The Dynamic Fault Tree Rare Event Simulator

The dynamic-fault-tree rare event simulator, DFTRES, is a statistical model checker for dynamic fault trees (DFTs), supporting the analysis of highly dependable systems, e.g. with unavailability or unreliability under 10^(-30). To efficiently estimate such low probabilities, we apply the Path-ZVA algorithm to implement Importance Sampling with minimal user input. Calculation speed is further improved by selective automata composition and bisimulation reduction. DFTRES reads DFTs in the Galileo or JANI textual formats. The tool is written in Java 11 with multi-platform support, and it is released under the GPLv3. In this paper we describe the architecture, setup, and input language of DFTRES, and showcase its accurate estimation of dependability metrics of (resilient) repairable DFTs from the FFORT benchmark suite.</p

Bulk Mediated Surface Diffusion: Non Markovian Desorption with Finite First Moment

Here we address a fundamental issue in surface physics: the dynamics of adsorbed molecules. We study this problem when the particle's desorption is characterized by a non Markovian process, while the particle's adsorption and its motion in the bulk are governed by a Markovian dynamics. We study the diffusion of particles in a semi-infinite cubic lattice, and focus on the effective diffusion process at the interface $z = 1$. We calculate analytically the conditional probability to find the particle on the $z=1$ plane as well as the surface dispersion as functions of time. The comparison of these results with Monte Carlo simulations show an excellent agreement.Comment: 16 pages, 7 figs. European Physical Journal B (in press

A pilot study comparing the metabolic profiles of elite-level athletes from different sporting disciplines

Background: The outstanding performance of an elite athlete might be associated with changes in their blood metabolic profile. The aims of this study were to compare the blood metabolic profiles between moderate- and high-power and endurance elite athletes and to identify the potential metabolic pathways underlying these differences. Methods: Metabolic profiling of serum samples from 191 elite athletes from different sports disciplines (121 high- and 70 moderate-endurance athletes, including 44 high- and 144 moderate-power athletes), who participated in national or international sports events and tested negative for doping abuse at anti-doping laboratories, was performed using non-targeted metabolomics-based mass spectroscopy combined with ultrahigh-performance liquid chromatography. Multivariate analysis was conducted using orthogonal partial least squares discriminant analysis. Differences in metabolic levels between high- and moderate-power and endurance sports were assessed by univariate linear models. Results: Out of 743 analyzed metabolites, gamma-glutamyl amino acids were significantly reduced in both high-power and high-endurance athletes compared to moderate counterparts, indicating active glutathione cycle. High-endurance athletes exhibited significant increases in the levels of several sex hormone steroids involved in testosterone and progesterone synthesis, but decreases in diacylglycerols and ecosanoids. High-power athletes had increased levels of phospholipids and xanthine metabolites compared to moderate-power counterparts. Conclusions: This pilot data provides evidence that high-power and high-endurance athletes exhibit a distinct metabolic profile that reflects steroid biosynthesis, fatty acid metabolism, oxidative stress, and energy-related metabolites. Replication studies are warranted to confirm differences in the metabolic profiles associated with athletes’ elite performance in independent data sets, aiming ultimately for deeper understanding of the underlying biochemical processes that could be utilized as biomarkers with potential therapeutic implications

Mix-and-Match System for the Enzymatic Synthesis of Enantiopure Glycerol-3-Phosphate-Containing Capsule Polymer Backbones from Actinobacillus pleuropneumoniae, Neisseria meningitidis, and Bibersteinia trehalosi

Capsule polymers are crucial virulence factors of pathogenic bacteria and are used as antigens in glycoconjugate vaccine formulations. Some Gram-negative pathogens express poly(glycosylglycerol phosphate) capsule polymers that resemble Gram-positive wall teichoic acids and are synthesized by TagF-like capsule polymerases. So far, the biotechnological use of these enzymes for vaccine developmental studies was restricted by the unavailability of enantiopure CDP-glycerol, one of the donor substrates required for polymer assembly. Here, we use CTP:glycerol-phosphate cytidylyltransferases (GCTs) and TagF-like polymerases to synthesize the poly(glycosylglycerol phosphate) capsule polymer backbones of the porcine pathogen Actinobacillus pleuropneumoniae, serotypes 3 and 7 (App3 and App7). GCT activity was confirmed by high-performance liquid chromatography, and polymers were analyzed using comprehensive nuclear magnetic resonance studies. Solid-phase synthesis protocols were established to allow potential scale-up of polymer production. In addition, one-pot reactions exploiting glycerol-kinase allowed us to start the reaction from inexpensive, widely available substrates. Finally, this study highlights that multidomain TagF-like polymerases can be transformed by mutagenesis of active site residues into single-action transferases, which in turn can act in trans to build-up structurally new polymers. Overall, our protocols provide enantiopure, nature-identical capsule polymer backbones from App2, App3, App7, App9, and App11, Neisseria meningitidis serogroup H, and Bibersteinia trehalosi serotypes T3 and T15

HIF-1 and SKN-1 Coordinate the Transcriptional Response to Hydrogen Sulfide in Caenorhabditis elegans

Hydrogen sulfide (H2S) has dramatic physiological effects on animals that are associated with improved survival. C. elegans grown in H2S are long-lived and thermotolerant. To identify mechanisms by which adaptation to H2S effects physiological functions, we have measured transcriptional responses to H2S exposure. Using microarray analysis we observe rapid changes in the abundance of specific mRNAs. The number and magnitude of transcriptional changes increased with the duration of H2S exposure. Functional annotation suggests that genes associated with protein homeostasis are upregulated upon prolonged exposure to H2S. Previous work has shown that the hypoxia-inducible transcription factor, HIF-1, is required for survival in H2S. In fact, we show that hif-1 is required for most, if not all, early transcriptional changes in H2S. Moreover, our data demonstrate that SKN-1, the C. elegans homologue of NRF2, also contributes to H2S-dependent changes in transcription. We show that these results are functionally important, as skn-1 is essential to survive exposure to H2S. Our results suggest a model in which HIF-1 and SKN-1 coordinate a broad transcriptional response to H2S that culminates in a global reorganization of protein homeostasis networks

Single phase nanocrystalline GaMnN thin films with high Mn content

Ga₁ˍₓ Mnₓ Nthin films with a Mn content as high as x=0.18 have been grown using ion-assisted deposition and a combination of Rutherford backscattering spectroscopy and nuclear reaction analysis was used to determine their composition. The structure of the films was determined from x-ray diffraction,transmission electron microscopy, and extended x-ray absorption fine structure(EXAFS). The films are comprised of nanocrystals of random stacked GaMnN and there is no evidence of Mn-rich secondary phases or clusters. EXAFS measurements at the Mn and Ga edge are almost identical to those at the Ga edge from Mn-free nanocrystallineGaNfilms, showing that the Mn occupies the Ga lattice sites, and simulated radial distribution functions of possible Mn-rich impurity phases bear no resemblance to the experimental data. The results indicate that these are the most heavily Mn-doped single phase GaNfilms studied to date.The authors gratefully acknowledge financial support from the New Zealand Foundation for Research Science and Technology through its New Economy Research Fund, and through a postdoctoral fellowship of one of the authors B.J.R.. The work of the MacDiarmid Institute is supported by a New Zealand Centre of Research Excellence award. Another author S.G. wishes to thank Education New Zealand for financial support of the EXAFS measurements

EU Agro Biogas Project

EU-AGRO-BIOGAS is a European Biogas initiative to improve the yield of agricultural biogas plants in Europe, to optimise biogas technology and processes and to improve the efficiency in all parts of the production chain from feedstock to biogas utilisation. Leading European research institutions and universities are cooperating with key industry partners in order to work towards a sustainable Europe. Fourteen partners from eight European countries are involved. EU-AGRO-BIOGAS aims at the development and optimisation of the entire value chain – to range from the production of raw materials, the production and refining of biogas to the utilisation of heat and electricity