Using schedulers to test probabilistic distributed systems

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s00165-012-0244-5. Copyright © 2012, British Computer Society.Formal methods are one of the most important approaches to increasing the confidence in the correctness of software systems. A formal specification can be used as an oracle in testing since one can determine whether an observed behaviour is allowed by the specification. This is an important feature of formal testing: behaviours of the system observed in testing are compared with the specification and ideally this comparison is automated. In this paper we study a formal testing framework to deal with systems that interact with their environment at physically distributed interfaces, called ports, and where choices between different possibilities are probabilistically quantified. Building on previous work, we introduce two families of schedulers to resolve nondeterministic choices among different actions of the system. The first type of schedulers, which we call global schedulers, resolves nondeterministic choices by representing the environment as a single global scheduler. The second type, which we call localised schedulers, models the environment as a set of schedulers with there being one scheduler for each port. We formally define the application of schedulers to systems and provide and study different implementation relations in this setting

Crop straw incorporation interacts with N fertilizer on N₂O emissions in an intensively cropped farmland

Nitrogen (N) fertilization and straw incorporation strongly influence nitrous oxide (N2O) emissions from agricultural fields. An in-situ micro-plot experiment on intensively farmed winter wheat (Triticum aestivum L.) was conducted to investigate the source and rate of N2O emissions from soils following labeled 15N fertilization with and without straw incorporation. Four treatments, i.e., no N fertilizer and no straw incorporation (N0S0), straw incorporation only (N0S1), N fertilizer only (N1S0), and N fertilization plus straw incorporation (N1S1), were established in the experiment. The N2O emissions mainly occurred after N fertilization and lasted for approximately 1–2 weeks, accounting for 60%–67% of the wheat seasonal N2O emissions. Within the 6 days after basal fertilization and 2–4 days after top-dressing, most of the N2O fluxes (>50%) were derived from fertilizer. Thereafter, soil-derived N2O dominated the total N2O emissions and within 10–20 days after N fertilization, fertilizer-derived N2O became negligible. Fertilizer N and soil N both accounted for 40%–60% of the seasonal N2O emissions, which may be explained by the high soil N stock due to long-term high N fertilization in the region. This implies the similar roles of soil N pool and fertilizer N in N2O generation under intensively farmed soils. The N fertilization had a significant priming effect on the turnover of soil N, which contributed 21.02%–50.47% of the total N2O emissions. During the basal fertilization/first irrigation event, straw incorporation significantly (P < 0.05) stimulated CO2 fluxes both in N-fertilized and non-N-fertilized plots; however, after the top-dressing/second irrigation event, the significant increase of CO2 fluxes induced by straw incorporation was only observed in the N-fertilized treatment. Straw incorporation interacted with N fertilization, and tended to enhance N2O emissions in the basal fertilization and lower N2O emissions in the top-dressing period. In N-fertilized plots, the seasonal N2O emissions from straw-incorporated and straw-removed treatments were similar, indicating that straw incorporation enhanced the N supply without increasing the N2O emissions. Our study highlights that there are significant benefits of straw incorporation to soil fertility improvement; however, the long-term impacts of straw incorporation on greenhouse gas emissions should be further examined

cij: A Python code for quasiharmonic thermoelasticity

The Wu-Wentzcovitch semi-analytical method (SAM) is a concise and predictive formalism to calculate the high-pressure and high-temperature (high-PT) thermoelastic tensor (Cij) of crystalline materials. This method has been successfully applied to materials across different crystal systems in conjunction with ab initio calculations of static elastic coefficients and phonon frequencies. Such results have offered first-hand insights into the composition and structure of the Earth's mantle. Here we introduce the cij package, a Python implementation of the SAM-Cij formalism. It enables a thermoelasticity calculation to be initiated from a single command and fully configurable from a calculation settings file to work with solids within any crystalline system. These features allow SAM-Cij calculations to work on a personal computer and to be easily integrated as a part of high-throughput workflows. Here we show the performance of this code for three minerals from different crystal systems at their relevant PTs: diopside (monoclinic), akimotoite (trigonal), and bridgmanite (orthorhombic)

Crystal structure of the type IV secretion system component CagX from Helicobacter pylori.

This is the final version.Available from the International Union of Crystallography via the DOI in this record.Helicobacter pylori, a Gram-negative bacterial pathogen prevalent in the human population, is the causative agent of severe gastric diseases. An H. pylori type IV secretion (T4S) system encoded by the cytotoxin-associated gene pathogenicity island (cagPAI) is responsible for communication with host cells. As a component of the cagPAI T4S system core complex, CagX plays an important role in virulence-protein translocation into the host cells. In this work, the crystal structure of the C-terminal domain of CagX (CagXct), which is a homologue of the VirB9 protein from the VirB/D4 T4S system, is presented. CagXct is only the second three-dimensional structure to be elucidated of a VirB9-like protein. Another homologue, TraO, which is encoded on the Escherichia coli conjugative plasmid pKM101, shares only 19% sequence identity with CagXct; however, there is a remarkable similarity in tertiary structure between these two β-sandwich protein domains. Most of the residues that are conserved between CagXct and TraO are located within the protein core and appear to be responsible for the preservation of this domain fold. The studies presented here will contribute to our understanding of different bacterial T4S systems.The authors thank the staff of beamline BL17U1 at Shanghai Synchrotron Radiation Facility (SSRF) for support during diffraction data collection. We thank the National Natural Science Foundation of China (Grant Nos. 31470741 and 31270790) and the National Thousand Talents Program of China for their support of this work

Quantum phase transition to unconventional multi-orbital superfluidity in optical lattices

Orbital physics plays a significant role for a vast number of important phenomena in complex condensed matter systems such as high-T$_c$ superconductivity and unconventional magnetism. In contrast, phenomena in superfluids -- especially in ultracold quantum gases -- are commonly well described by the lowest orbital and a real order parameter. Here, we report on the observation of a novel multi-orbital superfluid phase with a {\it complex} order parameter in binary spin mixtures. In this unconventional superfluid, the local phase angle of the complex order parameter is continuously twisted between neighboring lattice sites. The nature of this twisted superfluid quantum phase is an interaction-induced admixture of the p-orbital favored by the graphene-like band structure of the hexagonal optical lattice used in the experiment. We observe a second-order quantum phase transition between the normal superfluid (NSF) and the twisted superfluid phase (TSF) which is accompanied by a symmetry breaking in momentum space. The experimental results are consistent with calculated phase diagrams and reveal fundamentally new aspects of orbital superfluidity in quantum gas mixtures. Our studies might bridge the gap between conventional superfluidity and complex phenomena of orbital physics.Comment: 5 pages, 4 figure

Screening of knee-joint vibroarthrographic signals using statistical parameters and radial basis functions

Externally detected vibroarthrographic (VAG) signals bear diagnostic information related to the roughness, softening, breakdown, or the state of lubrication of the articular cartilage surfaces of the knee joint. Analysis of VAG signals could provide quantitative indices for noninvasive diagnosis of articular cartilage breakdown and staging of osteoarthritis. We propose the use of statistical parameters of VAG signals, including the form factor involving the variance of the signal and its derivatives, skewness, kurtosis, and entropy, to classify VAG signals as normal or abnormal. With a database of 89 VAG signals, screening efficiency of up to 0.82 was achieved, in terms of the area under the receiver operating characteristics curve, using a neural network classifier based on radial basis functions

Age-related changes in the effects of strength training on lower leg muscles in healthy individuals measured using MRI

BACKGROUND: We previously measured the rate of regaining muscle strength during rehabilitation of lower leg muscles in patients following lower leg casting. Our primary aim in this study was to measure the rate of gain of strength in healthy individuals undergoing a similar training regime. Our secondary aim was to test the ability of MRI to provide a biomarker for muscle function. METHODS: Men and women were recruited in three age groups: 20-30, 50-65 and over 70 years. Their response to resistance training of the right lower leg twice a week for 8 weeks was monitored using a dynamometer and MRI of tibialis anterior, soleus and gastrocnemius muscles at 2 weekly intervals to measure muscle size (anatomical cross-sectional area (ACSA)) and quality (T2 relaxation). Forty-four volunteers completed the study. RESULTS: Baseline strength declined with age. Training had no effect in middle-aged females or in elderly men in dorsiflexion. Other groups significantly increased both plantarflexion and dorsiflexion strength at rates up to 5.5 N m week(-1) in young females in plantarflexion and 1.25 N m week(-1) in young males in dorsiflexion. No changes were observed in ACSA or T2 in any age group in any muscle. CONCLUSION: Exercise training improves muscle strength in males at all ages except the elderly in dorsiflexion. Responses in females were less clear with variation across age and muscle groups. These results were not reflected in simple MRI measures that do not, therefore, provide a good biomarker for muscle atrophy or the efficacy of rehabilitation

Synergistic Antibacterial Effects of Metallic Nanoparticle Combinations

© The Author(s) 2019.Metallic nanoparticles have unique antimicrobial properties that make them suitable for use within medical and pharmaceutical devices to prevent the spread of infection in healthcare. The use of nanoparticles in healthcare is on the increase with silver being used in many devices. However, not all metallic nanoparticles can target and kill all disease-causing bacteria. To overcome this, a combination of several different metallic nanoparticles were used in this study to compare effects of multiple metallic nanoparticles when in combination than when used singly, as single elemental nanoparticles (SENPs), against two common hospital acquired pathogens (Staphylococcus aureus and Pseudomonas. aeruginosa). Flow cytometry LIVE/DEAD assay was used to determine rates of cell death within a bacterial population when exposed to the nanoparticles. Results were analysed using linear models to compare effectiveness of three different metallic nanoparticles, tungsten carbide (WC), silver (Ag) and copper (Cu), in combination and separately. Results show that when the nanoparticles are placed in combination (NPCs), antimicrobial effects significantly increase than when compared with SENPs (P < 0.01). This study demonstrates that certain metallic nanoparticles can be used in combination to improve the antimicrobial efficiency in destroying morphologically distinct pathogens within the healthcare and pharmaceutical industry.Peer reviewe