Assessing uncertainties from physical parameters and modelling choices in an atmospheric large eddy simulation model

In this study, we investigate uncertainties in a large eddy simulation of the atmosphere, employing modern uncertainty quantification methods that have hardly been used yet in this context. When analysing the uncertainty of model results, one can distinguish between uncertainty related to physical parameters whose values are not exactly known, and uncertainty related to modelling choices such as the selection of numerical discretization methods, of the spatial domain size and resolution, and the use of different model formulations. While the former kind is commonly studied e.g. with forward uncertainty propagation, we explore the use of such techniques to also assess the latter kind. From a climate modelling perspective, uncertainties in the convective response and cloud formation are of particular interest, since these affect the cloud-climate feedback, one of the dominant sources of uncertainty in current climate models. Therefore we analyse the DALES model in the RICO case, a well-studied convection benchmark. We use the VECMA toolkit for uncertainty propagation, assessing uncertainties stemming from physical parameters as well as from modelling choices. We find substantial uncertainties due to small random initial state perturbations, and that the choice of advection scheme is the most influential of the modelling choices we assessed. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.Atmospheric Remote Sensin

The Road Accident Fund and serious injuries: the narrative test.

The Road Accident Fund Amendment Act 19 of 2005 came into effect on 1 August 2008. This Act limits the Road Accident Fund’s liability for compensation in respect of claims for non-pecuniary loss to instances where a “serious injury” has been sustained. A medical practitioner has to determine whether or not the claimant has suffered a serious injury by undertaking an assessment prescribed in the Regulations to the Act. The practitioner has to complete a RAF 4 report. In doing so the practitioner must assess the injury in terms of the American Medical Association’s Guides to the Evaluation of Permanent Impairment (6th ed). If the injury is considered to have resulted in less than 30 per cent of the whole person impairment the medical practitioner should apply the narrative test. The article focuses on the narrative test but also discusses reasons why the regulations do not fulfil the requirements of the Act; reasons why the Guides is not adequate to the task; the impact of the circumstances of an injured person on disability; problems with the existing wording of the narrative test; shortcomings on the RAf 4 form; the administrative process as well as the appeal tribunals.     &nbsp

HPCSA Serious Injury Narrative Test guideline

Current South African Road Accident Fund (RAF) legislation requires a medical determination of the seriousness of injuries sustained in motor vehicle accidents to determine whether the claimant is entitled to a claim for general damages. Such medical assessments are submitted in the form of RAF 4 Serious Injury Assessment Reports. Contested claims for serious injury are referred to the Health Professions Council of South Africa (HPCSA) Appeal Tribunals for final determination. The legislation prescribes 2 instruments, namely the American Medical Association (AMA) Guides (6th edition) and the Narrative Test for this purpose. Whereas the AMA Guides are published in a comprehensive book, and training courses are provided in their use, existing legislation does not provide any indication of the required structure, content or criteria of a Narrative Test report. This document is published by the HPCSA Appeal Tribunals as a guideline to the performance of the Narrative Test; what it is, reasons for applying it and who should compile it, as well as the required structure, content and criteria thereof. A Narrative Test Report should include relevant and meaningful comment in relation to each of the 6 sections described in the article.

Crystallization and preliminary diffraction studies of native and selenomethionine CcmG (CycY, DsbE)

t Disulfide-bond (Dsb) proteins are a family of redox proteins containing a Cys-X-X-Cys motif. They are essential for disulfide-bond exchange in the bacterial periplasm and are necessary for the correct folding and function of many secreted proteins. CcmG (DsbE) is a reducing Dsb protein required for cytochrome c maturation. Crystals of Bradyrhizobium japonicum CcmG have been obtained that diffract X-rays to 1.14 Angstrom resolution. The crystals are orthorhombic, space group P2(1)2(1)2(1), with unit-cell parameters a = 35.1, b = 48.2, c = 90.2 Angstrom. Selenomethionine CcmG was expressed without using a methionine auxotroph or methionine-pathway inhibition and was purified without reducing agents

Sensitivity Analysis of High-Dimensional Models with Correlated Inputs

The file archived on this repository is a preprint. It has not been certified by peer reviewSensitivity analysis is an important tool used in many domains of computational science to either gain insight into the mathematical model and interaction of its parameters or study the uncertainty propagation through the input-output interactions. In many applications, the inputs are stochastically dependent, which violates one of the essential assumptions in the state-of-the-art sensitivity analysis methods. Consequently, the results obtained ignoring the correlations provide values which do not reflect the true contributions of the input parameters. This study proposes an approach to address the parameter correlations using a polynomial chaos expansion method and Rosenblatt and Cholesky transformations to reflect the parameter dependencies. Treatment of the correlated variables is discussed in context of variance and derivative-based sensitivity analysis. We demonstrate that the sensitivity of the correlated parameters can not only differ in magnitude, but even the sign of the derivative-based index can be inverted, thus significantly altering the model behavior compared to the prediction of the analysis disregarding the correlations. Numerous experiments are conducted using workflow automation tools within the VECMA toolkit.This research is part of the activities of the Innosuisse project no 34394.1 entitled “High-Performance Data Analytics Framework for Power Markets Simulation” which is financially supported by the Swiss Innovation Agency. This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under project ID d120. DS and DG have been supported by the SEAVEA ExCALIBUR project, which has received funding from EPSRC under grant agreement EP/W007711/1

The Fc region of an antibody impacts the neutralization of West Nile viruses in different maturation states

Flavivirus-infected cells secrete a structurally heterogeneous population of viruses because of an inefficient virion maturation process. Flaviviruses assemble as noninfectious, immature virions composed of trimers of envelope (E) and precursor membrane (prM) protein heterodimers. Cleavage of prM is a required process during virion maturation, although this often remains incomplete for infectious virus particles. Previous work demonstrated that the efficiency of virion maturation could impact antibody neutralization through changes in the accessibility of otherwise cryptic epitopes on the virion. In this study, we show that the neutralization potency of monoclonal antibody (MAb) E33 is sensitive to the maturation state of West Nile virus (WNV), despite its recognition of an accessible epitope, the domain III lateral ridge (DIII-LR). Comprehensive epitope mapping studies with 166 E protein DIII-LR variants revealed that the functional footprint of MAb E33 on the E protein differs subtly from that of the well-characterized DIII-LR MAb E16. Remarkably, aromatic substitutions at E protein residue 306 ablated the maturation state sensitivity of E33 IgG, and the neutralization efficacy of E33 Fab fragments was not affected by changes in the virion maturation state. We propose that E33 IgG binding on mature virions orients the Fc region in a manner that impacts subsequent antibody binding to nearby sites. This Fc-mediated steric constraint is a novel mechanism by which the maturation state of a virion modulates the efficacy of the humoral immune response to flavivirus infection

Assessing uncertainties from physical parameters and modelling choices in an atmospheric large eddy simulation model

In this study, we investigate uncertainties in a large eddy simulation of the atmosphere, employing modern uncertainty quantification methods that have hardly been used yet in this context. When analysing the uncertainty of model results, one can distinguish between uncertainty related to physical parameters whose values are not exactly known, and uncertainty related to modelling choices such as the selection of numerical discretization methods, of the spatial domain size and resolution, and the use of