Maximal good step graph methods for reducing the generation of the state space

This paper proposes an effective method based on the two main partial order techniques which are persistent sets and covering step graph techniques, to deal with the state explosion problem. First, we introduce a new definition of sound steps, the firing of which enables to extremely reduce the state space. Then, we propose a weaker sufficient condition about how to find the set of sound steps at each current marking. Next, we illustrate the relation between maximal sound steps and persistent sets, and propose a concept of good steps. Based on the maximal sound steps and good steps, a construction algorithm for generating a maximal good step graph (MGSG) of a Petri net (PN) is established. This algorithm first computes the maximal good step at each marking if there exists one, otherwise maximal sound steps are fired at the marking. Furthermore, we have proven that an MGSG can effectively preserve deadlocks of a Petri net. Finally, the change performance evaluation is made to demonstrate the superiority of our proposed method, compared with other related partial order techniques

Study on mechanical properties and damage characteristics of granite under thermal shock based on CT scanning

During the exploitation of deep geothermal resources, the thermal fractures of high-temperature rocks are usually induced by the impact of low-temperature fluids to improve the permeability of reservoir rocks. In order to reveal the damage and fracture mechanism of rock after thermal shock, the granites heated at high temperature (20 ℃, 150 ℃, 300 ℃, 450 ℃, 600 ℃ and 750 ℃) were treated by natural cooling and water cooling respectively, and the wave velocity test, uniaxial compression test and CT scanning were carried out on the treated granites. The mechanical effect of thermal shock on P-wave velocity, compressive strength and elastic modulus of granite were also discussed. The experimental results show that with the increase of heat treatment temperature, the P-wave velocity, compressive strength, and elastic modulus of rock gradually decrease, and the peak strain gradually increases. Compared with natural cooling, the wave velocity and mechanical properties of rock deteriorate more significantly after water cooling. Based on CT scanning, the spatial distribution characteristics of pore and fracture structure of granite under different heating temperatures and heat treatment methods were obtained, which can directly reflect the thermal damage degree of rock microstructure. When the heat treatment temperature is not higher than 450 ℃, the number and size of thermally induced cracks in granite scanning slices are less and the connectivity of cracks is relatively poor. When the temperature exceeds 450 ℃, the micro-cracks in granite develop and expand rapidly, and tend to form fracture network gradually, and the damage and cracking effect of water cooling on the microscomic-structure of granite is more obvious than that of natural cooling. In addition, based on triangular mesh discretization technique, ellipsoid model reconstruction algorithm and fracture tensor calculation theory, the three-dimensional fracture field of granite after thermal shock is quantitatively characterized, and the relationship between fracture fabric tensor and peak strength was established, which further reveals the influence mechanism of granite microscomic-structure on its mechanical properties under thermal shock

A Systematic Survey of Mini-Proteins in Bacteria and Archaea

BACKGROUND: Mini-proteins, defined as polypeptides containing no more than 100 amino acids, are ubiquitous in prokaryotes and eukaryotes. They play significant roles in various biological processes, and their regulatory functions gradually attract the attentions of scientists. However, the functions of the majority of mini-proteins are still largely unknown due to the constraints of experimental methods and bioinformatic analysis. METHODOLOGY/PRINCIPAL FINDINGS: In this article, we extracted a total of 180,879 mini-proteins from the annotations of 532 sequenced genomes, including 491 strains of Bacteria and 41 strains of Archaea. The average proportion of mini-proteins among all genomic proteins is approximately 10.99%, but different strains exhibit remarkable fluctuations. These mini-proteins display two notable characteristics. First, the majority are species-specific proteins with an average proportion of 58.79% among six representative phyla. Second, an even larger proportion (70.03% among all strains) is hypothetical proteins. However, a fraction of highly conserved hypothetical proteins potentially play crucial roles in organisms. Among mini-proteins with known functions, it seems that regulatory and metabolic proteins are more abundant than essential structural proteins. Furthermore, domains in mini-proteins seem to have greater distributions in Bacteria than Eukarya. Analysis of the evolutionary progression of these domains reveals that they have diverged to new patterns from a single ancestor. CONCLUSIONS/SIGNIFICANCE: Mini-proteins are ubiquitous in bacterial and archaeal species and play significant roles in various functions. The number of mini-proteins in each genome displays remarkable fluctuation, likely resulting from the differential selective pressures that reflect the respective life-styles of the organisms. The answers to many questions surrounding mini-proteins remain elusive and need to be resolved experimentally

A three-stage deadlock prevention strategy for S3PR nets

In this paper we focus on a particular class of Petri nets, called Systems of Simple Sequential Processes with Resources (S3PR). We propose a deadlock prevention strategy consisting of three stages, and based on Mixed Integer Programming (MIP). The advantage of the proposed approach is a usually higher permissiveness and a lower structural and computational complexity with respect to other approaches. Indeed exhaustive siphon enumeration is not required, as well as reachability analysis. Several numerical examples are illustrated to highlight the effectiveness of the approach

A Novel Approach for Constraint Transformation in Petri Nets with Uncontrollable Transitions

The main contribution of this correspondence paper consists in a linear algebraic characterization of the admissible marking set relative to a Petri net with uncontrollable transitions, subject to a linear constraint. In more detail, given a linear constraint that limits the number of tokens in one place, an algorithm is proposed to compute an approximation of the admissible marking set in terms of a disjunction of transformed linear constraints. The optimality of the solution is guaranteed provided that certain conditions are satisfied during the intermediate steps of the iterative approach. In all the other cases, the set of markings described by the transformed constraints could be surely contained in the admissible marking set

DsbA of Pseudomonas aeruginosa Is Essential for Multiple Virulence Factors

DsbA is a periplasmic thiol:disulfide oxidoreductase which contributes to the process of protein folding by catalyzing the formation of disulfide bonds. In this study, we demonstrate that the dsbA gene is required for the expression of the type III secretion system under low-calcium inducing conditions, intracellular survival of P. aeruginosa upon infection of HeLa cells, and twitching motility. The diverse phenotypes of the dsbA mutant are likely due to its defect in the folding of proteins that are involved in various biological processes, such as signal sensing, protein secretion, and defense against host clearing. In light of its effect on various virulence factors, DsbA could be an important target for the control of P. aeruginosa infections

Regulation of Membrane Permeability by a Two-Component Regulatory System in Pseudomonas aeruginosa

Membrane impermeability is the major contributing factor to multidrug resistance in clinical isolates of Pseudomonas aeruginosa. By using laboratory strain PAK, a spontaneous P. aeruginosa mutant (mutant PAK1-3) whose membrane had reduced permeability and which displayed increased levels of resistance to various antibiotics, especially aminoglycosides, was isolated. By complementation of the mutant with a genomic clone library derived from wild-type strain PAK, a novel two-component regulatory system (PprA and PprB) was identified and was found to be able to increase the permeability of the bacterial membrane and render PAK1-3 sensitive to antibiotics. Furthermore, specific phosphorylation of the response regulator (PprB) by histidine kinase (PprA) was observed in vitro, demonstrating that they are cognate two-component regulatory genes. Introduction of a plasmid expressing the pprB gene into randomly chosen clinical isolates (n = 17) resulted in increased sensitivity to aminoglycosides in the majority of isolates (n = 13) tested. This is the first demonstration that P. aeruginosa membrane permeability can be regulated, providing an important clue in the understanding of the mechanism of membrane impermeability-mediated multidrug resistance in P. aeruginosa