Development and Implementation of a Sustainable Modelling Platform for NanoInformatics.

Resultado final

Strategy to calculate in vivo exposure dose based on the modelling strategies developed in NanoInformaTIX

TMK will develop a strategy based on the collected in vitro and in vivo data to predict exposure doses

Report on application and integration of data analysis method for data curation and data exploration

Report on the methods applied andor developed and their impact on the NanoInformaTIX database

Overview of available data, modelling methods and modelling tools requirements

This report will provide overview of data of interest to NanoInformaTIX framework, modelling methods and tools envisaged for integration, and their specific requirements (data quality, e.g. input and output formats)

Workflows integrating ontology into data curation , data validation and input/output of modelling tools will be defined

Workflows for ontology supported data curation and validation including data quality and completeness criteria will be described

Human exposure models

This deliverable will present the final human NanoInformaTIX models that describe indoor exposure modeling of ENM

Test design recommendations for an ENM systems toxicology approach using non animal alternative test methods,

Based on systems biology guidance on best practices and test design will be given focussing on the specificities of testing ENM UAVR will draft and all WP5 partners will contribute

Human PBPK Modeling

This deliverable will report the final development of the human PBPK models developed within NanoInformaTIX

Developing an integrative analysis pipeline for multi-omics data for defining MIEs and Key Events of ENM

UFZ will report on the development of an integrative analysis pipeline for multiomics data

Environmental exposure models

This deliverable will present the final environmental NanoInformaTIX models that describe release and environmental fate modeling of ENM providing the environmental dose

eport on ontology usage and requirements Workflow for ontological development and maintenance

-Existing ontologies will be analysed and list of new ontology entries will be proposed to maintainers of eNanoMapper and EMMO ontology. A workflow enabling continuous update and maintenance of the ontology will be described, in collaboration with existing ontology development communities.

Open source libraries for interaction with NanoInformaTIX database

This deliverable will describe the open source libraries implemented by T24 enabling interoperable communication with NanoInformaTIX database Application to answering specific scientific questions and integration with modelling tools will be described

1 NanoInformaTIX database release

This report will describe the technical implementation and content of NanoInformaTIX database release Iterative development and releases at M12 M24 and M36 are planned based on requirement identified by T22 partners feedback and developments in T23T25

Mode of action grouping of ENM based on advanced material descriptors

NTUA will provide a report on the mode of action grouping of ENM based on advanced material descriptors

Plan for stakeholder events and trainings

We will have two stakeholder events (together with WP7) to gather feedback on the development of the SNF Platform. We will also run annual training schools, if possible together with other EC funded initiatives, to transfer knowledge to the next generation of researchers, and a final event to disseminate the projects’ results to stakeholders

Dose-response modelling

Report summarizing the doseresponse models developed within task 51

NanoInformaTIX Data Management Plan

This report will provide the first version of DMP describing the NanoInfomaTIX approach to data collection, management and curation.

Safe-by-Design approach and corresponding platform

DEMOKRITOS will provide a description of the developed approach for “safe-by-design”, which will take into account the feedbacks collected also by WP4, WP5 and WP6. NCSR will be responsible for developing a software tool to guide the reverse engineering towards safe-by-design materials.

Communication Basics

Logo, website, brochure, presentation template

Hybrid material models for computing physicochemical descriptors of ENM

This deliverable is an update of the D31 and hence the same format applies In particular the same consistency requirements with regards to EMMC httpsemmcinfo recommendations will be adopted This deliverable will include a set of datasheets about material models which may also include experimental results and hence are defined as hybrid This corresponds to the critical decision main path or alternative which will be taken at M24 by D31 These datasheets will report i the hybrid material modelling workflows and ii the corresponding estimated values about advanced descriptors as specified in WP45 Each estimated descriptor will be reported with the corresponding uncertainty for validation purposes in WP6

Pure material models for computing physicochemical descriptors of ENM

POLITO will prepare a set of datasheets about material models for computing physicochemical descriptors of ENM in a format agreed with the leading partners involved in material modelling in T3a beforehand The datasheets will be in line with the requirements of the MOdelling DAta MODA approach httpswwwceneuNewsWorkshopsPagesWS2017012aspx and with the European Materials Modelling Ontology EMMO for semantic interoperability httpsemmcinfo These datasheets will report i the material modelling workflows and ii the corresponding computed values about the preliminary list of advanced descriptors WP45 agreed in D33 at M12 Each computed descriptor will be reported with the corresponding uncertainty for validation WP6

Publicaciones

International Network Initiative on Safe and Sustainable Nanotechnologies (INISS-nano)

Autores: Falk, Andreas
Publicado en: Edición 12, 2021
Editor: BioNanoNet
DOI: 10.5281/zenodo.5004929

Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects

Autores: Pia Anneli Sofia Kinaret, Angela Serra, Antonio Federico, Pekka Kohonen, Penny Nymark, Irene Liampa, My Kieu Ha , Jang-Sik Choi, Karolina Jagiello, Natasha Sanabri, Georgia Melagraki, Luca Cattelani, Michele Fratello, Haralambos Sarimveis6, Antreas Afantitis , Tae-Hyun Yoon, Mary Gulumian, Roland Grafström, Tomasz Puzyn, Dario Greco
Publicado en: Nanomaterials, Edición 10(4), 750, 2020, ISSN 2079-4991
Editor: MDPI
DOI: 10.3390/nano10040750

Size-Specific, Dynamic, Probabilistic Material Flow Analysis of Titanium Dioxide Releases into the Environment.

Autores: Yuanfang Zheng; Bernd Nowack
Publicado en: Environmental Science & Technology, Edición 55, 4, 2021, Página(s) 2392–2402, ISSN 1520-5851
Editor: American Chemical Society
DOI: 10.1021/acs.est.0c07446

Annelid genomes: Enchytraeus crypticus, a soil model for innate (and primed) immune system

Autores: Mónica J.B. Amorim, Yannick Gansemans, Susana I.L. Gomes, Filip Van Nieuwerburgh and Janeck J. Scott-Fordsmand
Publicado en: Lab Animal, Edición 50, 285–294 (2021), 2021, ISSN 0093-7355
Editor: Nature Publishing Group
DOI: 10.1038/s41684-021-00831-x

Effects of natural organic matter on the joint toxicity and accumulation of Cu nanoparticles and ZnO nanoparticles in Daphnia magna

Autores: Qi Yu, Zhuang Wang, Guiyin Wang, Willie J. G. M. Peijnenburg, Martina G. Vijver
Publicado en: Environmental Pollution, Edición Volume 292, Part B, 1 January 2022, 118413, 2022, ISSN 0269-7491
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.envpol.2021.118413

"""Systems toxicology to advance human and environmental hazard assessment: A roadmap for advanced materials"""

Autores: M.J.B. Amorim, W. Peijnenburg, D. Greco, L.A. Saarimäki, V.I. Dumit f, A. Bahl, A. Haase, L. Tran, J. Hackermüller, S. Canzler, J.J. Scott-Fordsmand
Publicado en: Nano Today, Edición 48 (February 2023), 2023, ISSN 1748-0132
Editor: Elsevier BV
DOI: 10.1016/j.nantod.2022.101735

Probing Nano-QSAR to Assess the Interactions between Carbon Nanoparticles and a SARS-CoV-2 RNA Fragment

Autores: Fan Zhang, Zhuang Wang, Martina G. Vijver, Willie J.G.M. Peijnenburg
Publicado en: Ecotoxicology and Environmental Safety, Edición Volume 219, August 2021, 112357, 2021, ISSN 1090-2414
Editor: Orlando, Fla. Academic Press
DOI: 10.1016/j.ecoenv.2021.112357

Machine learning and materials modelling interpretation of in vivo toxicological response to TiO2 nanoparticles library (UV and non-UV exposure)

Autores: Susana I. L. Gomes; Mónica J. B. Amorim; Suman Pokhrel; Lutz Mädler; Matteo Fasano; Eliodoro Chiavazzo; Pietro Asinari; Jaak Jänes; Kaido Tämm; Jaanus Burk; Janeck J. Scott-Fordsmand
Publicado en: Nanoscale, Edición 35/2021, 2021, ISSN 2040-3372
Editor: Royal Society of Chemistry
DOI: 10.1039/d1nr03231c

BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data

Autores: Angela Serra, Laura Aliisa Saarimäki, Michele Fratello, Veer Singh Marwah, Dario Greco
Publicado en: Bioinformatics, Edición Volume 36, Edición 9, 2020, ISSN 1367-4811
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa030

Pulmonary toxicity of silver vapours, nanoparticles and fine dusts: A review

Autores: Niels Hadrup, Anoop K. Sharma, Katrin Loeschner, Nicklas R. Jacobsen
Publicado en: Regulatory Toxicology and Pharmacology, Edición 115, 2020, Página(s) 104690, ISSN 0273-2300
Editor: Academic Press
DOI: 10.1016/j.yrtph.2020.104690

Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields

Autores: Brajesh Narayan; Colm Herbert; Brian J. Rodriguez; Bernard R. Brooks; Nicolae-Viorel Buchete
Publicado en: The Journal of Physical Chemistry. B, Edición 125, 20, 2021, Página(s) 5233–5242, ISSN 1089-5639
Editor: American Chemical Society
DOI: 10.1021/acs.jpcb.1c01939

Trophic transfer of Cu nanoparticles in simulated aquatic food chains

Autores: Qi Yu, Zhuang Wang, Willie J. G. M. Peijnenburg, Martina G. Vijver
Publicado en: Ecotoxicology and Environmental Safety, Edición Volume 242, 1 September 2022, 113920, 2022, ISSN 1090-2414
Editor: Orlando, Fla. Academic Press
DOI: 10.1016/j.ecoenv.2022.113920

A systematic quality evaluation and review of nanomaterial genotoxicity studies – a regulatory perspective

Autores: Siivola KM, Burgum MJ, Suárez-Merino B, Clift M, Doak S and Catalán J
Publicado en: Particle and Fibre Toxicology, Edición 2022; 19: 59, 2022, ISSN 1743-8977
Editor: BioMed Central
DOI: 10.1186/s12989-022-00499-2

Computer Simulations of the Dissociation Mechanism of Gleevec from Abl Kinase with Milestoning

Autores: Brajesh Narayan; Nicolae-Viorel Buchete; Ron Elber
Publicado en: Jorunal of Physical Chemistry B, 2021, ISSN 1089-5639
Editor: American Chemical Society
DOI: 10.1021/acs.jpcb.1c00264

Core, Coating, or Corona? The Importance of Considering Protein Coronas in nano-QSPR Modeling of Zeta Potential.

Autores: Selvaraj Sengottiyan, Alicja Mikolajczyk, Karolina Jagiełło, Marta Swirog, and Tomasz Puzyn
Publicado en: ACS Nano, Edición Vol 17, Edición 3, 2023, ISSN 1936-0851
Editor: American Chemical Society
DOI: 10.1021/acsnano.2c06977

Assembling Biocompatible Polymers on Gold Nanoparticles: Towards a Rational Design of Particle Shape by Molecular Dynamics

Autores: Roberta Cappabianca, Paolo De Angelis, Annalisa Cardellini, Eliodoro Chiavazzo and Pietro Asinari
Publicado en: ACS Omega, Edición 2022, 7, 46, 2022, ISSN 2470-1343
Editor: ACS Publications
DOI: 10.1021/acsomega.2c05218

PROTEOMAS: a workflow enabling harmonized proteomic meta-analysis and proteomic signature mapping

Autores: Aileen Bahl, Celine Ibrahim, Kristina Plate, Andrea Haase, Jörn Dengjel, Penny Nymark & Verónica I. Dumit
Publicado en: Journal of Cheminformatics, Edición 15, Article number:34, 2023, ISSN 1758-2946
Editor: Chemistry Central
DOI: 10.1186/s13321-023-00710-2

Development of a quasi-QSAR model for prediction of the immobilization response of Daphnia magna exposed to metal-based nanomaterials

Autores: Warisa Bunmahotama, Martina G. Vijver, Willie Peijnenburg
Publicado en: Environmental Toxicology and Chemistry, Edición 2022 Jun; 41(6): 1439–1450., 2022, ISSN 1552-8618
Editor: Society of Environmental Toxicology and Chemistry
DOI: 10.1002/etc.5322

Multi-Scale Modelling of Aggregation of TiO2 Nanoparticle Suspensions in Water

Autores: G.Mancardi(POLITO), M.Alberghini(POLITO), N.Aguilera-Porta(Sorbonne), M.Calatayud(Sorbonne), P.Asinari(POLITO&INRIM) and E.Chiavazzo(POLITO)
Publicado en: nanomaterials, Edición 2(2), 217, 2022, ISSN 2079-4991
Editor: MDPI
DOI: 10.3390/nano12020217

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data.

Autores: Sebastian Canzler; Jörg Hackermüller
Publicado en: BMC Bioinformatics, Edición 21/2020, 2020, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-020-03910-x

Meta‐analysis of Bioaccumulation Data for Nondissolvable Engineered Nanomaterials in Freshwater Aquatic Organisms

Autores: Yuanfang Zheng; Bernd Nowack
Publicado en: Environmental Toxicology and Chemistry, Edición Volume 41, Edición 5, 2022, Página(s) Pages 1202-1214, ISSN 1552-8618
Editor: SETAC
DOI: 10.1002/etc.5312

Multiomics assessment in Enchytraeus crypticus exposed to Ag nanomaterials (Ag NM300K) and ions (AgNO3) – Metabolomics, proteomics (& transcriptomics)

Autores: Vera L. Maria; David Licha; Janeck J. Scott-Fordsmand; Christian G. Huber; Mónica J.B. Amorim
Publicado en: Environmental Pollution, Edición 286, 2021, ISSN 1873-6424
Editor: Elsevier
DOI: 10.1016/j.envpol.2021.117571

Alternative test methods for (nano)materials hazards assessment: challenges and recommendations for regulatory preparedness

Autores: Susana I.L. Gomes, Janeck J. Scott-Fordsmand and Monica J.B. Amorim
Publicado en: Nano Today, Edición Volume 40, October 2021, 101242, 2021, ISSN 1748-0132
Editor: Elsevier BV
DOI: 10.1016/j.nantod.2021.101242

Toxicokinetics and toxicodynamics of Ag nanomaterials (NM300K) in the soil environment – impact on Enchytraeus crypticus (Oligochaeta)

Autores: Fátima C.F. Santosa, Rudo A. Verweijb, Cornelis A.M. van Gestelb and Mónica J.B. Amorima
Publicado en: Ecotoxicology and Environmental Safety, Edición Volume 252, 1 March 2023, 114599, 2023, ISSN 0147-6513
Editor: Academic Press
DOI: 10.1016/j.ecoenv.2023.114599

Graphene nanoplatelets and reduced graphene oxide elevate the microalgal cytotoxicity of nano-zirconium oxide.

Autores: Zhuang Wang; Fan Zhang; Martina G. Vijver; Willie J.G.M. Peijnenburg
Publicado en: Chemosphere, Edición 276, 2021, ISSN 1879-1298
Editor: Elsevier
DOI: 10.1016/j.chemosphere.2021.130015

Epigenetic effects of (nano)materials in environmental species – Cu case study in Enchytraeus crypticus

Autores: Rita C. Bicho, Dick Roelofs, Janine Mariën, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim
Publicado en: Environment International, Edición 136, 2020, Página(s) 105447, ISSN 0160-4120
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.envint.2019.105447

Aquatic Mesocosm Strategies for the Environmental Fate and Risk Assessment of Engineered Nanomaterials.

Autores: Andrea Carboni; Danielle L. Slomberg; Mohammad Nassar; Catherine Santaella; Armand Masion; Jérôme Rose; Mélanie Auffan
Publicado en: https://hal-cnrs.archives-ouvertes.fr/hal-03468409, Edición 2, 2021, ISSN 0013-936X
Editor: American Chemical Society
DOI: 10.1021/acs.est.1c02221

Comparison of Biokinetic Models for Non-dissolvable Engineered Nanomaterials in Freshwater Aquatic Organisms

Autores: Yuanfang Zheng, Bernd Nowack
Publicado en: Environmental Science: Nano, Edición 2023,10, 1065-1076, 2023, ISSN 2051-8161
Editor: Royal Society of Chemistry
DOI: 10.1039/d2en01039a

Editorial for the Special Issue From Nanoinformatics to Nanomaterials Risk Assessment and Governance.

Autores: Iseult Lynch; Antreas Afantitis; Dario Greco; Maria Dusinska; Miguel A. Bañares; Georgia Melagraki
Publicado en: Nanomaterials, Edición 11/2021, 2021, Página(s) p 121, ISSN 2079-4991
Editor: MDPI
DOI: 10.3390/nano11010121

Multivariate analysis of the exposure and hazard of ceria nanomaterials in indoor aquatic mesocosms

Autores: Mohammad Nassar; Mélanie Auffan; Mélanie Auffan; Catherine Santaella; Armand Masion; Jérôme Rose; Jérôme Rose
Publicado en: Environmental Science Nano, Edición 6/2020, 2020, ISSN 2051-8161
Editor: Royal Society of Chemistry
DOI: 10.1039/c9en01439j

The role of size and nature in nanoparticle binding to a model lung membrane: an atomistic study

Autores: Ankush Singhal; Geert Jan Agur Sevink
Publicado en: Nanoscale Advances, Edición 23/2021, 2021, ISSN 2516-0230
Editor: Royal Society of Chemistry
DOI: 10.1039/d1na00578b

Your Spreadsheets Can Be FAIR: A Tool and FAIRification Workflow for the eNanoMapper Database

Autores: Nikolay Kochev, Nina Jeliazkova, Vesselina Paskaleva, Gergana Tancheva, Luchesar Iliev, Peter Ritchie, Vedrin Jeliazkov
Publicado en: Nanomaterials, Edición 10/10, 2020, Página(s) 1908, ISSN 2079-4991
Editor: MDPI
DOI: 10.3390/nano10101908

Predicting electrophoretic mobility of TiO2, ZnO and CeO2 nanoparticles in natural waters: The importance of environment descriptors in nanoinformatics models

Autores: Marta Swirog, Alicja Mikołajczyk, Karolina Jagiello, Jaak Jänes, Kaido Tämm, Tomasz Puzyn
Publicado en: Science of the Total Environment, Edición Volume 840, 20 September 2022, 156572, 2022, ISSN 1879-1026
Editor: Elsevier
DOI: 10.1016/j.scitotenv.2022.156572

Multigenerational Exposure to WCCo Nanomaterials—Epigenetics in the Soil Invertebrate Enchytraeus crypticus

Autores: Rita C. Bicho, Janeck J. Scott-Fordsmand, Mónica J.B. Amorim
Publicado en: Nanomaterials, Edición 10/5, 2020, Página(s) 836, ISSN 2079-4991
Editor: MDPI
DOI: 10.3390/nano10050836

How Does the Study MD of pH-Dependent Exposure of Nanoparticles Affect Cellular Uptake of Anticancer Drugs?

Autores: Selvaraj Sengottiyan, Alicja Mikolajczyk, Tomasz Puzyn
Publicado en: International Journal of Molecular Sciences, Edición Vol 24, Edición 4, 2023, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24043479

"""Fostering EU-US Cooperation in Nanosafety"""

Autores: Miguel Bañares
Publicado en: 2019
Editor: Harvard University

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