Monte Carlo Particle Lists: MCPL

A binary format with lists of particle state information, for interchanging particles between various Monte Carlo simulation applications, is presented. Portable C code for file manipulation is made available to the scientific community, along with converters and plugins for several popular simulation packages

Simulation Tools for Detector and Instrument Design

The high performance requirements at the European Spallation Source have been driving the technological advances on the neutron detector front. Now more than ever is it important to optimize the design of detectors and instruments, to fully exploit the ESS source brilliance. Most of the simulation tools the neutron scattering community has at their disposal target the instrument optimization until the sample position, with little focus on detectors. The ESS Detector Group has extended the capabilities of existing detector simulation tools to bridge this gap. An extensive software framework has been developed, enabling efficient and collaborative developments of required simulations and analyses -- based on the use of the Geant4 Monte Carlo toolkit, but with extended physics capabilities where relevant (like for Bragg diffraction of thermal neutrons in crystals). Furthermore, the MCPL (Monte Carlo Particle Lists) particle data exchange file format, currently supported for the primary Monte Carlo tools of the community (McStas, Geant4 and MCNP), facilitates the integration of detector simulations with existing simulations of instruments using these software packages. These means offer a powerful set of tools to tailor the detector and instrument design to the instrument application

A C. elegans Screening Platform for the Rapid Assessment of Chemical Disruption of Germline Function

Background: Despite the developmental impact of chromosome segregation errors, we lack the tools to assess environmental effects on the integrity of the germline in animals. Objectives: We developed an assay in Caenorhabditis elegans that fluorescently marks aneuploid embryos after chemical exposure. Methods: We qualified the predictive value of the assay against chemotherapeutic agents as well as environmental compounds from the ToxCast Phase I library by comparing results from the C. elegans assay with the comprehensive mammalian in vivo end point data from the ToxRef database. Results: The assay was highly predictive of mammalian reproductive toxicities, with a 69% maximum balanced accuracy. We confirmed the effect of select compounds on germline integrity by monitoring germline apoptosis and meiotic progression. Conclusions: This C. elegans assay provides a comprehensive strategy for assessing environmental effects on germline function

Disruption of VEGFR signaling leading to developmental defects

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Pluripotent stem cell assays: Modalities and applications for predictive developmental toxicity

This manuscript provides a review focused on embryonic stem cell-based models and their place within the landscape of alternative developmental toxicity assays. Against the background of the principles of developmental toxicology, the wide diversity of alternative methods using pluripotent stem cells developed in this area over the past half century is reviewed. In order to provide an overview of available models, a systematic scoping review was conducted following a published protocol with inclusion criteria, which were applied to select the assays. Critical aspects including biological domain, readout endpoint, availability of standardized protocols, chemical domain, reproducibility and predictive power of each assay are described in detail, in order to review the applicability and limitations of the platform in general and progress moving forward to implementation. The horizon of innovative routes of promoting regulatory implementation of alternative methods is scanned, and recommendations for further work are given