Direction Matters : On Influence-Preserving Graph Summarization and Max-Cut Principle for Directed Graphs

Summarizing large-scale directed graphs into small-scale representations is a useful but less-studied problem setting. Conventional clustering approaches, based on Min-Cut-style criteria, compress both the vertices and edges of the graph into the communities, which lead to a loss of directed edge information. On the other hand, compressing the vertices while preserving the directed-edge information provides a way to learn the small-scale representation of a directed graph. The reconstruction error, which measures the edge information preserved by the summarized graph, can be used to learn such representation. Compared to the original graphs, the summarized graphs are easier to analyze and are capable of extracting group-level features, useful for efficient interventions of population behavior. In this letter, we present a model, based on minimizing reconstruction error with nonnegative constraints, which relates to a Max-Cut criterion that simultaneously identifies the compressed nodes and the directed compressed relations between these nodes. A multiplicative update algorithm with column-wise normalization is proposed. We further provide theoretical results on the identifiability of the model and the convergence of the proposed algorithms. Experiments are conducted to demonstrate the accuracy and robustness of the proposed method.Peer reviewe

A Survey of DeFi Security: Challenges and Opportunities

DeFi, or Decentralized Finance, is based on a distributed ledger called blockchain technology. Using blockchain, DeFi may customize the execution of predetermined operations between parties. The DeFi system use blockchain technology to execute user transactions, such as lending and exchanging. The total value locked in DeFi decreased from \$200 billion in April 2022 to \$80 billion in July 2022, indicating that security in this area remained problematic. In this paper, we address the deficiency in DeFi security studies. To our best knowledge, our paper is the first to make a systematic analysis of DeFi security. First, we summarize the DeFi-related vulnerabilities in each blockchain layer. Additionally, application-level vulnerabilities are also analyzed. Then we classify and analyze real-world DeFi attacks based on the principles that correlate to the vulnerabilities. In addition, we collect optimization strategies from the data, network, consensus, smart contract, and application layers. And then, we describe the weaknesses and technical approaches they address. On the basis of this comprehensive analysis, we summarize several challenges and possible future directions in DeFi to offer ideas for further research

Identification and characterization of capsule depolymerase Dpo48 from Acinetobacter baumannii phage IME200

Background The emergence of multidrug- or extensively drug-resistant Acinetobacter baumannii has made it difficult to treat and control infections caused by this bacterium. It is urgently necessary to search for alternatives to conventional antibiotics for control of severe A. baumannii infections. In recent years, bacteriophages and their derivatives, such as depolymerases, showed great potential as antibacterial or antivirulence agents against bacterial infections. Nonetheless, unlike broad-spectrum bactericidal antibiotics, phage-encoded depolymerase targets only a limited number of bacterial strains. Therefore, identification of novel depolymerases and evaluation of their ability to control A. baumannii infections is important. Methods A bacteriophage was isolated from hospital sewage using an extensively drug-resistant A. baumannii strain as the host bacterium, and the phage’s plaque morphology and genomic composition were studied. A polysaccharide depolymerase (Dpo48) was expressed and identified, and the effects of pH and temperature on its activity were determined. Besides, a serum killing assay was conducted, and amino acid sequences homologous to those of putative polysaccharide depolymerases were compared. Results Phage IME200 yielded clear plaques surrounded by enlarged halos, with polysaccharide depolymerase activity against the host bacterium. A tail fiber protein with a Pectate_lyase_3 domain was identified as Dpo48 and characterized . Dpo48 was found to degrade the capsule polysaccharide of the bacterial surface, as revealed by Alcian blue staining. Dpo48 manifested stable activity over a broad range of pH (5.0–9.0) and temperatures (20–70 °C). Results from in vitro serum killing assays indicated that 50% serum was sufficient to cause a five log reduction of overnight enzyme-treated bacteria, with serum complement playing an important role in these killing assays. Moreover, Dpo48 had a spectrum of activity exactly the same as its parental phage IME200, which was active against 10 out of 41 A. baumannii strains. Amino acid sequence alignment showed that the putative tail fiber proteins had a relatively short, highly conserved domain in their N-terminal sequences, but their amino acid sequences containing pectate lyase domains, found in the C-terminal regions, were highly diverse. Conclusions Phage-encoded capsule depolymerases may become promising antivirulence agents for preventing and controlling A. baumannii infections

Development and Applications of Geometrically Nonlinear Piezoelectric Shell Elements

The investigation in this dissertation is concerned with development and applications of geometrically nonlinear triangular shell finite elements for the studies of highly geometrical nonlinear piezoelectric structures. In engineering practice, a nonlinear approach for piezoelectric shell structures is needed. This method is to enable one to (a) reveal the changing of configurations more precisely comparing with linear approach, and (b) deal with practical situations where large mechanical/electrical inputs and, in turn, large deformation phenomena exist. Hybrid strain and mixed formulation-based three node flat triangular shell elements are obtained for linear and nonlinear piezoelectric shell structures analyses. The elements are obtained by combining geometrically nonlinear shell elements with drilling degree-of-freedom and a piezoelectric shell element with assumed electrical field. For the nonlinear analysis the updated Lagrangian formulation and incremental Hellinger-Reissner variational principle are applied, with incremental displacements and strains being independent assumed fields. The hybrid strain and mixed formulation-based elements have features, such as finite strain, director formulation and updating thickness. The actuator and sensor equations as well as control algorithms are also introduced. A collection of geometrically nonlinear piezoelectric structures is treated by using the developed elements. The collection includes bimorph beam, sandwich beam, simply-supported sandwich plate, cylindrical ring, spherical cap, cylindrical panel, energy bender, simply-supported square plate, and cylindrical shell. These structures are analyzed for static and dynamic behaviors with piezoelectric actuating and sensing. Considerations of large deformations and strong electrical fields are emphasized. Computed results are compared with available analytical or numerical results reported in the literature. These numerical results have demonstrated the excellent performance of the geometrically nonlinear piezoelectric shell elements. Recommendations for further investigations are finally included in this dissertation

Regulation of S1P receptors and sphingosine kinases expression in acute pulmonary endothelial cell injury

Background Acute lung injury and acute respiratory distress syndrome (ALI/ARDS) is a severe clinical syndrome with mortality rate as high as 30–40%. There is no treatment yet to improve pulmonary endothelial barrier function in patients with severe pulmonary edema. Developing therapies to protect endothelial barrier integrity and stabilizing gas exchange is getting more and more attention. Sphingosine-1-phosphate (S1P) is able to enhance the resistance of endothelial cell barrier. S1P at physiological concentrations plays an important role in maintaining endothelial barrier function. Proliferation, regeneration and anti-inflammatory activity that mesenchymal stem cells (MSCs) exhibit make it possible to regulate the homeostatic control of S1P. Methods By building a pulmonary endothelial cell model of acute injury, we investigated the regulation of S1P receptors and sphingosine kinases expression by MSCs during the treatment of acute lung injury using RT-PCR, and investigated the HPAECs Micro-electronics impedance using Real Time Cellular Analysis. Results It was found that the down-regulation of TNF-α expression was more significant when MSC was used in combination with S1P. The combination effection mainly worked on S1PR2, S1PR3 and SphK2. The results show that when MSCs were used in combination with S1P, the selectivity of S1P receptors was increased and the homeostatic control of S1P concentration was improved through regulation of expression of S1P metabolic enzymes. Discussions The study found that, as a potential treatment, MSCs could work on multiple S1P related genes simultaneously. When it was used in combination with S1P, the expression regulation result of related genes was not simply the superposition of each other, but more significant outcome was obtained. This study establishes the experimental basis for further exploring the efficacy of improving endothelial barrier function in acute lung injury, using MSCs in combination with S1P and their possible synergistic mechanism

Establishment and Validation of a Prognostic Risk Model for Autophagy-Related Genes in Clear Cell Renal Cell Carcinoma

Background. Autophagy plays an essential role in tumorigenesis. At present, due to the unclear role of autophagy in renal clear cell carcinoma, we studied the potential value of autophagy-related genes (ARGs) in renal clear cell carcinoma (ccRCC). Methods. We obtained all ccRCC data from The Cancer Genome Atlas (TCGA). We extracted the expression data of ARGs for difference analysis and carried out biological function analysis on the different results. The autophagy risk model was constructed. The 5-year survival rate was assessed using the model, and the predictive power of the model was evaluated from multiple perspectives. Cox regression analysis was use to assess whether the model could be an independent prognostic factor. Finally, the correlation between the model and clinical indicators is analyzed. Results. The patients were divided into the high-risk group and low-risk group according to the median of autophagy risk score, and the results showed that the prognosis of the low-risk group was better than that of a high-risk group. The validation results of external data sets show that our model has good predictive value for ccRCC patients. The model can be an independent prognostic factor. Finally, the results show that our model has a stable predictive ability. Conclusion. The autophagy gene model we constructed can be used as an excellent prognostic indicator for ccRCC. Our study provides the possibility of individualized and precise treatment for ccRCC patients

Identification and Characterization of a Serious Multidrug Resistant Stenotrophomonas maltophilia Strain in China

An S. maltophilia strain named WJ66 was isolated from a patient; WJ66 showed resistance to more antibiotics than the other S. maltophilia strains. This bacteraemia is resistant to sulphonamides, or fluoroquinolones, while the representative strain of S. maltophilia, K279a, is sensitive to both. To explore drug resistance determinants of this strain, the draft genome sequence of WJ66 was determined and compared to other S. maltophilia sequences. Genome sequencing and genome-wide evolutionary analysis revealed that WJ66 was highly homologous with the strain K279a, but strain WJ66 contained additional antibiotic resistance genes. Further analysis confirmed that strain WJ66 contained an amino acid substitution (Q83L) in fluoroquinolone target GyrA and carried a class 1 integron, with an aadA2 gene in the resistance gene cassette. Homology analysis from the pathogen-host interaction database showed that strain WJ66 lacks raxST and raxA, which is consistent with K279a. Comparative genomic analyses revealed that subtle nucleotide differences contribute to various significant phenotypes in close genetic relationship strains

Isolation and Whole-genome Sequence Analysis of the Imipenem Heteroresistant Acinetobacter baumannii Clinical Isolate HRAB-85

Objectives: Heteroresistance is a phenomenon in which there are various responses to antibiotics from bacterial cells within the same population. Here, we isolated and characterised an imipenem heteroresistant Acinetobacter baumannii strain (HRAB-85). Methods: The genome of strain HRAB-85 was completely sequenced and analysed to understand its antibiotic resistance mechanisms. Population analysis and multilocus sequence typing were performed. Results: Subpopulations grew in the presence of imipenem at concentrations of up to 64 μg/mL, and the strain was found to belong to ST208. The total length of strain HRAB-85 was 4,098,585 bp with a GC content of 39.98%. The genome harboured at least four insertion sequences: the common ISAba1, ISAba22, ISAba24, and newly reported ISAba26. Additionally, 19 antibiotic-resistance genes against eight classes of antimicrobial agents were found, and 11 genomic islands (GIs) were identified. Among them, GI3, GI10, and GI11 contained many ISs and antibiotic-resistance determinants. Conclusions: The existence of imipenem heteroresistant phenotypes in A. baumannii was substantiated in this hospital, and imipenem pressure, which could induce imipenem-heteroresistant subpopulations, may select for highly resistant strains. The complete genome sequencing and bioinformatics analysis of HRAB-85 could improve our understanding of the epidemiology and resistance mechanisms of carbapenem-heteroresistant A. baumannii