On the validation of variable fidelity multi-physics simulations

The difficulties encountered in applying current normative approaches for validation to computational models of complex multi-physics engineering systems are identified and are associated with the untestable, and sometimes unprincipled, nature of these models. The behaviour of a structural panel on the surface of a hypersonic flight vehicle when subject to complex interactions between aerothermal, aeroelastic and material responses is employed as a key exemplar. A wide range of positions in the philosophy of science, that are applicable to validation, are discussed within the context of a schematic matrix, which allows models to be categorised according to whether they are testable and principled. In the absence of test data against which to assess the accuracy of predictions, it is proposed that a model's credibility should be established based on its epistemic values, theoretical ancestry and the credentials of the modelling techniques. This shift from an objectivist to a relativist approach requires the assignment of experts who acknowledge their biases while engaging intellectually and ethically with the model, the community of knowledge and stakeholders, in a hermeneutical approach.JRC.F.3-Chemicals Safety and Alternative Method

Calibration and evaluation of optical systems for full-field strain measurement

The design and testing of a reference material for the calibration of optical systems for strain measurement is described, together with the design and testing of a standardized test material that allows the evaluation and assessment of fitness for purpose of the most sophisticated optical system for strain measurement. A classification system for the steps in the measurement process is also proposed and allows the development of a unified approach to diagnostic testing of components or sub-systems in an optical system for strain measurement based on any optical technique. The results described arise from a European study known as SPOTS whose objectives were to begin to fill the gap caused by a lack of standards

Real-time large-scale dense RGB-D SLAM with volumetric fusion

We present a new simultaneous localization and mapping (SLAM) system capable of producing high-quality globally consistent surface reconstructions over hundreds of meters in real time with only a low-cost commodity RGB-D sensor. By using a fused volumetric surface reconstruction we achieve a much higher quality map over what would be achieved using raw RGB-D point clouds. In this paper we highlight three key techniques associated with applying a volumetric fusion-based mapping system to the SLAM problem in real time. First, the use of a GPU-based 3D cyclical buffer trick to efficiently extend dense every-frame volumetric fusion of depth maps to function over an unbounded spatial region. Second, overcoming camera pose estimation limitations in a wide variety of environments by combining both dense geometric and photometric camera pose constraints. Third, efficiently updating the dense map according to place recognition and subsequent loop closure constraints by the use of an ‘as-rigid-as-possible’ space deformation. We present results on a wide variety of aspects of the system and show through evaluation on de facto standard RGB-D benchmarks that our system performs strongly in terms of trajectory estimation, map quality and computational performance in comparison to other state-of-the-art systems.Science Foundation Ireland (Strategic Research Cluster Grant 07/SRC/I1168)Irish Research Council (Embark Initiative)United States. Office of Naval Research (Grant N00014-10-1-0936)United States. Office of Naval Research (Grant N00014-11-1-0688)United States. Office of Naval Research (Grant N00014-12-1-0093)United States. Office of Naval Research (Grant N00014-12-10020)National Science Foundation (U.S.) (Grant IIS-1318392

Lessons from Toxicology: Developing a 21st‑Century Paradigm for Medical Research

Biomedical developments in the 21st century provide an unprecedented opportunity to gain a dynamic systems-level and human-specific understanding of the causes and pathophysiologies of disease. This understanding is a vital need, in view of continuing failures in health research, drug discovery, and clinical translation. The full potential of advanced approaches may not be achieved within a 20th-century conceptual framework dominated by animal models. Novel technologies are being integrated into environmental health research and are also applicable to disease research, but these advances need a new medical research and drug discovery paradigm to gain maximal benefits. We suggest a new conceptual framework that repurposes the 21st-century transition underway in toxicology. Human disease should be conceived as resulting from integrated extrinsic and intrinsic causes, with research focused on modern human-specific models to understand disease pathways at multiple biological levels that are analogous to adverse outcome pathways in toxicology. Systems biology tools should be used to integrate and interpret data about disease causation and pathophysiology. Such an approach promises progress in overcoming the current roadblocks to understanding human disease and successful drug discovery and translation. A discourse should begin now to identify and consider the many challenges and questions that need to be solved

Incorporating New Technologies Into Toxicity Testing and Risk Assessment: Moving From 21st Century Vision to a Data-Driven Framework

Based on existing data and previous work, a series of studies is proposed as a basis toward a pragmatic early step in transforming toxicity testing. These studies were assembled into a data-driven framework that invokes successive tiers of testing with margin of exposure (MOE) as the primary metric. The first tier of the framework integrates data from high-throughput in vitro assays, in vitro-to-in vivo extrapolation (IVIVE) pharmacokinetic modeling, and exposure modeling. The in vitro assays are used to separate chemicals based on their relative selectivity in interacting with biological targets and identify the concentration at which these interactions occur. The IVIVE modeling converts in vitro concentrations into external dose for calculation of the point of departure (POD) and comparisons to human exposure estimates to yield a MOE. The second tier involves short-term in vivo studies, expanded pharmacokinetic evaluations, and refined human exposure estimates. The results from the second tier studies provide more accurate estimates of the POD and the MOE. The third tier contains the traditional animal studies currently used to assess chemical safety. In each tier, the POD for selective chemicals is based primarily on endpoints associated with a proposed mode of action, whereas the POD for nonselective chemicals is based on potential biological perturbation. Based on the MOE, a significant percentage of chemicals evaluated in the first 2 tiers could be eliminated from further testing. The framework provides a risk-based and animal-sparing approach to evaluate chemical safety, drawing broadly from previous experience but incorporating technological advances to increase efficiency

Phylogeny of Echinoderm Hemoglobins

Recent genomic information has revealed that neuroglobin and cytoglobin are the two principal lineages of vertebrate hemoglobins, with the latter encompassing the familiar myoglobin and α-globin/β-globin tetramer hemoglobin, and several minor groups. In contrast, very little is known about hemoglobins in echinoderms, a phylum of exclusively marine organisms closely related to vertebrates, beyond the presence of coelomic hemoglobins in sea cucumbers and brittle stars. We identified about 50 hemoglobins in sea urchin, starfish and sea cucumber genomes and transcriptomes, and used Bayesian inference to carry out a molecular phylogenetic analysis of their relationship to vertebrate sequences, specifically, to assess the hypothesis that the neuroglobin and cytoglobin lineages are also present in echinoderms.The genome of the sea urchin Strongylocentrotus purpuratus encodes several hemoglobins, including a unique chimeric 14-domain globin, 2 androglobin isoforms and a unique single androglobin domain protein. Other strongylocentrotid genomes appear to have similar repertoires of globin genes. We carried out molecular phylogenetic analyses of 52 hemoglobins identified in sea urchin, brittle star and sea cucumber genomes and transcriptomes, using different multiple sequence alignment methods coupled with Bayesian and maximum likelihood approaches. The results demonstrate that there are two major globin lineages in echinoderms, which are related to the vertebrate neuroglobin and cytoglobin lineages. Furthermore, the brittle star and sea cucumber coelomic hemoglobins appear to have evolved independently from the cytoglobin lineage, similar to the evolution of erythroid oxygen binding globins in cyclostomes and vertebrates.The presence of echinoderm globins related to the vertebrate neuroglobin and cytoglobin lineages suggests that the split between neuroglobins and cytoglobins occurred in the deuterostome ancestor shared by echinoderms and vertebrates

The effect of the geomagnetic field on cosmic ray energy estimates and large scale anisotropy searches on data from the Pierre Auger Observatory

We present a comprehensive study of the influence of the geomagnetic field on the energy estimation of extensive air showers with a zenith angle smaller than $60^\circ$, detected at the Pierre Auger Observatory. The geomagnetic field induces an azimuthal modulation of the estimated energy of cosmic rays up to the ~2% level at large zenith angles. We present a method to account for this modulation of the reconstructed energy. We analyse the effect of the modulation on large scale anisotropy searches in the arrival direction distributions of cosmic rays. At a given energy, the geomagnetic effect is shown to induce a pseudo-dipolar pattern at the percent level in the declination distribution that needs to be accounted for.Comment: 20 pages, 14 figure

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Complicated intra-abdominal infections worldwide : the definitive data of the CIAOW Study

Peer reviewe