-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 02/20/2024] [Indexed: 05/18/2024]
Abstract
Making research data findable, accessible, interoperable and reusable (FAIR) is typically hampered by a lack of skills in technical aspects of data management by data generators and a lack of resources. We developed a Template Wizard for researchers to easily create templates suitable for consistently capturing data and metadata from their experiments. The templates are easy to use and enable the compilation of machine-readable metadata to accompany data generation and align them to existing community standards and databases, such as eNanoMapper, streamlining the adoption of the FAIR principles. These templates are citable objects and are available as online tools. The Template Wizard is designed to be user friendly and facilitates using and reusing existing templates for new projects or project extensions. The wizard is accompanied by an online template validator, which allows self-evaluation of the template (to ensure mapping to the data schema and machine readability of the captured data) and transformation by an open-source parser into machine-readable formats, compliant with the FAIR principles. The templates are based on extensive collective experience in nanosafety data collection and include over 60 harmonized data entry templates for physicochemical characterization and hazard assessment (cell viability, genotoxicity, environmental organism dose-response tests, omics), as well as exposure and release studies. The templates are generalizable across fields and have already been extended and adapted for microplastics and advanced materials research. The harmonized templates improve the reliability of interlaboratory comparisons, data reuse and meta-analyses and can facilitate the safety evaluation and regulation process for (nano) materials.
Collapse
Affiliation(s)
| | - Eleonora Longhin
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Naouale El Yamani
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Elise Rundén-Pran
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway
| | - Elisa Moschini
- Environmental Health group, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Tommaso Serchi
- Environmental Health group, Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | | | - Michael J Burgum
- In Vitro Toxicology Group, Faculty of Medicine, Health and Life Sciences, Institute of Life Sciences, Swansea University Medical School, Singleton Park, Swansea, Wales, UK
| | - Shareen H Doak
- In Vitro Toxicology Group, Faculty of Medicine, Health and Life Sciences, Institute of Life Sciences, Swansea University Medical School, Singleton Park, Swansea, Wales, UK
| | | | | | - Emil Cimpan
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | | | - Cecilia Bossa
- Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Rositsa Tsekovska
- Medical and Biological Research Laboratory, Roumen Tsanev Institute of Molecular Biology-Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Neža Repar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ammar Ammar
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Veronica Di Battista
- BASF SE, Material Physics, Carl Bosch straße, Ludwigshafen, Germany
- Department of Environmental and Resource Engineering, DTU, Kgs. Lyngby, Denmark
| | - Anita Sosnowska
- QSAR Lab Ltd., Gdańsk, Poland
- University of Gdańsk, Faculty of Chemistry, Gdansk, Poland
| | - Tomasz Puzyn
- QSAR Lab Ltd., Gdańsk, Poland
- University of Gdańsk, Faculty of Chemistry, Gdansk, Poland
| | - Nikolay Kochev
- Ideaconsult Ltd., Sofia, Bulgaria
- Department of Analytical Chemistry and Computer Chemistry, Faculty of Chemistry, University of Plovdiv, Plovdiv, Bulgaria
| | | | | | - Katie Reilly
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Martine Bakker
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - Araceli Sánchez Jiménez
- Spanish National Institute of Health and Safety, Centro Nacional de Verificación de Maquinaria, Barakaldo, Spain
| | - Ana Sofia Fonseca
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Nicolas Manier
- Ecotoxicology of Substances and Environmental Matrices Unit, French National Institute for Industrial Environment and Risks, Verneuil-en-Halatte, France
| | - María Luisa Fernandez-Cruz
- Department of Environment and Agronomy, National Institute for Agriculture and Food Research and Technology, Spanish National Research Council, Madrid, Spain
| | - Shahzad Rashid
- Institute of Occupational Medicine, Research Avenue North, Edinburgh, UK
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Margarita D Apostolova
- Medical and Biological Research Laboratory, Roumen Tsanev Institute of Molecular Biology-Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry & Health Effects, The Climate and Environmental Research Institute NILU, Kjeller, Norway.
| |
Collapse
|
4
|
Ammar A, Evelo C, Willighagen E. FAIR assessment of nanosafety data reusability with community standards. Sci Data 2024; 11:503. [PMID: 38755173 PMCID: PMC11099147 DOI: 10.1038/s41597-024-03324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
Nanomaterials hold great promise for improving our society, and it is crucial to understand their effects on biological systems in order to enhance their properties and ensure their safety. However, the lack of consistency in experimental reporting, the absence of universally accepted machine-readable metadata standards, and the challenge of combining such standards hamper the reusability of previously produced data for risk assessment. Fortunately, the research community has responded to these challenges by developing minimum reporting standards that address several of these issues. By converting twelve published minimum reporting standards into a machine-readable representation using FAIR maturity indicators, we have created a machine-friendly approach to annotate and assess datasets' reusability according to those standards. Furthermore, our NanoSafety Data Reusability Assessment (NSDRA) framework includes a metadata generator web application that can be integrated into experimental data management, and a new web application that can summarize the reusability of nanosafety datasets for one or more subsets of maturity indicators, tailored to specific computational risk assessment use cases. This approach enhances the transparency, communication, and reusability of experimental data and metadata. With this improved FAIR approach, we can facilitate the reuse of nanosafety research for exploration, toxicity prediction, and regulation, thereby advancing the field and benefiting society as a whole.
Collapse
Affiliation(s)
- Ammar Ammar
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
| | - Chris Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - Egon Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands.
| |
Collapse
|
5
|
Wohlleben W, Bossa N, Mitrano DM, Scott K. Everything falls apart: How solids degrade and release nanomaterials, composite fragments, and microplastics. NANOIMPACT 2024; 34:100510. [PMID: 38759729 DOI: 10.1016/j.impact.2024.100510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
To ensure the safe use of materials, one must assess the identity and quantity of exposure. Solid materials, such as plastics, metals, coatings and cements, degrade to some extent during their life cycle, and releases can occur during manufacturing, use and end-of-life. Releases (e.g., what is released, how does release happen, and how much material is released) depend on the composition and internal (nano)structures of the material as well as the applied stresses during the lifecycle. We consider, in some depth, releases from mechanical, weathering and thermal stresses and specifically address the use cases of fused-filament 3D printing, dermal contact, food contact and textile washing. Solid materials can release embedded nanomaterials, composite fragments, or micro- and nanoplastics, as well as volatile organics, ions and dissolved organics. The identity of the release is often a heterogenous mixture and requires adapted strategies for sampling and analysis, with suitable quality control measures. Control materials enhance robustness by enabling comparative testing, but reference materials are not always available as yet. The quantity of releases is typically described by time-dependent rates that are modulated by the nature and intensity of the applied stress, the chemical identity of the polymer or other solid matrix, and the chemical identity and compatibility of embedded engineered nanomaterials (ENMs) or other additives. Standardization of methods and the documentation of metadata, including all the above descriptors of the tested material, applied stresses, sampling and analytics, are identified as important needs to advance the field and to generate robust, comparable assessments. In this regard, there are strong methodological synergies between the study of all solid materials, including the study of micro- and nanoplastics. From an outlook perspective, we review the hazard of the released entities, and show how this informs risk assessment. We also address the transfer of methods to related issues such as tyre wear, advanced materials and advanced manufacturing, biodegradable polymers, and non-solid matrices. As the consideration of released entities will become more routine in industry via lifecycle assessment in Safe-and-Sustainable-by-Design practices, release assessments will require careful design of the study with quality controls, the use of agreed-on test materials and standardized methods where these exist and the adoption of clearly defined data reporting practices that enable data reuse, meta-analyses, and comparative studies.
Collapse
Affiliation(s)
- Wendel Wohlleben
- BASF SE, Dept. of Analytical and Materials Science, 67056 Ludwigshafen, Germany.
| | - Nathan Bossa
- TEMAS Solutions GmbH, Lätterweg 5, 5212 Hausen, Switzerland; Department of Civil & Environmental Engineering, Duke University, Durham, NC 27708, United States
| | - Denise M Mitrano
- Environmental Systems Science Department, ETH Zurich, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Keana Scott
- Materials Measurement Science Division, National Institute of Standards and Technology, 100 Bureau Drive, MS-8372, Gaithersburg, MD 20899, United States
| |
Collapse
|
6
|
Amos JD, Zhang Z, Tian Y, Lowry GV, Wiesner MR, Hendren CO. Knowledge and Instance Mapping: architecture for premeditated interoperability of disparate data for materials. Sci Data 2024; 11:173. [PMID: 38321063 PMCID: PMC10847415 DOI: 10.1038/s41597-024-03006-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/26/2024] [Indexed: 02/08/2024] Open
Abstract
Predicting and elucidating the impacts of materials on human health and the environment is an unending task that has taken on special significance in the context of nanomaterials research over the last two decades. The properties of materials in environmental and physiological media are dynamic, reflecting the complex interactions between materials and these media. This dynamic behavior requires special consideration in the design of databases and data curation that allow for subsequent comparability and interrogation of the data from potentially diverse sources. We present two data processing methods that can be integrated into the experimental process to encourage pre-mediated interoperability of disparate material data: Knowledge Mapping and Instance Mapping. Originally developed as a framework for the NanoInformatics Knowledge Commons (NIKC) database, this architecture and associated methods can be used independently of the NIKC and applied across multiple subfields of nanotechnology and material science.
Collapse
Affiliation(s)
- Jaleesia D Amos
- Center for the Environmental Implications of Nano Technology (CEINT), Durham, USA
- Civil & Environmental Engineering, Duke University, Durham, North Carolina, 2770y8, USA
| | - Zhao Zhang
- Center for the Environmental Implications of Nano Technology (CEINT), Durham, USA
- Civil & Environmental Engineering, Duke University, Durham, North Carolina, 2770y8, USA
- Lucideon M+P, Morrisville, North Carolina, 27560, USA
| | - Yuan Tian
- Center for the Environmental Implications of Nano Technology (CEINT), Durham, USA
- Civil & Environmental Engineering, Duke University, Durham, North Carolina, 2770y8, USA
| | - Gregory V Lowry
- Center for the Environmental Implications of Nano Technology (CEINT), Durham, USA
- Civil & Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, 15213, USA
| | - Mark R Wiesner
- Center for the Environmental Implications of Nano Technology (CEINT), Durham, USA.
- Civil & Environmental Engineering, Duke University, Durham, North Carolina, 2770y8, USA.
| | - Christine Ogilvie Hendren
- Center for the Environmental Implications of Nano Technology (CEINT), Durham, USA
- Civil & Environmental Engineering, Duke University, Durham, North Carolina, 2770y8, USA
- Department of Geological and Environmental Sciences, Appalachian State University, Boone, North Carolina, 28608, USA
| |
Collapse
|
7
|
Del Giudice G, Serra A, Saarimäki LA, Kotsis K, Rouse I, Colibaba SA, Jagiello K, Mikolajczyk A, Fratello M, Papadiamantis AG, Sanabria N, Annala ME, Morikka J, Kinaret PAS, Voyiatzis E, Melagraki G, Afantitis A, Tämm K, Puzyn T, Gulumian M, Lobaskin V, Lynch I, Federico A, Greco D. An ancestral molecular response to nanomaterial particulates. NATURE NANOTECHNOLOGY 2023; 18:957-966. [PMID: 37157020 PMCID: PMC10427433 DOI: 10.1038/s41565-023-01393-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 03/31/2023] [Indexed: 05/10/2023]
Abstract
The varied transcriptomic response to nanoparticles has hampered the understanding of the mechanism of action. Here, by performing a meta-analysis of a large collection of transcriptomics data from various engineered nanoparticle exposure studies, we identify common patterns of gene regulation that impact the transcriptomic response. Analysis identifies deregulation of immune functions as a prominent response across different exposure studies. Looking at the promoter regions of these genes, a set of binding sites for zinc finger transcription factors C2H2, involved in cell stress responses, protein misfolding and chromatin remodelling and immunomodulation, is identified. The model can be used to explain the outcomes of mechanism of action and is observed across a range of species indicating this is a conserved part of the innate immune system.
Collapse
Affiliation(s)
- G Del Giudice
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - A Serra
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere, Finland
| | - L A Saarimäki
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - K Kotsis
- School of Physics, University College Dublin, Dublin, Ireland
| | - I Rouse
- School of Physics, University College Dublin, Dublin, Ireland
| | - S A Colibaba
- School of Physics, University College Dublin, Dublin, Ireland
| | - K Jagiello
- Group of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | - A Mikolajczyk
- Group of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | - M Fratello
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - A G Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
- Novamechanics Ltd, Nicosia, Cyprus
| | - N Sanabria
- National Institute for Occupational Health, National Health Laboratory Services, Johannesburg, South Africa
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - M E Annala
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - J Morikka
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - P A S Kinaret
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland
| | | | - G Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece
| | | | - K Tämm
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - T Puzyn
- Group of Environmental Chemoinformatics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
- QSAR Lab Ltd, Gdańsk, Poland
| | - M Gulumian
- National Institute for Occupational Health, National Health Laboratory Services, Johannesburg, South Africa
- Haematology and Molecular Medicine Department, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Water Research Group, Unit for Environmental Sciences and Management, North West University, Potchefstroom, South Africa
| | - V Lobaskin
- School of Physics, University College Dublin, Dublin, Ireland
| | - I Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - A Federico
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere Institute for Advanced Study, Tampere, Finland
| | - D Greco
- FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLife), University of Helsinki, Helsinki, Finland.
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
8
|
Furxhi I, Willighagen E, Evelo C, Costa A, Gardini D, Ammar A. A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability. NANOIMPACT 2023; 31:100475. [PMID: 37423508 DOI: 10.1016/j.impact.2023.100475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
INTRODUCTION The current effort towards the digital transformation across multiple scientific domains requires data that is Findable, Accessible, Interoperable and Reusable (FAIR). In addition to the FAIR data, what is required for the application of computational tools, such as Quantitative Structure Activity Relationships (QSARs), is a sufficient data volume and the ability to merge sources into homogeneous digital assets. In the nanosafety domain there is a lack of FAIR available metadata. METHODOLOGY To address this challenge, we utilized 34 datasets from the nanosafety domain by exploiting the NanoSafety Data Reusability Assessment (NSDRA) framework, which allowed the annotation and assessment of dataset's reusability. From the framework's application results, eight datasets targeting the same endpoint (i.e. numerical cellular viability) were selected, processed and merged to test several hypothesis including universal versus nanogroup-specific QSAR models (metal oxide and nanotubes), and regression versus classification Machine Learning (ML) algorithms. RESULTS Universal regression and classification QSARs reached an 0.86 R2 and 0.92 accuracy, respectively, for the test set. Nanogroup-specific regression models reached 0.88 R2 for nanotubes test set followed by metal oxide (0.78). Nanogroup-specific classification models reached 0.99 accuracy for nanotubes test set, followed by metal oxide (0.91). Feature importance revealed different patterns depending on the dataset with common influential features including core size, exposure conditions and toxicological assay. Even in the case where the available experimental knowledge was merged, the models still failed to correctly predict the outputs of an unseen dataset, revealing the cumbersome conundrum of scientific reproducibility in realistic applications of QSAR for nanosafety. To harness the full potential of computational tools and ensure their long-term applications, embracing FAIR data practices is imperative in driving the development of responsible QSAR models. CONCLUSIONS This study reveals that the digitalization of nanosafety knowledge in a reproducible manner has a long way towards its successful pragmatic implementation. The workflow carried out in the study shows a promising approach to increase the FAIRness across all the elements of computational studies, from dataset's annotation, selection, merging to FAIR modeling reporting. This has significant implications for future research as it provides an example of how to utilize and report different tools available in the nanosafety knowledge system, while increasing the transparency of the results. One of the main benefits of this workflow is that it promotes data sharing and reuse, which is essential for advancing scientific knowledge by making data and metadata FAIR compliant. In addition, the increased transparency and reproducibility of the results can enhance the trustworthiness of the computational findings.
Collapse
Affiliation(s)
- Irini Furxhi
- Transgero Limited, Cullinagh, Newcastle West, Co. Limerick, Ireland; Dept. of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93, Ireland.
| | - Egon Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, the Netherlands.
| | - Chris Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, the Netherlands.
| | - Anna Costa
- National Research Council, Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy.
| | - Davide Gardini
- National Research Council, Institute of Science, Technology and Sustainability for Ceramics, Faenza, Italy.
| | - Ammar Ammar
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, the Netherlands.
| |
Collapse
|
9
|
Fux AC, Casonato Melo C, Michelini S, Swartzwelter BJ, Neusch A, Italiani P, Himly M. Heterogeneity of Lipopolysaccharide as Source of Variability in Bioassays and LPS-Binding Proteins as Remedy. Int J Mol Sci 2023; 24:ijms24098395. [PMID: 37176105 PMCID: PMC10179214 DOI: 10.3390/ijms24098395] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Lipopolysaccharide (LPS), also referred to as endotoxin, is the major component of Gram-negative bacteria's outer cell wall. It is one of the main types of pathogen-associated molecular patterns (PAMPs) that are known to elicit severe immune reactions in the event of a pathogen trespassing the epithelial barrier and reaching the bloodstream. Associated symptoms include fever and septic shock, which in severe cases, might even lead to death. Thus, the detection of LPS in medical devices and injectable pharmaceuticals is of utmost importance. However, the term LPS does not describe one single molecule but a diverse class of molecules sharing one common feature: their characteristic chemical structure. Each bacterial species has its own pool of LPS molecules varying in their chemical composition and enabling the aggregation into different supramolecular structures upon release from the bacterial cell wall. As this heterogeneity has consequences for bioassays, we aim to examine the great variability of LPS molecules and their potential to form various supramolecular structures. Furthermore, we describe current LPS quantification methods and the LPS-dependent inflammatory pathway and show how LPS heterogeneity can affect them. With the intent of overcoming these challenges and moving towards a universal approach for targeting LPS, we review current studies concerning LPS-specific binders. Finally, we give perspectives for LPS research and the use of LPS-binding molecules.
Collapse
Affiliation(s)
- Alexandra C Fux
- Division of Allergy & Immunology, Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg (PLUS), Hellbrunnerstraße 34, 5020 Salzburg, Austria
- Chemical Biology Department, R&D Reagents, Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Cristiane Casonato Melo
- Division of Allergy & Immunology, Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg (PLUS), Hellbrunnerstraße 34, 5020 Salzburg, Austria
- Chemical Biology Department, R&D Reagents, Miltenyi Biotec B.V. & Co. KG, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
| | - Sara Michelini
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Benjamin J Swartzwelter
- Department of Microbiology, Immunology, and Pathology, 1601 Campus Delivery, Colorado State University, Fort Collins, CO 80523, USA
| | - Andreas Neusch
- Experimental Medical Physics, Heinrich-Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Paola Italiani
- Institute of Biochemistry and Cell Biology, Consiglio Nazionale delle Ricerche (CNR), Via P. Castellino 111, 80131 Naples, Italy
- Stazione Zoologica Anton Dohrn (SZN), Villa Comunale, 80121 Naples, Italy
| | - Martin Himly
- Division of Allergy & Immunology, Department of Biosciences & Medical Biology, Paris Lodron University of Salzburg (PLUS), Hellbrunnerstraße 34, 5020 Salzburg, Austria
| |
Collapse
|
10
|
Cano MA, Tsueng G, Zhou X, Xin J, Hughes LD, Mullen JL, Su AI, Wu C. Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data. BMC Bioinformatics 2023; 24:159. [PMID: 37081398 PMCID: PMC10116472 DOI: 10.1186/s12859-023-05258-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging Schema.org could benefit biomedical research resource providers, but it can be challenging to apply Schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize Schema.org or other biomedical schema projects. RESULTS Our browser-based tool includes features which can help address many of the barriers towards Schema.org-compliance such as: The ability to easily browse for relevant Schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schema-a large multi-class schema for harmonizing various COVID-19 related resources. CONCLUSIONS We have created a browser-based tool to empower biomedical research resource providers to leverage Schema.org classes to make their research outputs more FAIR.
Collapse
Affiliation(s)
| | | | | | - Jiwen Xin
- The Scripps Research Institute, San Diego, USA
| | | | | | - Andrew I Su
- The Scripps Research Institute, San Diego, USA
| | - Chunlei Wu
- The Scripps Research Institute, San Diego, USA
| |
Collapse
|
11
|
Furxhi I, Bengalli R, Motta G, Mantecca P, Kose O, Carriere M, Haq EU, O’Mahony C, Blosi M, Gardini D, Costa A. Data-Driven Quantitative Intrinsic Hazard Criteria for Nanoproduct Development in a Safe-by-Design Paradigm: A Case Study of Silver Nanoforms. ACS APPLIED NANO MATERIALS 2023; 6:3948-3962. [PMID: 36938492 PMCID: PMC10012170 DOI: 10.1021/acsanm.3c00173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The current European (EU) policies, that is, the Green Deal, envisage safe and sustainable practices for chemicals, which include nanoforms (NFs), at the earliest stages of innovation. A theoretically safe and sustainable by design (SSbD) framework has been established from EU collaborative efforts toward the definition of quantitative criteria in each SSbD dimension, namely, the human and environmental safety dimension and the environmental, social, and economic sustainability dimensions. In this study, we target the safety dimension, and we demonstrate the journey toward quantitative intrinsic hazard criteria derived from findable, accessible, interoperable, and reusable data. Data were curated and merged for the development of new approach methodologies, that is, quantitative structure-activity relationship models based on regression and classification machine learning algorithms, with the intent to predict a hazard class. The models utilize system (i.e., hydrodynamic size and polydispersity index) and non-system (i.e., elemental composition and core size)-dependent nanoscale features in combination with biological in vitro attributes and experimental conditions for various silver NFs, functional antimicrobial textiles, and cosmetics applications. In a second step, interpretable rules (criteria) followed by a certainty factor were obtained by exploiting a Bayesian network structure crafted by expert reasoning. The probabilistic model shows a predictive capability of ≈78% (average accuracy across all hazard classes). In this work, we show how we shifted from the conceptualization of the SSbD framework toward the realistic implementation with pragmatic instances. This study reveals (i) quantitative intrinsic hazard criteria to be considered in the safety aspects during synthesis stage, (ii) the challenges within, and (iii) the future directions for the generation and distillation of such criteria that can feed SSbD paradigms. Specifically, the criteria can guide material engineers to synthesize NFs that are inherently safer from alternative nanoformulations, at the earliest stages of innovation, while the models enable a fast and cost-efficient in silico toxicological screening of previously synthesized and hypothetical scenarios of yet-to-be synthesized NFs.
Collapse
Affiliation(s)
- Irini Furxhi
- Transgero
Ltd, Limerick V42V384, Ireland
- Department
of Accounting and Finance, Kemmy Business School, University of Limerick, Limerick V94T9PX, Ireland
| | - Rossella Bengalli
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza
della Scienza 1, Milano 20126, Italy
| | - Giulia Motta
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza
della Scienza 1, Milano 20126, Italy
| | - Paride Mantecca
- Department
of Earth and Environmental Sciences, University
of Milano-Bicocca, Piazza
della Scienza 1, Milano 20126, Italy
| | - Ozge Kose
- Univ.
Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SYMMES, Grenoble 38000, France
| | - Marie Carriere
- Univ.
Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SYMMES, Grenoble 38000, France
| | - Ehtsham Ul Haq
- Department
of Physics, and Bernal Institute, University
of Limerick, Limerick V94TC9PX, Ireland
| | - Charlie O’Mahony
- Department
of Physics, and Bernal Institute, University
of Limerick, Limerick V94TC9PX, Ireland
| | - Magda Blosi
- Istituto
di Scienza e Tecnologia dei Materiali Ceramici (CNR-ISTEC), Via Granarolo, 64, Faenza 48018, Ravenna, Italy
| | - Davide Gardini
- Istituto
di Scienza e Tecnologia dei Materiali Ceramici (CNR-ISTEC), Via Granarolo, 64, Faenza 48018, Ravenna, Italy
| | - Anna Costa
- Istituto
di Scienza e Tecnologia dei Materiali Ceramici (CNR-ISTEC), Via Granarolo, 64, Faenza 48018, Ravenna, Italy
| |
Collapse
|
12
|
Mashoufi M, Ayatollahi H, Khorasani-Zavareh D, Talebi Azad Boni T. Data Quality in Health Care: Main Concepts and Assessment Methodologies. Methods Inf Med 2023; 62:5-18. [PMID: 36716776 DOI: 10.1055/s-0043-1761500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION In the health care environment, a huge volume of data is produced on a daily basis. However, the processes of collecting, storing, sharing, analyzing, and reporting health data usually face with numerous challenges that lead to producing incomplete, inaccurate, and untimely data. As a result, data quality issues have received more attention than before. OBJECTIVE The purpose of this article is to provide an insight into the data quality definitions, dimensions, and assessment methodologies. METHODS In this article, a scoping literature review approach was used to describe and summarize the main concepts related to data quality and data quality assessment methodologies. Search terms were selected to find the relevant articles published between January 1, 2012 and September 31, 2022. The retrieved articles were then reviewed and the results were reported narratively. RESULTS In total, 23 papers were included in the study. According to the results, data quality dimensions were various and different methodologies were used to assess them. Most studies used quantitative methods to measure data quality dimensions either in paper-based or computer-based medical records. Only two studies investigated respondents' opinions about data quality. CONCLUSION In health care, high-quality data not only are important for patient care, but also are vital for improving quality of health care services and better decision making. Therefore, using technical and nontechnical solutions as well as constant assessment and supervision is suggested to improve data quality.
Collapse
Affiliation(s)
- Mehrnaz Mashoufi
- Department of Health Information Management, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Haleh Ayatollahi
- Health Management and Economics Research Center, Health Management Research Institute, Iran University of Medical Sciences, Tehran, Iran.,Department of Health Information Management, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Davoud Khorasani-Zavareh
- Department of Health in Emergencies and Disasters, Safety Promotion and Injury Prevention Research Center, School of Public Health and Safety, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tahere Talebi Azad Boni
- Department of Health Information Management, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran.,Social Determinants of Health Research Center, Saveh University of Medical Sciences, Saveh, Iran
| |
Collapse
|
13
|
van Rijn J, Afantitis A, Culha M, Dusinska M, Exner TE, Jeliazkova N, Longhin EM, Lynch I, Melagraki G, Nymark P, Papadiamantis AG, Winkler DA, Yilmaz H, Willighagen E. European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterials. J Cheminform 2022; 14:57. [PMID: 36002868 PMCID: PMC9400299 DOI: 10.1186/s13321-022-00614-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/21/2022] [Indexed: 11/25/2022] Open
Abstract
Management of nanomaterials and nanosafety data needs to operate under the FAIR (findability, accessibility, interoperability, and reusability) principles and this requires a unique, global identifier for each nanomaterial. Existing identifiers may not always be applicable or sufficient to definitively identify the specific nanomaterial used in a particular study, resulting in the use of textual descriptions in research project communications and reporting. To ensure that internal project documentation can later be linked to publicly released data and knowledge for the specific nanomaterials, or even to specific batches and variants of nanomaterials utilised in that project, a new identifier is proposed: the European Registry of Materials Identifier. We here describe the background to this new identifier, including FAIR interoperability as defined by FAIRSharing, identifiers.org, Bioregistry, and the CHEMINF ontology, and show how it complements other identifiers such as CAS numbers and the ongoing efforts to extend the InChI identifier to cover nanomaterials. We provide examples of its use in various H2020-funded nanosafety projects.
Collapse
Affiliation(s)
- Jeaphianne van Rijn
- Department of Bioinformatics-BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, The Netherlands.
| | | | - Mustafa Culha
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956, Istanbul, Turkey
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, Norwegian Institute for Air Research, 2007, Kjeller, Norway
| | | | | | - Eleonora Marta Longhin
- Health Effects Laboratory, Department of Environmental Chemistry, Norwegian Institute for Air Research, 2007, Kjeller, Norway
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | | | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Anastasios G Papadiamantis
- NovaMechanics Ltd., 1070, Nicosia, Cyprus.,School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - David A Winkler
- School of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.,Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia.,School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Hulya Yilmaz
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956, Istanbul, Turkey
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, The Netherlands
| |
Collapse
|
14
|
Mullins M, Himly M, Llopis IR, Furxhi I, Hofer S, Hofstätter N, Wick P, Romeo D, Küehnel D, Siivola K, Catalán J, Hund-Rinke K, Xiarchos I, Linehan S, Schuurbiers D, Bilbao AG, Barruetabeña L, Drobne D. (Re)Conceptualizing decision-making tools in a risk governance framework for emerging technologies-the case of nanomaterials. ENVIRONMENT SYSTEMS & DECISIONS 2022; 43:3-15. [PMID: 35912374 PMCID: PMC9309004 DOI: 10.1007/s10669-022-09870-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 12/03/2022]
Abstract
The utility of decision-making tools for the risk governance of nanotechnology is at the core of this paper. Those working in nanotechnology risk management have been prolific in creating such tools, many derived from European FP7 and H2020-funded projects. What is less clear is how such tools might assist the overarching ambition of creating a fair system of risk governance. In this paper, we reflect upon the role that tools might and should play in any system of risk governance. With many tools designed for the risk governance of this emerging technology falling into disuse, this paper provides an overview of extant tools and addresses their potential shortcomings. We also posit the need for a data readiness tool. With the EUs NMP13 family of research consortia about to report to the Commission on ways forward in terms of risk governance of this domain, this is a timely intervention on an important element of any risk governance system.
Collapse
Affiliation(s)
- Martin Mullins
- Transgero Limited, Cullinagh, Newcastle West, Co., Limerick, Ireland
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, Limerick, Ireland
| | - Martin Himly
- Department of Biosciences, Paris Lodron University of Salzburg (PLUS), 5020 Salzburg, Austria
| | - Isabel Rodríguez Llopis
- GAIKER Technology Centre, Basque Research and Technology Alliance, (BRTA) ES, Gipuzkoa, Spain
| | - Irini Furxhi
- Transgero Limited, Cullinagh, Newcastle West, Co., Limerick, Ireland
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, Limerick, Ireland
| | - Sabine Hofer
- Department of Biosciences, Paris Lodron University of Salzburg (PLUS), 5020 Salzburg, Austria
| | - Norbert Hofstätter
- Department of Biosciences, Paris Lodron University of Salzburg (PLUS), 5020 Salzburg, Austria
| | - Peter Wick
- Particles-Biology Interactions Laboratory, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Daina Romeo
- Particles-Biology Interactions Laboratory, Empa, Swiss Federal Laboratories for Materials Science and Technology, Lerchenfeldstrasse 5, 9014 St. Gallen, Switzerland
| | - Dana Küehnel
- Department Bioanalytical Ecotoxicology (BIOTOX), Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Kirsi Siivola
- Finnish Institute of Occupational Health, Työterveyslaitos, Box 40, 00032 Helsinki, Finland
| | - Julia Catalán
- Finnish Institute of Occupational Health, Työterveyslaitos, Box 40, 00032 Helsinki, Finland
- Department of Anatomy, Embryology and Genetics, University of Zaragoza, Saragossa, Spain
| | - Kerstin Hund-Rinke
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Auf dem Aberg 1, 57392 Schmallenberg, Germany
| | - Ioannis Xiarchos
- Research Lab of Advanced Composite, Nanomaterials, and Nanotechnology (R-NanoLab), School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou str, 15780 Zographos, Athens Greece
| | - Shona Linehan
- Management, Cairnes School of Business and Economics, National University of Ireland Galway, Galway, Ireland
| | - Daan Schuurbiers
- De Proeffabriek Josef Israelslaan 63, NL-6813 JB Arnhem, The Netherlands
| | - Amaia García Bilbao
- GAIKER Technology Centre, Basque Research and Technology Alliance, (BRTA) ES, Gipuzkoa, Spain
| | - Leire Barruetabeña
- GAIKER Technology Centre, Basque Research and Technology Alliance, (BRTA) ES, Gipuzkoa, Spain
| | - Damjana Drobne
- Department Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
15
|
Elberskirch L, Sofranko A, Liebing J, Riefler N, Binder K, Bonatto Minella C, Razum M, Mädler L, Unfried K, Schins RPF, Kraegeloh A, van Thriel C. How Structured Metadata Acquisition Contributes to the Reproducibility of Nanosafety Studies: Evaluation by a Round-Robin Test. NANOMATERIALS 2022; 12:nano12071053. [PMID: 35407172 PMCID: PMC9000531 DOI: 10.3390/nano12071053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/19/2022]
Abstract
It has been widely recognized that nanosafety studies are limited in reproducibility, caused by missing or inadequate information and data gaps. Reliable and comprehensive studies should be performed supported by standards or guidelines, which need to be harmonized and usable for the multidisciplinary field of nanosafety research. The previously described minimal information table (MIT), based on existing standards or guidelines, represents one approach towards harmonization. Here, we demonstrate the applicability and advantages of the MIT by a round-robin test. Its modular structure enables describing individual studies comprehensively by a combination of various relevant aspects. Three laboratories conducted a WST-1 cell viability assay using A549 cells to analyze the effects of the reference nanomaterials NM101 and NM110 according to predefined (S)OPs. The MIT contains relevant and defined descriptive information and quality criteria and thus supported the implementation of the round-robin test from planning, investigation to analysis and data interpretation. As a result, we could identify sources of variability and justify deviating results attributed to differences in specific procedures. Consequently, the use of the MIT contributes to the acquisition of reliable and comprehensive datasets and therefore improves the significance and reusability of nanosafety studies.
Collapse
Affiliation(s)
- Linda Elberskirch
- INM—Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany;
| | - Adriana Sofranko
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.S.); (K.U.); (R.P.F.S.)
| | - Julia Liebing
- IfADo—Leibniz Research Centre for Working Environment and Human Factors, Ardeystraße 67, 44139 Dortmund, Germany;
| | - Norbert Riefler
- IWT—Leibniz-Institut für Werkstofforientierte Technologien, Badgasteiner Str. 3, 28359 Bremen, Germany; (N.R.); (L.M.)
| | - Kunigunde Binder
- FIZ Karlsruhe—Leibniz Institute for Information Infrastructure, Hermann-von-Helmholtz-Platz 1, 76133 Eggenstein-Leopoldshafen, Germany; (K.B.); (C.B.M.); (M.R.)
| | - Christian Bonatto Minella
- FIZ Karlsruhe—Leibniz Institute for Information Infrastructure, Hermann-von-Helmholtz-Platz 1, 76133 Eggenstein-Leopoldshafen, Germany; (K.B.); (C.B.M.); (M.R.)
| | - Matthias Razum
- FIZ Karlsruhe—Leibniz Institute for Information Infrastructure, Hermann-von-Helmholtz-Platz 1, 76133 Eggenstein-Leopoldshafen, Germany; (K.B.); (C.B.M.); (M.R.)
| | - Lutz Mädler
- IWT—Leibniz-Institut für Werkstofforientierte Technologien, Badgasteiner Str. 3, 28359 Bremen, Germany; (N.R.); (L.M.)
| | - Klaus Unfried
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.S.); (K.U.); (R.P.F.S.)
| | - Roel P. F. Schins
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany; (A.S.); (K.U.); (R.P.F.S.)
| | - Annette Kraegeloh
- INM—Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany;
- Correspondence: (A.K.); (C.v.T.)
| | - Christoph van Thriel
- IfADo—Leibniz Research Centre for Working Environment and Human Factors, Ardeystraße 67, 44139 Dortmund, Germany;
- Correspondence: (A.K.); (C.v.T.)
| |
Collapse
|
16
|
Furxhi I, Perucca M, Blosi M, Lopez de Ipiña J, Oliveira J, Murphy F, Costa AL. ASINA Project: Towards a Methodological Data-Driven Sustainable and Safe-by-Design Approach for the Development of Nanomaterials. Front Bioeng Biotechnol 2022; 9:805096. [PMID: 35155410 PMCID: PMC8832976 DOI: 10.3389/fbioe.2021.805096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/20/2021] [Indexed: 12/27/2022] Open
Abstract
The novel chemical strategy for sustainability calls for a Sustainable and Safe-by-Design (SSbD) holistic approach to achieve protection of public health and the environment, industrial relevance, societal empowerment, and regulatory preparedness. Based on it, the ASINA project expands a data-driven Management Methodology (ASINA-SMM) capturing quality, safety, and sustainability criteria across the Nano-Enabled Products’ (NEPs) life cycle. We base the development of this methodology through value chains of highly representative classes of NEPs in the market, namely, (i) self-cleaning/air-purifying/antimicrobial coatings and (ii) nano-structured capsules delivering active phases in cosmetics. These NEPs improve environmental quality and human health/wellness and have innovative competence to industrial sectors such as healthcare, textiles, cosmetics, and medical devices. The purpose of this article is to visually exhibit and explain the ASINA approach, which allows identifying, combining, and addressing the following pillars: environmental impact, techno-economic performance, functionality, and human and environmental safety when developing novel NEPs, at an early stage. A metamodel supports the above by utilizing quality data collected throughout the NEPs’ life cycle, for maximization of functionality (to meet stakeholders needs) and nano-safety (regulatory obligations) and for the minimization of costs (to meet business requirements) and environmental impacts (to achieve sustainability). Furthermore, ASINA explores digitalization opportunities (digital twins) to speed the nano-industry translation into automatic progress towards economic, social, environmental, and governance sustainability.
Collapse
Affiliation(s)
- Irini Furxhi
- Transgero Limited, Limerick, Ireland
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, Limerick, Ireland
- *Correspondence: Irini Furxhi, ; Massimo Perucca, ; Anna Luisa Costa,
| | - Massimo Perucca
- PROJECT-SAS, Faenza, Italy
- *Correspondence: Irini Furxhi, ; Massimo Perucca, ; Anna Luisa Costa,
| | - Magda Blosi
- National Research Council, Institute of Science and Technology for Ceramics, Faenza, Italy
| | - Jesús Lopez de Ipiña
- TECNALIA Research and Innovation—Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Alava, Miñano, Spain
| | - Juliana Oliveira
- CeNTI—Centre of Nanotechnology and Smart Materials, Vila Nova de Famalicão, Portugal
| | - Finbarr Murphy
- Transgero Limited, Limerick, Ireland
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, Limerick, Ireland
| | - Anna Luisa Costa
- National Research Council, Institute of Science and Technology for Ceramics, Faenza, Italy
- *Correspondence: Irini Furxhi, ; Massimo Perucca, ; Anna Luisa Costa,
| |
Collapse
|
17
|
Elberskirch L, Binder K, Riefler N, Sofranko A, Liebing J, Minella CB, Mädler L, Razum M, van Thriel C, Unfried K, Schins RPF, Kraegeloh A. Digital research data: from analysis of existing standards to a scientific foundation for a modular metadata schema in nanosafety. Part Fibre Toxicol 2022; 19:1. [PMID: 34983569 PMCID: PMC8728981 DOI: 10.1186/s12989-021-00442-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Assessing the safety of engineered nanomaterials (ENMs) is an interdisciplinary and complex process producing huge amounts of information and data. To make such data and metadata reusable for researchers, manufacturers, and regulatory authorities, there is an urgent need to record and provide this information in a structured, harmonized, and digitized way. RESULTS This study aimed to identify appropriate description standards and quality criteria for the special use in nanosafety. There are many existing standards and guidelines designed for collecting data and metadata, ranging from regulatory guidelines to specific databases. Most of them are incomplete or not specifically designed for ENM research. However, by merging the content of several existing standards and guidelines, a basic catalogue of descriptive information and quality criteria was generated. In an iterative process, our interdisciplinary team identified deficits and added missing information into a comprehensive schema. Subsequently, this overview was externally evaluated by a panel of experts during a workshop. This whole process resulted in a minimum information table (MIT), specifying necessary minimum information to be provided along with experimental results on effects of ENMs in the biological context in a flexible and modular manner. The MIT is divided into six modules: general information, material information, biological model information, exposure information, endpoint read out information and analysis and statistics. These modules are further partitioned into module subdivisions serving to include more detailed information. A comparison with existing ontologies, which also aim to electronically collect data and metadata on nanosafety studies, showed that the newly developed MIT exhibits a higher level of detail compared to those existing schemas, making it more usable to prevent gaps in the communication of information. CONCLUSION Implementing the requirements of the MIT into e.g., electronic lab notebooks (ELNs) would make the collection of all necessary data and metadata a daily routine and thereby would improve the reproducibility and reusability of experiments. Furthermore, this approach is particularly beneficial regarding the rapidly expanding developments and applications of novel non-animal alternative testing methods.
Collapse
Affiliation(s)
- Linda Elberskirch
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
| | - Kunigunde Binder
- FIZ Karlsruhe - Leibniz Institute for Information Infrastructure, Hermann-von-Helmholtz-Platz 1, 76133, Eggenstein-Leopoldshafen, Germany
| | - Norbert Riefler
- IWT - Leibniz-Institut für Werkstofforientierte Technologien, Badgasteiner Str. 3, 28359, Bremen, Germany
| | - Adriana Sofranko
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
| | - Julia Liebing
- IfADo - Leibniz Research Centre for Working Environment and Human Factors, Ardeystraße 67, 44139, Dortmund, Germany
| | - Christian Bonatto Minella
- FIZ Karlsruhe - Leibniz Institute for Information Infrastructure, Hermann-von-Helmholtz-Platz 1, 76133, Eggenstein-Leopoldshafen, Germany
| | - Lutz Mädler
- IWT - Leibniz-Institut für Werkstofforientierte Technologien, Badgasteiner Str. 3, 28359, Bremen, Germany
| | - Matthias Razum
- FIZ Karlsruhe - Leibniz Institute for Information Infrastructure, Hermann-von-Helmholtz-Platz 1, 76133, Eggenstein-Leopoldshafen, Germany
| | - Christoph van Thriel
- IfADo - Leibniz Research Centre for Working Environment and Human Factors, Ardeystraße 67, 44139, Dortmund, Germany
| | - Klaus Unfried
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
| | - Roel P F Schins
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
| | - Annette Kraegeloh
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany.
| |
Collapse
|
18
|
Saarimäki LA, Melagraki G, Afantitis A, Lynch I, Greco D. Prospects and challenges for FAIR toxicogenomics data. NATURE NANOTECHNOLOGY 2022; 17:17-18. [PMID: 34949777 DOI: 10.1038/s41565-021-01049-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Laura A Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | | | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
19
|
Hofer S, Hofstätter N, Punz B, Hasenkopf I, Johnson L, Himly M. Immunotoxicity of nanomaterials in health and disease: Current challenges and emerging approaches for identifying immune modifiers in susceptible populations. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1804. [PMID: 36416020 PMCID: PMC9787548 DOI: 10.1002/wnan.1804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 11/24/2022]
Abstract
Nanosafety assessment has experienced an intense era of research during the past decades driven by a vivid interest of regulators, industry, and society. Toxicological assays based on in vitro cellular models have undergone an evolution from experimentation using nanoparticulate systems on singular epithelial cell models to employing advanced complex models more realistically mimicking the respective body barriers for analyzing their capacity to alter the immune state of exposed individuals. During this phase, a number of lessons were learned. We have thus arrived at a state where the next chapters have to be opened, pursuing the following objectives: (1) to elucidate underlying mechanisms, (2) to address effects on vulnerable groups, (3) to test material mixtures, and (4) to use realistic doses on (5) sophisticated models. Moreover, data reproducibility has become a significant demand. In this context, we studied the emerging concept of adverse outcome pathways (AOPs) from the perspective of immune activation and modulation resulting in pro-inflammatory versus tolerogenic responses. When considering the interaction of nanomaterials with biological systems, protein corona formation represents the relevant molecular initiating event (e.g., by potential alterations of nanomaterial-adsorbed proteins). Using this as an example, we illustrate how integrated experimental-computational workflows combining in vitro assays with in silico models aid in data enrichment and upon comprehensive ontology-annotated (meta)data upload to online repositories assure FAIRness (Findability, Accessibility, Interoperability, Reusability). Such digital twinning may, in future, assist in early-stage decision-making during therapeutic development, and hence, promote safe-by-design innovation in nanomedicine. Moreover, it may, in combination with in silico-based exposure-relevant dose-finding, serve for risk monitoring in particularly loaded areas, for example, workplaces, taking into account pre-existing health conditions. This article is categorized under: Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials.
Collapse
Affiliation(s)
- Sabine Hofer
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Norbert Hofstätter
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Benjamin Punz
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Ingrid Hasenkopf
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Litty Johnson
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| | - Martin Himly
- Division of Allergy & Immunology, Department of Biosciences & Medical BiologyParis Lodron University of SalzburgSalzburgAustria
| |
Collapse
|
20
|
Furxhi I. Health and environmental safety of nanomaterials: O Data, Where Art Thou? NANOIMPACT 2022; 25:100378. [PMID: 35559884 DOI: 10.1016/j.impact.2021.100378] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 06/15/2023]
Abstract
Nanotechnology keeps drawing attention due to the great tunable properties of nanomaterials in comparison to their bulk conventional materials. The growth of nanotechnology in combination with the digitization era has led to an increased need of safety related data. In addition to safety, new data-driven paradigms on safe and sustainable by design materials are stressing the necessity of data even more. Data is a fundamental asset to the scientific community in studying and analysing the entire life-cycle of nanomaterials. Unfortunately, data exist in a scattered fashion, in different sources and formats. To our knowledge, there is no study focusing on aspects of actual data-structure knowledge that exists in literature and databases. The purpose of this review research is to transparently and comprehensively, display to the nanoscience community the datasets readily available for machine learning purposes making it convenient and more efficient for the next users such as modellers or data curators to retrieve information. We systematically recorded the features and descriptors available in the datasets and provide synopsised information on their ranges, forms and metrics in the supplementary material.
Collapse
Affiliation(s)
- Irini Furxhi
- Transgero Limited, Cullinagh, Newcastle West, Co. Limerick, Ireland; Dept. of Accounting and Finance, Kemmy Business School, University of Limerick, V94PH93, Ireland.
| |
Collapse
|
21
|
Thwala MM, Afantitis A, Papadiamantis AG, Tsoumanis A, Melagraki G, Dlamini LN, Ouma CNM, Ramasami P, Harris R, Puzyn T, Sanabria N, Lynch I, Gulumian M. Using the Isalos platform to develop a (Q)SAR model that predicts metal oxide toxicity utilizing facet-based electronic, image analysis-based, and periodic table derived properties as descriptors. Struct Chem 2021. [DOI: 10.1007/s11224-021-01869-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractEngineered nanoparticles (NPs) are being studied for their potential to harm humans and the environment. Biological activity, toxicity, physicochemical properties, fate, and transport of NPs must all be evaluated and/or predicted. In this work, we explored the influence of metal oxide nanoparticle facets on their toxicity towards bronchial epithelial (BEAS-2B), Murine myeloid (RAW 264.7), and E. coli cell lines. To estimate the toxicity of metal oxide nanoparticles grown to a low facet index, a quantitative structure–activity relationship ((Q)SAR) approach was used. The novel model employs theoretical (density functional theory calculations) and experimental studies (transmission electron microscopy images from which several particle descriptors are extracted and toxicity data extracted from the literature) to investigate the properties of faceted metal oxides, which are then utilized to construct a toxicity model. The classification mode of the k-nearest neighbour algorithm (EnaloskNN, Enalos Chem/Nanoinformatics) was used to create the presented model for metal oxide cytotoxicity. Four descriptors were identified as significant: core size, chemical potential, enthalpy of formation, and electronegativity count of metal oxides. The relationship between these descriptors and metal oxide facets is discussed to provide insights into the relative toxicities of the nanoparticle. The model and the underpinning dataset are freely available on the NanoSolveIT project cloud platform and the NanoPharos database, respectively.
Collapse
|
22
|
Lynch I, Nymark P, Doganis P, Gulumian M, Yoon TH, Martinez DST, Afantitis A. Methods, models, mechanisms and metadata: Introducing the Nanotoxicology collection at F1000Research. F1000Res 2021; 10:1196. [PMID: 34853679 PMCID: PMC8613506 DOI: 10.12688/f1000research.75113.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/03/2021] [Indexed: 11/28/2022] Open
Abstract
Nanotoxicology is a relatively new field of research concerning the study and application of nanomaterials to evaluate the potential for harmful effects in parallel with the development of applications. Nanotoxicology as a field spans materials synthesis and characterisation, assessment of fate and behaviour, exposure science, toxicology / ecotoxicology, molecular biology and toxicogenomics, epidemiology, safe and sustainable by design approaches, and chemoinformatics and nanoinformatics, thus requiring scientists to work collaboratively, often outside their core expertise area. This interdisciplinarity can lead to challenges in terms of interpretation and reporting, and calls for a platform for sharing of best-practice in nanotoxicology research. The F1000Research Nanotoxicology collection, introduced via this editorial, will provide a place to share accumulated best practice, via original research reports including no-effects studies, protocols and methods papers, software reports and living systematic reviews, which can be updated as new knowledge emerges or as the domain of applicability of the method, model or software is expanded. This editorial introduces the Nanotoxicology Collection in
F1000Research. The aim of the collection is to provide an open access platform for nanotoxicology researchers, to support an improved culture of
data sharing and documentation of evolving protocols, biological and computational models, software tools and datasets, that can be applied and built upon to develop predictive models and move towards
in silico nanotoxicology and nanoinformatics. Submissions will be assessed for fit to the collection and subjected to the F1000Research open peer review process.
Collapse
Affiliation(s)
- Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, Nobels väg 13, Stockholm, 17 177, Sweden
| | - Philip Doganis
- School of Chemical Engineering, National Technical University of Athens, Athens, 10682, Greece
| | - Mary Gulumian
- National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg, 2192, South Africa.,Haematology and Molecular Medicine, University of the Witwatersrand, 1 Jan Smuts Ave, Johannesburg, 2000, South Africa.,Water Research Group, Unit for Environmental Sciences and Management Potchefstroom, North West University, Potchefstroom, South Africa
| | - Tae-Hyun Yoon
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea.,Institute of Next Generation Material Design, Hanyang University, Seoul, 04763, South Korea
| | - Diego S T Martinez
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas,, Sao Paulo, CEP 13083-970, Brazil
| | | |
Collapse
|
23
|
Bossa C, Andreoli C, Bakker M, Barone F, De Angelis I, Jeliazkova N, Nymark P, Battistelli CL. FAIRification of nanosafety data to improve applicability of (Q)SAR approaches: A case study on in vitro Comet assay genotoxicity data. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 20:100190. [PMID: 34820591 PMCID: PMC8591730 DOI: 10.1016/j.comtox.2021.100190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 12/30/2022]
Abstract
(Quantitative) structure-activity relationship ([Q]SAR) methodologies are widely applied to predict the (eco)toxicological effects of chemicals, and their use is envisaged in different regulatory frameworks for filling data gaps of untested substances. However, their application to the risk assessment of nanomaterials is still limited, also due to the scarcity of large and curated experimental datasets. Despite a great amount of nanosafety data having been produced over the last decade in international collaborative initiatives, their interpretation, integration and reuse has been hampered by several obstacles, such as poorly described (meta)data, non-standard terminology, lack of harmonized reporting formats and criteria. Recently, the FAIR (Findable, Accessible, Interoperable, and Reusable) principles have been established to guide the scientific community in good data management and stewardship. The EU H2020 Gov4Nano project, together with other international projects and initiatives, is addressing the challenge of improving nanosafety data FAIRness, for maximizing their availability, understanding, exchange and ultimately their reuse. These efforts are largely supported by the creation of a common Nanosafety Data Interface, which connects a row of project-specific databases applying the eNanoMapper data model. A wide variety of experimental data relating to characterization and effects of nanomaterials are stored in the database; however, the methods, protocols and parameters driving their generation are not fully mature. This article reports the progress of an ongoing case study in the Gov4nano project on the reuse of in vitro Comet genotoxicity data, focusing on the issues and challenges encountered in their FAIRification through the eNanoMapper data model. The case study is part of an iterative process in which the FAIRification of data supports the understanding of the phenomena underlying their generation and, ultimately, improves their reusability.
Collapse
Key Words
- (Q)SAR approaches
- (Q)SAR, (Quantitative) structure-activity relationship
- AOP, Adverse Outcome Pathway
- ECHA, European Chemicals Agency
- FAIR principles
- FAIR, Findable, Accessible, Interoperable, and Reusable
- Fpg, Formamido pyrimidine glycosilase
- Genotoxicity
- IATA, Integrated Approaches to Testing and Assessment
- ISA–Tab, Investigation/Study/Assay Tab-delimited
- JRC, Joint Research Centre
- MIRCA, Minimum Information for Reporting Comet Assay
- NMBP, Horizon 2020 Advisory Group for Nanotechnologies, Advanced Materials, Biotechnology and Advanced Manufacturing and Processing
- NMBP-13-2018 projects, Gov4Nano, NANORIGO and RiskGONE
- NMs, nanomaterials
- Nano-EHS, Nano Environment, Health and Safety
- Nanomaterials
- Nanosafety data
- OECD, Organisation for Economic Co-operation and Development
- OTM, Olive tail moment
- REACH, Registration, Evaluation Authorisation and Restriction of Chemicals
- SCGE, Single Cell Gel Electrophoresis
- SOPs, Standard Operating Procedures
- in vitro Comet assay
Collapse
Affiliation(s)
- Cecilia Bossa
- Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Cristina Andreoli
- Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Martine Bakker
- Centre for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Flavia Barone
- Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Isabella De Angelis
- Environment and Health Department, Istituto Superiore di Sanità, Rome, Italy
| | | | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | |
Collapse
|
24
|
Cano M, Tsueng G, Zhou X, Hughes LD, Mullen JL, Xin J, Su AI, Wu C. Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data.. [PMID: 35677074 PMCID: PMC9176648 DOI: 10.1101/2021.09.02.458726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Background: Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging schema.org could benefit biomedical research resource providers, but it can be challenging to apply schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize schema.org or other biomedical schema projects. Results: Our browser-based tool includes features which can help address many of the barriers towards schema.org-compliance such as: The ability to easily browse for relevant schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schema—a large multi-class schema for harmonizing various COVID-19 related resources. Conclusions: We have created a browser-based tool to empower biomedical research resource providers to leverage schema.org classes to make their research outputs more FAIR.
Collapse
|
25
|
Guo Z, Chakraborty S, Monikh FA, Varsou DD, Chetwynd AJ, Afantitis A, Lynch I, Zhang P. Surface Functionalization of Graphene-Based Materials: Biological Behavior, Toxicology, and Safe-By-Design Aspects. Adv Biol (Weinh) 2021; 5:e2100637. [PMID: 34288601 DOI: 10.1002/adbi.202100637] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/11/2021] [Indexed: 01/08/2023]
Abstract
The increasing exploitation of graphene-based materials (GBMs) is driven by their unique properties and structures, which ignite the imagination of scientists and engineers. At the same time, the very properties that make them so useful for applications lead to growing concerns regarding their potential impacts on human health and the environment. Since GBMs are inert to reaction, various attempts of surface functionalization are made to make them reactive. Herein, surface functionalization of GBMs, including those intentionally designed for specific applications, as well as those unintentionally acquired (e.g., protein corona formation) from the environment and biota, are reviewed through the lenses of nanotoxicity and design of safe materials (safe-by-design). Uptake and toxicity of functionalized GBMs and the underlying mechanisms are discussed and linked with the surface functionalization. Computational tools that can predict the interaction of GBMs behavior with their toxicity are discussed. A concise framing of current knowledge and key features of GBMs to be controlled for safe and sustainable applications are provided for the community.
Collapse
Affiliation(s)
- Zhiling Guo
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Swaroop Chakraborty
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar, Gujarat, 382355, India
| | - Fazel Abdolahpur Monikh
- Department of Environmental & Biological Sciences, University of Eastern Finland, P.O. Box 111, Joensuu, FI-80101, Finland
| | - Dimitra-Danai Varsou
- School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| | - Andrew J Chetwynd
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Antreas Afantitis
- Department of ChemoInformatics, NovaMechanics Ltd., Nicosia, 1046, Cyprus
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Peng Zhang
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| |
Collapse
|
26
|
Furxhi I, Koivisto AJ, Murphy F, Trabucco S, Del Secco B, Arvanitis A. Data Shepherding in Nanotechnology. The Exposure Field Campaign Template. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1818. [PMID: 34361203 PMCID: PMC8308211 DOI: 10.3390/nano11071818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022]
Abstract
In this paper, we demonstrate the realization process of a pragmatic approach on developing a template for capturing field monitoring data in nanomanufacturing processes. The template serves the fundamental principles which make data scientifically Findable, Accessible, Interoperable and Reusable (FAIR principles), as well as encouraging individuals to reuse it. In our case, the data shepherds' (the guider of data) template creation workflow consists of the following steps: (1) Identify relevant stakeholders, (2) Distribute questionnaires to capture a general description of the data to be generated, (3) Understand the needs and requirements of each stakeholder, (4) Interactive simple communication with the stakeholders for variables/descriptors selection, and (5) Design of the template and annotation of descriptors. We provide an annotated template for capturing exposure field campaign monitoring data, and increase their interoperability, while comparing it with existing templates. This paper enables the data creators of exposure field campaign data to store data in a FAIR way and helps the scientific community, such as data shepherds, by avoiding extensive steps for template creation and by utilizing the pragmatic structure and/or the template proposed herein, in the case of a nanotechnology project (Anticipating Safety Issues at the Design of Nano Product Development, ASINA).
Collapse
Affiliation(s)
- Irini Furxhi
- Transgero Limited, Cullinagh, Newcastle West, V42V384 Limerick, Ireland;
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, V94T9PX Limerick, Ireland
| | - Antti Joonas Koivisto
- Air Pollution Management, Willemoesgade 16, st tv, DK-2100 Copenhagen, Denmark;
- ARCHE Consulting, Liefkensstraat 35D, B-9032 Wondelgem, Belgium
- Institute for Atmospheric and Earth System Research (INAR), University of Helsinki, PL 64, FI-00014 Helsinki, Finland
| | - Finbarr Murphy
- Transgero Limited, Cullinagh, Newcastle West, V42V384 Limerick, Ireland;
- Department of Accounting and Finance, Kemmy Business School, University of Limerick, V94T9PX Limerick, Ireland
| | - Sara Trabucco
- Institute of Atmospheric Sciences and Climate (CNR-ISAC) Via Gobetti 101, 40129 Bologna, Italy; (S.T.); (B.D.S.)
| | - Benedetta Del Secco
- Institute of Atmospheric Sciences and Climate (CNR-ISAC) Via Gobetti 101, 40129 Bologna, Italy; (S.T.); (B.D.S.)
| | - Athanasios Arvanitis
- Environmental Informatics Research Group, Department of Mechanical Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| |
Collapse
|
27
|
Zhang P, Guo Z, Ullah S, Melagraki G, Afantitis A, Lynch I. Nanotechnology and artificial intelligence to enable sustainable and precision agriculture. NATURE PLANTS 2021; 7:864-876. [PMID: 34168318 DOI: 10.1038/s41477-021-00946-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Climate change, increasing populations, competing demands on land for production of biofuels and declining soil quality are challenging global food security. Finding sustainable solutions requires bold new approaches and integration of knowledge from diverse fields, such as materials science and informatics. The convergence of precision agriculture, in which farmers respond in real time to changes in crop growth with nanotechnology and artificial intelligence, offers exciting opportunities for sustainable food production. Coupling existing models for nutrient cycling and crop productivity with nanoinformatics approaches to optimize targeting, uptake, delivery, nutrient capture and long-term impacts on soil microbial communities will enable design of nanoscale agrochemicals that combine optimal safety and functionality profiles.
Collapse
Affiliation(s)
- Peng Zhang
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK.
| | - Zhiling Guo
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Sami Ullah
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, Vari, Greece
| | | | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| |
Collapse
|
28
|
Data Shepherding in Nanotechnology. The Initiation. NANOMATERIALS 2021; 11:nano11061520. [PMID: 34201308 PMCID: PMC8230087 DOI: 10.3390/nano11061520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/25/2021] [Accepted: 06/07/2021] [Indexed: 01/26/2023]
Abstract
In this paper we describe the pragmatic approach of initiating, designing and implementing the Data Management Plan (DMP) and the data FAIRification process in the multidisciplinary Horizon 2020 nanotechnology project, Anticipating Safety Issues at the Design Stage of NAno Product Development (ASINA). We briefly describe the general DMP requirements, emphasizing that the initial steps in the direction towards data FAIRification must be conceptualized and visualized in a systematic way. We demonstrate the use of a generic questionnaire to capture primary data and metadata description from our consortium (data creators/experimentalists and data analysts/modelers). We then display the interactive process with external FAIR data initiatives (data curators/quality assessors), regarding guidance for data and metadata capturing and future integration into repositories. After the preliminary data capturing and FAIRification template is formed, the inner-communication process begins between the partners, which leads to developing case-specific templates. This paper assists future data creators, data analysts, stewards and shepherds engaged in the multi-faceted data shepherding process, in any project, by providing a roadmap, demonstrated in the case of ASINA.
Collapse
|
29
|
Da Silva GH, Franqui LS, Petry R, Maia MT, Fonseca LC, Fazzio A, Alves OL, Martinez DST. Recent Advances in Immunosafety and Nanoinformatics of Two-Dimensional Materials Applied to Nano-imaging. Front Immunol 2021; 12:689519. [PMID: 34149731 PMCID: PMC8210669 DOI: 10.3389/fimmu.2021.689519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 01/10/2023] Open
Abstract
Two-dimensional (2D) materials have emerged as an important class of nanomaterials for technological innovation due to their remarkable physicochemical properties, including sheet-like morphology and minimal thickness, high surface area, tuneable chemical composition, and surface functionalization. These materials are being proposed for new applications in energy, health, and the environment; these are all strategic society sectors toward sustainable development. Specifically, 2D materials for nano-imaging have shown exciting opportunities in in vitro and in vivo models, providing novel molecular imaging techniques such as computed tomography, magnetic resonance imaging, fluorescence and luminescence optical imaging and others. Therefore, given the growing interest in 2D materials, it is mandatory to evaluate their impact on the immune system in a broader sense, because it is responsible for detecting and eliminating foreign agents in living organisms. This mini-review presents an overview on the frontier of research involving 2D materials applications, nano-imaging and their immunosafety aspects. Finally, we highlight the importance of nanoinformatics approaches and computational modeling for a deeper understanding of the links between nanomaterial physicochemical properties and biological responses (immunotoxicity/biocompatibility) towards enabling immunosafety-by-design 2D materials.
Collapse
Affiliation(s)
- Gabriela H. Da Silva
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Lidiane S. Franqui
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- School of Technology, University of Campinas (Unicamp), Limeira, Brazil
| | - Romana Petry
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Center of Natural and Human Sciences, Federal University of ABC (UFABC), Santo Andre, Brazil
| | - Marcella T. Maia
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Leandro C. Fonseca
- NanoBioss Laboratory and Solid State Chemistry Laboratory (LQES), Institute of Chemistry, University of Campinas (Unicamp), Campinas, Brazil
| | - Adalberto Fazzio
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Center of Natural and Human Sciences, Federal University of ABC (UFABC), Santo Andre, Brazil
| | - Oswaldo L. Alves
- NanoBioss Laboratory and Solid State Chemistry Laboratory (LQES), Institute of Chemistry, University of Campinas (Unicamp), Campinas, Brazil
| | - Diego Stéfani T. Martinez
- Brazilian Nanotechnology National Laboratory (LNNano), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- School of Technology, University of Campinas (Unicamp), Limeira, Brazil
| |
Collapse
|
30
|
Papadiamantis AG, Afantitis A, Tsoumanis A, Valsami-Jones E, Lynch I, Melagraki G. Computational enrichment of physicochemical data for the development of a ζ-potential read-across predictive model with Isalos Analytics Platform. NANOIMPACT 2021; 22:100308. [PMID: 35559965 DOI: 10.1016/j.impact.2021.100308] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/01/2021] [Accepted: 03/01/2021] [Indexed: 06/15/2023]
Abstract
The physicochemical characterisation data from a library of 69 engineered nanomaterials (ENMs) has been exploited in silico following enrichment with a set of molecular descriptors that can be easily acquired or calculated using atomic periodicity and other fundamental atomic parameters. Based on the extended set of twenty descriptors, a robust and validated nanoinformatics model has been proposed to predict the ENM ζ-potential. The five critical parameters selected as the most significant for the model development included the ENM size and coating as well as three molecular descriptors, metal ionic radius (rion), the sum of metal electronegativity divided by the number of oxygen atoms present in a particular metal oxide (Σχ/nO) and the absolute electronegativity (χabs), each of which is thoroughly discussed to interpret their influence on ζ-potential values. The model was developed using the Isalos Analytics Platform and is available to the community as a web service through the Horizon 2020 (H2020) NanoCommons Transnational Access services and the H2020 NanoSoveIT Integrated Approach to Testing and Assessment (IATA).
Collapse
Affiliation(s)
- Anastasios G Papadiamantis
- NovaMechanics Ltd, 1065 Nicosia, Cyprus; School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | | | | | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom.
| | | |
Collapse
|
31
|
Saarimäki LA, Federico A, Lynch I, Papadiamantis AG, Tsoumanis A, Melagraki G, Afantitis A, Serra A, Greco D. Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials. Sci Data 2021; 8:49. [PMID: 33558569 PMCID: PMC7870661 DOI: 10.1038/s41597-021-00808-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023] Open
Abstract
Toxicogenomics (TGx) approaches are increasingly applied to gain insight into the possible toxicity mechanisms of engineered nanomaterials (ENMs). Omics data can be valuable to elucidate the mechanism of action of chemicals and to develop predictive models in toxicology. While vast amounts of transcriptomics data from ENM exposures have already been accumulated, a unified, easily accessible and reusable collection of transcriptomics data for ENMs is currently lacking. In an attempt to improve the FAIRness of already existing transcriptomics data for ENMs, we curated a collection of homogenized transcriptomics data from human, mouse and rat ENM exposures in vitro and in vivo including the physicochemical characteristics of the ENMs used in each study.
Collapse
Affiliation(s)
- Laura Aliisa Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, Birmingham, United Kingdom
| | - Anastasios G Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, Birmingham, United Kingdom
- NovaMechanics Ltd, P.O Box 26014 1666, Nicosia, Cyprus
| | | | | | | | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- BioMediTech Institute, Tampere University, Tampere, Finland.
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- Finnish Centre for Alternative Methods (FICAM), Faculty of Medicine and Heath Technology, Tampere University, Tampere, Finland.
| |
Collapse
|
32
|
Lynch I, Afantitis A, Greco D, Dusinska M, Banares MA, Melagraki G. Editorial for the Special Issue From Nanoinformatics to Nanomaterials Risk Assessment and Governance. NANOMATERIALS 2021; 11:nano11010121. [PMID: 33430326 PMCID: PMC7825746 DOI: 10.3390/nano11010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Iseult Lynch
- School of Geography, Earth & Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Correspondence:
| | - Antreas Afantitis
- Department of Cheminformatics, NovaMechanics Ltd., Nicosia 1065, Cyprus; (A.A.); (G.M.)
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland;
| | - Maria Dusinska
- Environmental Chemistry Department, Norwegian Institute for Air Research, 2027 Kjeller, Norway;
| | - Miguel A. Banares
- Institute for Catalysis, ICP-CSIC, Marie Curie 2, E-28049 Madrid, Spain;
| | - Georgia Melagraki
- Department of Cheminformatics, NovaMechanics Ltd., Nicosia 1065, Cyprus; (A.A.); (G.M.)
| |
Collapse
|
33
|
Halappanavar S, Ede JD, Mahapatra I, Krug HF, Kuempel ED, Lynch I, Vandebriel RJ, Shatkin JA. A methodology for developing key events to advance nanomaterial-relevant adverse outcome pathways to inform risk assessment. Nanotoxicology 2020; 15:289-310. [PMID: 33317378 DOI: 10.1080/17435390.2020.1851419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Significant advances have been made in the development of Adverse Outcome Pathways (AOPs) over the last decade, mainly focused on the toxicity mechanisms of chemicals. These AOPs, although relevant to manufactured nanomaterials (MNs), do not currently capture the reported roles of size-associated properties of MNs on toxicity. Moreover, some AOs of relevance to airborne exposures to MNs such as lung inflammation and fibrosis shown in animal studies may not be targeted in routine regulatory decision making. The primary objective of the present study was to establish an approach to advance the development of AOPs of relevance to MNs using existing, publicly available, nanotoxicology literature. A systematic methodology was created for curating, organizing and applying the available literature for identifying key events (KEs). Using a case study approach, the study applied the available literature to build the biological plausibility for 'tissue injury', a KE of regulatory relevance to MNs. The results of the analysis reveal the various endpoints, assays and specific biological markers used for assessing and reporting tissue injury. The study elaborates on the limitations and opportunities of the current nanotoxicology literature and provides recommendations for the future reporting of nanotoxicology results that will expedite not only the development of AOPs for MNs but also aid in application of existing data for decision making.
Collapse
Affiliation(s)
- Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | | | - Indrani Mahapatra
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Harald F Krug
- Retired International Research Cooperation Manager, Empa - Swiss Federal Laboratories for Science and Materials Technology, St. Gallen, Switzerland.,NanoCASE GmbH, Engelburg, Switzerland
| | - Eileen D Kuempel
- National Institute for Occupational Safety and Health, Nanotechnology Research Center, Cincinnati, OH, USA
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Rob J Vandebriel
- National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | |
Collapse
|
34
|
Lynch I, Afantitis A, Exner T, Himly M, Lobaskin V, Doganis P, Maier D, Sanabria N, Papadiamantis AG, Rybinska-Fryca A, Gromelski M, Puzyn T, Willighagen E, Johnston BD, Gulumian M, Matzke M, Green Etxabe A, Bossa N, Serra A, Liampa I, Harper S, Tämm K, Jensen ACØ, Kohonen P, Slater L, Tsoumanis A, Greco D, Winkler DA, Sarimveis H, Melagraki G. Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies? NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2493. [PMID: 33322568 PMCID: PMC7764592 DOI: 10.3390/nano10122493] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 12/16/2022]
Abstract
Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analyzed issues involved in developing an InChI for NMs (NInChI). The layers needed to capture NM structures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a "nano" extension to the InChI standard.
Collapse
Affiliation(s)
- Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Antreas Afantitis
- Nanoinformatics Department, NovaMechanics Ltd., 1666 Nicosia, Cyprus; (A.A.); (A.T.)
| | - Thomas Exner
- Edelweiss Connect GmbH, Hochbergerstrasse 60C, 4057 Basel, Switzerland;
| | - Martin Himly
- Department Biosciences, Paris Lodron University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria;
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Philip Doganis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece; (P.D.); (I.L.); (H.S.)
| | - Dieter Maier
- Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany;
| | - Natasha Sanabria
- National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg 2192, South Africa; (N.S.); (M.G.)
| | - Anastasios G. Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
- Nanoinformatics Department, NovaMechanics Ltd., 1666 Nicosia, Cyprus; (A.A.); (A.T.)
| | - Anna Rybinska-Fryca
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland; (A.R.-F.); (M.G.); (T.P.)
| | - Maciej Gromelski
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland; (A.R.-F.); (M.G.); (T.P.)
| | - Tomasz Puzyn
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland; (A.R.-F.); (M.G.); (T.P.)
| | - Egon Willighagen
- Department of Bioinformatics—BiGCaT, School of Nutrition and Translational Research in Metabolism, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands;
| | - Blair D. Johnston
- Department Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany;
| | - Mary Gulumian
- National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg 2192, South Africa; (N.S.); (M.G.)
- Haematology and Molecular Medicine, University of the Witwatersrand, 1 Jan Smuts Ave, Johannesburg 2000, South Africa
| | - Marianne Matzke
- UK Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford OX10 8BB, UK; (M.M.); (A.G.E.)
| | - Amaia Green Etxabe
- UK Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford OX10 8BB, UK; (M.M.); (A.G.E.)
| | - Nathan Bossa
- LEITAT Technological Center, Circular Economy Business Unit, C/de La Innovació 2, 08225 Terrassa, Barcelona, Spain;
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (D.G.)
| | - Irene Liampa
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece; (P.D.); (I.L.); (H.S.)
| | - Stacey Harper
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 116 Johnson Hall 105 SW 26th St., Corvallis, OR 97331, USA;
| | - Kaido Tämm
- Institute of Chemistry, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia;
| | - Alexander CØ Jensen
- The National Research Center for the Work Environment, Lersø Parkallé 105, 2100 Copenhagen, Denmark;
| | - Pekka Kohonen
- Misvik Biology OY, Karjakatu 35 B, 20520 Turku, Finland;
| | - Luke Slater
- Institute of Cancer and Genomics, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Andreas Tsoumanis
- Nanoinformatics Department, NovaMechanics Ltd., 1666 Nicosia, Cyprus; (A.A.); (A.T.)
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (D.G.)
| | - David A. Winkler
- Institute of Molecular Sciences, La Trobe University, Kingsbury Drive, Bundoora 3086, Australia;
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
- CSIRO Data61, Pullenvale 4069, Australia
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece; (P.D.); (I.L.); (H.S.)
| | - Georgia Melagraki
- Nanoinformatics Department, NovaMechanics Ltd., 1666 Nicosia, Cyprus; (A.A.); (A.T.)
| |
Collapse
|
35
|
A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences. NANOMATERIALS 2020; 10:nano10102068. [PMID: 33092028 PMCID: PMC7594074 DOI: 10.3390/nano10102068] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/28/2020] [Accepted: 10/14/2020] [Indexed: 12/27/2022]
Abstract
Data sharing and reuse are crucial to enhance scientific progress and maximize return of investments in science. Although attitudes are increasingly favorable, data reuse remains difficult due to lack of infrastructures, standards, and policies. The FAIR (findable, accessible, interoperable, reusable) principles aim to provide recommendations to increase data reuse. Because of the broad interpretation of the FAIR principles, maturity indicators are necessary to determine the FAIRness of a dataset. In this work, we propose a reproducible computational workflow to assess data FAIRness in the life sciences. Our implementation follows principles and guidelines recommended by the maturity indicator authoring group and integrates concepts from the literature. In addition, we propose a FAIR balloon plot to summarize and compare dataset FAIRness. We evaluated the feasibility of our method on three real use cases where researchers looked for six datasets to answer their scientific questions. We retrieved information from repositories (ArrayExpress, Gene Expression Omnibus, eNanoMapper, caNanoLab, NanoCommons and ChEMBL), a registry of repositories, and a searchable resource (Google Dataset Search) via application program interfaces (API) wherever possible. With our analysis, we found that the six datasets met the majority of the criteria defined by the maturity indicators, and we showed areas where improvements can easily be reached. We suggest that use of standard schema for metadata and the presence of specific attributes in registries of repositories could increase FAIRness of datasets.
Collapse
|
36
|
Papadiamantis AG, Jänes J, Voyiatzis E, Sikk L, Burk J, Burk P, Tsoumanis A, Ha MK, Yoon TH, Valsami-Jones E, Lynch I, Melagraki G, Tämm K, Afantitis A. Predicting Cytotoxicity of Metal Oxide Nanoparticles using Isalos Analytics Platform. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2017. [PMID: 33066094 PMCID: PMC7601995 DOI: 10.3390/nano10102017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 02/07/2023]
Abstract
A literature curated dataset containing 24 distinct metal oxide (MexOy) nanoparticles (NPs), including 15 physicochemical, structural and assay-related descriptors, was enriched with 62 atomistic computational descriptors and exploited to produce a robust and validated in silico model for prediction of NP cytotoxicity. The model can be used to predict the cytotoxicity (cell viability) of MexOy NPs based on the colorimetric lactate dehydrogenase (LDH) assay and the luminometric adenosine triphosphate (ATP) assay, both of which quantify irreversible cell membrane damage. Out of the 77 total descriptors used, 7 were identified as being significant for induction of cytotoxicity by MexOy NPs. These were NP core size, hydrodynamic size, assay type, exposure dose, the energy of the MexOy conduction band (EC), the coordination number of the metal atoms on the NP surface (Avg. C.N. Me atoms surface) and the average force vector surface normal component of all metal atoms (v⟂ Me atoms surface). The significance and effect of these descriptors is discussed to demonstrate their direct correlation with cytotoxicity. The produced model has been made publicly available by the Horizon 2020 (H2020) NanoSolveIT project and will be added to the project's Integrated Approach to Testing and Assessment (IATA).
Collapse
Affiliation(s)
- Anastasios G. Papadiamantis
- NovaMechanics Ltd., Nicosia 1065, Cyprus; (A.G.P.); (E.V.); (A.T.)
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK; (E.V.-J.); (I.L.)
| | - Jaak Jänes
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
| | | | - Lauri Sikk
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
| | - Jaanus Burk
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
| | - Peeter Burk
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
| | | | - My Kieu Ha
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Korea; (M.K.H.); (T.H.Y.)
| | - Tae Hyun Yoon
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Korea; (M.K.H.); (T.H.Y.)
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, Korea
| | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK; (E.V.-J.); (I.L.)
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK; (E.V.-J.); (I.L.)
| | - Georgia Melagraki
- Division of Physical Sciences and Applications, Hellenic Military Academy, 16672 Vari, Greece;
| | - Kaido Tämm
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia; (J.J.); (L.S.); (J.B.); (P.B.)
| | | |
Collapse
|
37
|
Ede JD, Lobaskin V, Vogel U, Lynch I, Halappanavar S, Doak SH, Roberts MG, Shatkin JA. Translating Scientific Advances in the AOP Framework to Decision Making for Nanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1229. [PMID: 32599945 PMCID: PMC7353114 DOI: 10.3390/nano10061229] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023]
Abstract
Much of the current innovation in advanced materials is occurring at the nanoscale, specifically in manufactured nanomaterials (MNs). MNs display unique attributes and behaviors, and may be biologically and physically unique, making them valuable across a wide range of applications. However, as the number, diversity and complexity of MNs coming to market continue to grow, assessing their health and environmental risks with traditional animal testing approaches is too time- and cost-intensive to be practical, and is undesirable for ethical reasons. New approaches are needed that meet current requirements for regulatory risk assessment while reducing reliance on animal testing and enabling safer-by-design product development strategies to be implemented. The adverse outcome pathway (AOP) framework presents a sound model for the advancement of MN decision making. Yet, there are currently gaps in technical and policy aspects of AOPs that hinder the adoption and use for MN risk assessment and regulatory decision making. This review outlines the current status and next steps for the development and use of the AOP framework in decision making regarding the safety of MNs. Opportunities and challenges are identified concerning the advancement and adoption of AOPs as part of an integrated approach to testing and assessing (IATA) MNs, as are specific actions proposed to advance the development, use and acceptance of the AOP framework and associated testing strategies for MN risk assessment and decision making. The intention of this review is to reflect the views of a diversity of stakeholders including experts, researchers, policymakers, regulators, risk assessors and industry representatives on the current status, needs and requirements to facilitate the future use of AOPs in MN risk assessment. It incorporates the views and feedback of experts that participated in two workshops hosted as part of an Organization for Economic Cooperation and Development (OECD) Working Party on Manufactured Nanomaterials (WPMN) project titled, "Advancing AOP Development for Nanomaterial Risk Assessment and Categorization", as well as input from several EU-funded nanosafety research consortia.
Collapse
Affiliation(s)
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Ulla Vogel
- National Research Centre for the Working Environment, DK-2100 Copenhagen, Denmark;
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada;
| | - Shareen H. Doak
- Institute of Life Sciences, Swansea University Medical School, Singleton Park, Swansea SA2 8PP, UK;
| | - Megan G. Roberts
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada;
| | | |
Collapse
|