Development of Deep Learning Models for Predicting the Effects of Exposure to Engineered Nanomaterials on Daphnia magna

2020, Publications

Abstract This study presents the results of applying deep learning methodologies within the ecotoxicology field, with the objective of training predictive models that can support hazard assessment and eventually the design of safer engineered nanomaterials (ENMs). A workflow applying two different deep learning architectures on microscopic images of Daphnia magna is proposed that can automatically…

Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data

2020, Publications

Abstract Preprocessing of transcriptomics data plays a pivotal role in the development of toxicogenomics-driven tools for chemical toxicity assessment. The generation and exploitation of large volumes of molecular profiles, following an appropriate experimental design, allows the employment of toxicogenomics (TGx) approaches for a thorough characterisation of the mechanism of action (MOA) of different compounds. To…

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

2020, Publications

Abstract The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in…

Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment

2020, Publications

Abstract Transcriptomics data are relevant to address a number of challenges in Toxicogenomics (TGx). After careful planning of exposure conditions and data preprocessing, the TGx data can be used in predictive toxicology, where more advanced modelling techniques are applied. The large volume of molecular profiles produced by omics-based technologies allows the development and application of…

Exposure medium and particle ageing moderate the toxicological effects of nanomaterials to Daphnia magna over multiple generations: a case for standard test review?

2020, Publications

Abstract Pristine engineered nanomaterials (NMs) entering the aquatic environment become ‘aged’ during their lifetime via chemical, physical and/or biological process. Therefore, traditional ecotoxicology tests which were designed for soluble chemicals prior to the emergence of NMs, use pristine NMs and salt-only media which are not representative of realistic NM exposure scenarios. Exposure medium and NM ageing moderation…

Zeta‐Potential Read‐Across Model Utilizing Nanodescriptors Extracted via the NanoXtract Image Analysis Tool Available on the Enalos Nanoinformatics Cloud Platform

2020, Publications

Abstract Zeta potential is one of the most critical properties of nanomaterials (NMs) which provides an estimation of the surface charge, and therefore electrostatic stability in medium and, in practical terms, influences the NM’s tendency to form agglomerates and to interact with cellular membranes. This paper describes a robust and accurate read‐across model to predict…

Mass Cytometry and Single‐Cell RNA‐seq Profiling of the Heterogeneity in Human Peripheral Blood Mononuclear Cells Interacting with Silver Nanoparticles

2020, Publications

Abstract Understanding the interactions between nanoparticles (NPs) and human immune cells is necessary for justifying their utilization in consumer products and biomedical applications. However, conventional assays may be insufficient in describing the complexity and heterogeneity of cell–NP interactions. Herein, mass cytometry and single‐cell RNA‐sequencing (scRNA‐seq) are complementarily used to investigate the heterogeneous interactions between silver…

NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment

2020, Publications

Abstract Nanotechnology has enabled the discovery of a multitude of novel materials exhibiting unique physicochemical (PChem) properties compared to their bulk analogues. These properties have led to a rapidly increasing range of commercial applications; this, however, may come at a cost, if an association to long-term health and environmental risks is discovered or even just…