OECD harmonised template 201: Structuring and reporting mechanistic information to foster the integration of new approach methodologies for hazard and risk assessment of chemicals.

In the European Union, the Chemicals Strategy for Sustainability (CSS) highlights the need to enhance the identification and assessment of substances of concern while reducing animal testing, thus fostering the development and use of New Approach Methodologies (NAMs) such as in silico, in vitro and in chemico. In the United States, the Tox21 strategy aims at shifting toxicological assessments away from traditional animal studies towards target-specific, mechanism-based and biological observations mainly obtained by using NAMs. Many other jurisdictions around the world are also increasing the use of NAMs. Hence, the provision of dedicated non-animal toxicological data and reporting formats as a basis for chemical risk assessment is necessary. Harmonising data reporting is crucial when aiming at re-using and sharing data for chemical risk assessment across jurisdictions. The OECD has developed a series of OECD Harmonised Templates (OHT), which are standard data formats designed for reporting information used for the risk assessment of chemicals relevant to their intrinsic properties, including effects on human health (e.g., toxicokinetics, skin sensitisation, repeated dose toxicity) and the environment (e.g., toxicity to test species and wildlife, biodegradation in soil, metabolism of residues in crops). The objective of this paper is to demonstrate the applicability of the OHT standard format for reporting information under various chemical risk assessment regimes, and to provide users with practical guidance on the use of OHT 201, in particular to report test results on intermediate effects and mechanistic information.

Lock-In Thermal Test Simulation, Influence, and Optimum Cycle Period for Infrared Thermal Testing in Non-Destructive Testing.

Lock-in thermal tests (LTTs) are one of the best ways to detect defects in composite materials. The parameter that most affects their performance is the cycle period of the stimulation wave. Its influence on the amplitude-phase results was determined by performing various numeric simulations and laboratory tests. The laboratory tests were used to infer part of the simulation parameters, namely the input and output heat, corresponding to the stimulation and natural convection. The simulations and the analysis of their results focus on the heat flow inside the sample and the manner they change for different geometries. This was performed for poly(methyl methacrylate (PMMA) and carbon fiber-reinforced polymers (CFRPs). The simulation of these materials was also used to create prediction surfaces and equations. These predict the amplitude and phase for a sample with a thickness l and a cycle period. These new findings were validated with new laboratory tests and two new samples. These validated the prediction surfaces and equations and can now be used as a reference for future works and industrial applications.

Extension of the Virtual Cell Based Assay from a 2-D to a 3-D Cell Culture Model.

Prediction of chemical toxicity is very useful in risk assessment. With the current paradigm shift towards the use of in vitro and in silico systems, we present herein a theoretical mathematical description of a quasi-diffusion process to predict chemical concentrations in 3-D spheroid cell cultures. By extending a 2-D Virtual Cell Based Assay (VCBA) model into a 3-D spheroid cell model, we assume that cells are arranged in a series of concentric layers within the sphere. We formulate the chemical quasi-diffusion process by simplifying the spheroid with respect to the number of cells in each layer. The system was calibrated and tested with acetaminophen (APAP). Simulated predictions of APAP toxicity were compared with empirical data from in vitro measurements by using a 3-D spheroid model. The results of this first attempt to extend the VCBA model are promising - they show that the VCBA model simulates close correlation between the influence of compound concentration and the viability of the HepaRG 3-D cell culture. The 3-D VCBA model provides a complement to current in vitro procedures to refine experimental setups, to fill data gaps and help in the interpretation of in vitro data for the purposes of risk assessment.

Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology.

Omics methodologies are widely used in toxicological research to understand modes and mechanisms of toxicity. Increasingly, these methodologies are being applied to questions of regulatory interest such as molecular point-of-departure derivation and chemical grouping/read-across. Despite its value, widespread regulatory acceptance of omics data has not yet occurred. Barriers to the routine application of omics data in regulatory decision making have been: 1) lack of transparency for data processing methods used to convert raw data into an interpretable list of observations; and 2) lack of standardization in reporting to ensure that omics data, associated metadata and the methodologies used to generate results are available for review by stakeholders, including regulators. Thus, in 2017, the Organisation for Economic Co-operation and Development (OECD) Extended Advisory Group on Molecular Screening and Toxicogenomics (EAGMST) launched a project to develop guidance for the reporting of omics data aimed at fostering further regulatory use. Here, we report on the ongoing development of the first formal reporting framework describing the processing and analysis of both transcriptomic and metabolomic data for regulatory toxicology. We introduce the modular structure, content, harmonization and strategy for trialling this reporting framework prior to its publication by the OECD.

Physiological Arousal Quantifying Perception of Safe and Unsafe Virtual Environments by Older and Younger Adults.

Physiological arousal has been increasingly applied to monitor exploration (or navigation) of a virtual environment (VE), especially when the VE is designed to evoke an anxiety-related response. The present work aims to evaluate human physiological reactions to safe and unsafe VEs. We compared the effect of the presence of handrails in the VE in two different samples, young and older adults, through self-reports and physiological data: Electrodermal activation (EDA) and electrocardiogram (ECG) sensors. After navigation, self-report questionnaires were administered. We found that the VEs evoked a clearly differentiated perception of safety and unsafety demonstrated through self-reports, with older adults being more discriminative in their responses and reporting a higher sense of presence. In terms of physiological data, the effect of handrails did not provoke significant differences in arousal. Safety was better operationalized by discriminating neutral/non-neutral spaces, where the reaction of older adults was more pronounced than young adults. Results serve as a basis for orienting future experiments in the line of VE and applied physiology usage in the architectural spaces design process. This specific work also provided a basis for the development of applications that integrate virtual reality and applied biofeedback, tapping into mobility and ageing.

The Hippo pathway effector YAP controls mouse hepatic stellate cell activation.

BACKGROUND & AIMS: Hepatic stellate cell activation is a wound-healing response to liver injury. However, continued activation of stellate cells during chronic liver damage causes excessive matrix deposition and the formation of pathological scar tissue leading to fibrosis and ultimately cirrhosis. The importance of sustained stellate cell activation for this pathological process is well recognized, and several signalling pathways that can promote stellate cell activation have been identified, such as the TGFß-, PDGF-, and LPS-dependent pathways. However, the mechanisms that trigger and drive the early steps in activation are not well understood. METHODS AND RESULTS: We identified the Hippo pathway and its effector YAP as a key pathway that controls stellate cell activation. YAP is a transcriptional co-activator and we found that it drives the earliest changes in gene expression during stellate cell activation. Activation of stellate cells in vivo by CCl4 administration to mice or activation in vitro caused rapid activation of YAP as revealed by its nuclear translocation and by the induction of YAP target genes. YAP was also activated in stellate cells of human fibrotic livers as evidenced by its nuclear localization. Importantly, knockdown of YAP expression or pharmacological inhibition of YAP prevented hepatic stellate cell activation in vitro and pharmacological inhibition of YAP impeded fibrogenesis in mice. CONCLUSIONS: YAP activation is a critical driver of hepatic stellate cell activation and inhibition of YAP presents a novel approach for the treatment of liver fibrosis.

PBTK modelling platforms and parameter estimation tools to enable animal-free risk assessment: recommendations from a joint EPAA--EURL ECVAM ADME workshop.

Information on toxicokinetics is critical for animal-free human risk assessment. Human external exposure must be translated into human tissue doses and compared with in vitro actual cell exposure associated to effects (in vitro-in vivo comparison). Data on absorption, distribution, metabolism and excretion in humans (ADME) could be generated using in vitro and QSAR tools. Physiologically-based toxicokinetic (PBTK) computer modelling could serve to integrate disparate in vitro and in silico findings. However, there are only few freely-available PBTK platforms currently available. And although some ADME parameters can be reasonably estimated in vitro or in silico, important gaps exist. Examples include unknown or limited applicability domains and lack of (high-throughput) tools to measure penetration of barriers, partitioning between blood and tissues and metabolic clearance. This paper is based on a joint EPAA--EURL ECVAM expert meeting. It provides a state-of-the-art overview of the availability of PBTK platforms as well as the in vitro and in silico methods to parameterise basic (Tier 1) PBTK models. Five high-priority issues are presented that provide the prerequisites for wider use of non-animal based PBTK modelling for animal-free chemical risk assessment.

Correction: Hierarchical growth in neural networks structure: Organizing inputs by Order of Hierarchical Complexity.

[This corrects the article DOI: 10.1371/journal.pone.0290743.].

Peer review of the pesticide risk assessment for the active substance difenoconazole in light of confirmatory data submitted.

The conclusions of the EFSA following the peer review of the initial risk assessment carried out by the competent authority of the rapporteur Member State, Spain, for the pesticide active substance difenoconazole are reported. The context of the peer review was that requested by the European Commission following the submission and evaluation of confirmatory information with regard to the consumer risk assessment. The conclusions were reached on the basis of the evaluation of the representative uses of difenoconazole as a fungicide on pome fruit, carrot, wheat, barley, triticale, rye and oats. The reliable endpoints concluded as being appropriate for use in regulatory risk assessment, derived from the available studies and/or literature in the dossier peer reviewed, are presented. Concerns were not identified.

Peer review of the pesticide risk assessment of the active substance clove oil.

The conclusions of the EFSA following the peer review of the initial risk assessments carried out by the competent authority of the rapporteur Member State, Malta, for the pesticide active substance clove oil are reported. The context of the peer review was that required by Regulation (EC) No 1107/2009 of the European Parliament and of the Council. The conclusions for the amendment of approval were reached on the basis of the evaluation of the representative use of clove oil as a preharvest nematicide on tomatoes and cucumbers (permanent greenhouse use). The representative use evaluated for the renewal of approval of clove oil was as post-harvest fungicide and bactericide on apples, pears and peaches (indoor uses). The reliable endpoints appropriate for use in regulatory risk assessment are presented. Endpoints not relevant to the scope of the proposed amendment of approval conditions will be addressed in the context of the renewal of approval procedure of clove oil running in parallel (AIR IV, EFSA Q-2016-00809). Missing information identified as being required by the regulatory framework is listed. Concerns are reported where identified.

Peer review of the pesticide risk assessment of the active substance quinolin-8-ol.

The conclusions of the European Food Safety Authority (EFSA) following the peer review of the initial risk assessments carried out by the competent authorities of the rapporteur Member State, Spain, and co-rapporteur Member State, the Netherlands, for the pesticide active substance quinolin-8-ol are reported. The context of the peer review was that required by Commission Implementing Regulation (EU) No 844/2012. The conclusions were reached on the basis of the evaluation of the representative use of quinolin-8-ol as a fungicide and bactericide against soil-borne pathogens in tomato cultivation in permanent greenhouses applied by drip irrigation. The reliable end points, appropriate for use in regulatory risk assessment are presented. Missing information identified as being required by the regulatory framework is listed. Concerns are reported where identified.

Updated peer review of the pesticide risk assessment of the active substance dichlorprop-P and variant dichlorprop-P-2-ethylhexyl.

The conclusions of the EFSA following the peer review of the initial risk assessments carried out by the competent authorities of the rapporteur Member State, Ireland, and co-rapporteur Member State, Poland, for the pesticide active substance dichlorprop-P and the variant dichlorprop-P-2-ethylhexyl and the assessment of applications for maximum residue levels (MRLs) are reported. The context of the peer review was that required by Commission Implementing Regulation (EU) No 844/2012. The conclusions were reached on the basis of the evaluation of the representative uses of dichlorprop-P as a herbicide on cereals, grassland and grass seed crops and of the variant dichlorprop-P-2-ethylhexyl as a plant growth regulator on citrus. MRLs were assessed in mandarin and lemon. The conclusions from 2018 were updated in 2024 following the request from the European Commission with regard to the endocrine-disrupting properties. The reliable end points, appropriate for use in regulatory risk assessment and the proposed MRLs, are presented. Missing information identified as being required by the regulatory framework is listed. Concerns are reported where identified.

Peer review of the pesticide risk assessment of the active substance paraffin oil (CAS 8042-47-5, chain lengths C17-C31).

The conclusions of the European Food Safety Authority (EFSA) following the peer review of the initial risk assessments carried out by the competent authorities of the rapporteur Member State, Greece, and co-rapporteur Member State, France, for the pesticide active substance paraffin oil are reported. The context of the peer review was that required by Commission Implementing Regulation (EU) No 844/2012, as amended by Commission Implementing Regulation (EU) No 2018/1659. The conclusions were reached on the basis of the evaluation of the representative uses of paraffin oil as an acaricide and insecticide on potatoes, ornamentals (flower bulbs) and orchards (pear/apple), on pome fruit and stone fruit, on field and permanent protected fruiting vegetables and on field and permanent protected roses and on citrus. The reliable end points appropriate for use in regulatory risk assessment are presented. Missing information identified as being required by the regulatory framework is listed. Concerns are reported where identified.

Peer review of the pesticide risk assessment of the active substance lenacil.

The conclusions of the European Food Safety Authority (EFSA) following the peer review of the initial risk assessments carried out by the competent authorities of the rapporteur Member State, Belgium, and co-rapporteur Member State, Austria, for the pesticide active substance lenacil are reported. The context of the peer review was that required by Commission Implementing Regulation (EU) No 844/2012, as amended by Commission Implementing Regulation (EU) No 2018/1659. The conclusions were reached on the basis of the evaluation of the representative uses of lenacil as a herbicide on sugar and fodder beet (field use). The reliable end points, appropriate for use in regulatory risk assessment, are presented. Missing information identified as being required by the regulatory framework is listed. Concerns are reported where identified.

Peer review of the pesticide risk assessment of the active substance mepiquat (evaluated variant mepiquat chloride).

The conclusions of the EFSA following the peer review of the initial risk assessments carried out by the competent authorities of the rapporteur Member State, Finland, and co-rapporteur Member State, Estonia, for the pesticide active substance mepiquat (evaluated variant mepiquat chloride) are reported. The context of the peer review was that required by Commission Implementing Regulation (EU) No 844/2012, as amended by Commission Implementing Regulation (EU) No 2018/1659. The conclusions were reached on the basis of the evaluation of the representative uses of mepiquat chloride as a plant growth regulator on cereals and grass (field uses). The reliable end points, appropriate for use in regulatory risk assessment, are presented. Missing information identified as being required by the regulatory framework is listed. Concerns are identified.

Updated peer review of the pesticide risk assessment of the active substance pydiflumetofen.

The conclusions of the EFSA following the peer review of the initial risk assessments carried out by the competent authority of the rapporteur Member State, France, and co-rapporteur Member State, Austria, for the pesticide active substance pydiflumetofen and the assessment of applications for maximum residue levels (MRLs) are reported. The context of the peer review was that required by Regulation (EC) No 1107/2009 of the European Parliament and of the Council. The conclusions were reached on the basis of the evaluation of the representative uses of pydiflumetofen as a fungicide field application on pome fruits, grapes, potato, fruiting vegetables, cucurbits and Brassica vegetables and updated following the request from Commission to consider additional information submitted and review the risk assessment. The reliable endpoints, appropriate for use in regulatory risk assessment and the proposed MRLs, are presented. Missing information identified as being required by the regulatory framework is listed. Concerns are reported where identified.

Human liver cell spheroids in extended perfusion bioreactor culture for repeated-dose drug testing.

UNLABELLED: Primary cultures of human hepatocyte spheroids are a promising in vitro model for long-term studies of hepatic metabolism and cytotoxicity. The lack of robust methodologies to culture cell spheroids, as well as a poor characterization of human hepatocyte spheroid architecture and liver-specific functionality, have hampered a widespread adoption of this three-dimensional culture format. In this work, an automated perfusion bioreactor was used to obtain and maintain human hepatocyte spheroids. These spheroids were cultured for 3-4 weeks in serum-free conditions, sustaining their phase I enzyme expression and permitting repeated induction during long culture times; rate of albumin and urea synthesis, as well as phase I and II drug-metabolizing enzyme gene expression and activity of spheroid hepatocyte cultures, presented reproducible profiles, despite basal interdonor variability (n = 3 donors). Immunofluorescence microscopy of human hepatocyte spheroids after 3-4 weeks of long-term culture confirmed the presence of the liver-specific markers, hepatocyte nuclear factor 4α, albumin, cytokeratin 18, and cytochrome P450 3A. Moreover, immunostaining of the atypical protein kinase C apical marker, as well as the excretion of a fluorescent dye, evidenced that these spheroids spontaneously assemble a functional bile canaliculi network, extending from the surface to the interior of the spheroids, after 3-4 weeks of culture. CONCLUSION: Perfusion bioreactor cultures of primary human hepatocyte spheroids maintain a liver-specific activity and architecture and are thus suitable for drug testing in a long-term, repeated-dose format.

Hierarchical growth in neural networks structure: Organizing inputs by Order of Hierarchical Complexity.

Several studies demonstrate that the structure of the brain increases in hierarchical complexity throughout development. We tested if the structure of artificial neural networks also increases in hierarchical complexity while learning a developing task, called the balance beam problem. Previous simulations of this developmental task do not reflect a necessary premise underlying development: a more complex structure can be built out of less complex ones, while ensuring that the more complex structure does not replace the less complex one. In order to address this necessity, we segregated the input set by subsets of increasing Orders of Hierarchical Complexity. This is a complexity measure that has been extensively shown to underlie the complexity behavior and hypothesized to underlie the complexity of the neural structure of the brain. After segregating the input set, minimal neural network models were trained separately for each input subset, and adjacent complexity models were analyzed sequentially to observe whether there was a structural progression. Results show that three different network structural progressions were found, performing with similar accuracy, pointing towards self-organization. Also, more complex structures could be built out of less complex ones without substituting them, successfully addressing catastrophic forgetting and leveraging performance of previous models in the literature. Furthermore, the model structures trained on the two highest complexity subsets performed better than simulations of the balance beam present in the literature. As a major contribution, this work was successful in addressing hierarchical complexity structural growth in neural networks, and is the first that segregates inputs by Order of Hierarchical Complexity. Since this measure can be applied to all domains of data, the present method can be applied to future simulations, systematizing the simulation of developmental and evolutionary structural growth in neural networks.

Proceedings of a workshop to address animal methods bias in scientific publishing.

Animal methods bias in scientific publishing is a newly defined type of publishing bias describing a preference for animal-based methods where they may not be necessary or where nonanimal-based methods may already be suitable, which impacts the likelihood or timeliness of a manuscript being accepted for publication. This article covers the output from a workshop between stakeholders in publishing, academia, industry, government, and non-governmental organizations. The intent of the workshop was to exchange perspectives on the prevalence, causes, and impact of animal methods bias in scientific publishing, as well as to explore mitigation strategies. Output from the workshop includes summaries of presentations, breakout group discussions, participant polling results, and a synthesis of recommendations for mitigation. Overall, participants felt that animal methods bias has a meaningful impact on scientific publishing, though more evidence is needed to demonstrate its prevalence. Significant consequences of this bias that were identified include the unnecessary use of animals in scientific procedures, the continued reliance on animals in research ­ even where suitable nonanimal methods exist, poor rates of clinical translation, delays in publication, and negative impacts on career trajectories in science. Workshop participants offered recommendations for journals, publishers, funders, governments, and other policy makers, as well as the scientific community at large, to reduce the prevalence and impacts of animal methods bias. The workshop resulted in the creation of working groups committed to addressing animal methods bias, and activities are ongoing.

Considerations from an International Regulatory and Pharmaceutical Industry (IQ MPS Affiliate) Workshop on the Standardization of Complex In Vitro Models in Drug Development.

In May 2022, there is an International Regulatory and Pharmaceutical Industry (Innovation and Quality [IQ] Microphysiological Systems [MPS] Affiliate) Workshop on the standardization of complex in vitro models (CIVMs) in drug development. This manuscript summarizes the discussions and conclusions of this joint workshop organized and executed by the IQ MPS Affiliate and the United States Food and Drug Administration (FDA). A key objective of the workshop is to facilitate discussions around opportunities and/or needs for standardization of MPS and chart potential pathways to increase model utilization in the context of regulatory decision making. Participation in the workshop included 200 attendees from the FDA, IQ MPS Affiliate, and 26 global regulatory organizations and affiliated parties representing Europe, Japan, and Canada. It is agreed that understanding global perspectives regarding the readiness of CIVM/MPS models for regulatory decision making and potential pathways to gaining acceptance is useful to align on globally. The obstacles are currently too great to develop standards for every context of use (COU). Instead, it is suggested that a more tractable approach may be to think of broadly applicable standards that can be applied regardless of COU and/or organ system. Considerations and next steps for this effort are described.