Recommending Analogical APIs via Knowledge Graph Embedding

Library migration, which re-implements the same software behavior by using a different library instead of using the current one, has been widely observed in software evolution. One essential part of library migration is to find an analogical API that could provide the same functionality as current ones. However, given the large number of libraries/APIs, manually finding an analogical API could be very time-consuming and error-prone. Researchers have developed multiple automated analogical API recommendation techniques. Documentation-based methods have particularly attracted significant interest. Despite their potential, these methods have limitations, such as a lack of comprehensive semantic understanding in documentation and scalability challenges. In this work, we propose KGE4AR, a novel documentation-based approach that leverages knowledge graph (KG) embedding to recommend analogical APIs during library migration. Specifically, KGE4AR proposes a novel unified API KG to comprehensively and structurally represent three types of knowledge in documentation, which can better capture the high-level semantics. Moreover, KGE4AR then proposes to embed the unified API KG into vectors, enabling more effective and scalable similarity calculation. We build KGE4AR' s unified API KG for 35,773 Java libraries and assess it in two API recommendation scenarios: with and without target libraries. Our results show that KGE4AR substantially outperforms state-of-the-art documentation-based techniques in both evaluation scenarios in terms of all metrics (e.g., 47.1%-143.0% and 11.7%-80.6% MRR improvements in each scenario). Additionally, we explore KGE4AR' s scalability, confirming its effective scaling with the growing number of libraries.Comment: Accepted by FSE 202

The identification and characterization of nucleic acid chaperone activity of human enterovirus 71 nonstructural protein 3AB

AbstractHuman enterovirus 71 (EV71) belongs to the genus Enterovirus in the family Picornaviridae and has been recognized as one of the most important pathogens that cause emerging infectious disease. Despite of the importance of EV71, the nonstructural protein 3AB from this virus is little understood for its function during EV71 replication. Here we expressed EV71 3AB protein as recombinant protein in a eukaryotic expression system and uncovered that this protein possesses a nucleic acid helix-destabilizing and strand annealing acceleration activity in a dose-dependent manner, indicating that EV71 3AB is a nucleic acid chaperone protein. Moreover, we characterized the RNA chaperone activity of EV71 3AB, and revealed that divalent metal ions, such as Mg2+ and Zn2+, were able to inhibit the RNA helix-destabilizing activity of 3AB to different extents. Moreover, we determined that 3B plus the last 7 amino acids at the C-terminal of 3A (termed 3B+7) possess the RNA chaperone activity, and five amino acids, i.e. Lys-80, Phe-82, Phe-85, Tyr-89, and Arg-103, are critical and probably the active sites of 3AB for its RNA chaperone activity. This report reveals that EV71 3AB displays an RNA chaperone activity, adds a new member to the growing list of virus-encoded RNA chaperones, and provides novel knowledge about the virology of EV71

Doublade: Unknown Vulnerability Detection in Smart Contracts Via Abstract Signature Matching and Refined Detection Rules

With the prosperity of smart contracts and the blockchain technology, various security analyzers have been proposed from both the academia and industry to address the associated risks. Yet, there does not exist a high-quality benchmark of smart contract vulnerability for security research. In this study, we propose an approach towards building a high-quality vulnerability benchmark. Our approach consists of two parts. First, to improve recall, we propose to search for similar vulnerabilities in an automated way by leveraging the abstract vulnerability signature (AVS). Second, to remove the false positives (FPs) due to AVS-based matching, we summarize the detection rules of existing tools and apply the refined rules by considering various defense mechanisms (DMs). By integrating AVS-based code matching and the refined detection rules (RDR), our approach achieves higher precision and recall. On the collected 76,354 contracts, we build a benchmark consisting of 1,219 vulnerabilities covering five different vulnerability types identified together by our tool (DOUBLADE) and other three scanners. Additionally, we conduct a comparison between DOUBLADE and the others, on an additional 17,770 contracts. Results show that DOUBLADE can yield a better detection accuracy with similar execution time

IL-8 Enhances Therapeutic Effects of BMSCs on Bone Regeneration via CXCR2-Mediated PI3k/Akt Signaling Pathway

Background/Aims: Tissue engineering bone transplantation with bone marrow mesenchymal stem cells (BMSCs) is an effective technology to treat massive bone loss, while molecular regulation of the bone regeneration processes remains poorly understood. Here, we aimed to assess the role of interleukin-8 (IL-8) in the recruitment of host cells by seeded BMSCs and in the bone regeneration. Methods: A transwell assay was performed to examine the role of IL-8/CXCR1/CXCR2/PI3k/Akt on the migration potential of hBMSCs. The in vitro chondrogenic differentiation of hBMSCs was assessed by examination of 2 chondrogenic markers, Sox9 and type 2 collagen (COL2). mBMSCs were used in tissue engineered bone (TEB) with/without IL-8 implanted into bone defect area with CXCR2 or Akt inhibitors. Density and Masson staining of the regenerated bone were assessed. The chondrogenesis was assessed by expression levels of associated proteins, Sox9 and COL2, by RT-qPCR and by immunohistochemistry. Results: IL-8 may trigger in vitro migration of hBMSCs via CXCR2-mediated PI3k/Akt signaling pathway. IL-8 enhances osteogenesis in the TEB-implanted bone defect in mice. IL-8 induces chondrogenic differentiation of hBMSCs via CXCR2-mediated PI3k/Akt signaling pathway in vitro and in vivo. Conclusions: IL-8 enhances therapeutic effects of MSCs on bone regeneration via CXCR2-mediated PI3k/Akt signaling pathway

The Roles of Different Sources of Social Support on Emotional Well-Being among Chinese Elderly

Background: Social support has been widely known as a protective factor for the emotional well-being (EWB) of older adults, but less studies have investigated the roles of different sources of social support (i.e., family and friend support) on different facets of EWB (i.e., positive affect and negative affect) simultaneously

Investigating the Influence of Magnesium Ions on p53–DNA Binding Using Atomic Force Microscopy

p53 is a tumor suppressor protein that plays a significant role in apoptosis and senescence, preserving genomic stability, and preventing oncogene expression. Metal ions, such as magnesium and zinc ions, have important influences on p53–DNA interactions for stabilizing the structure of the protein and enhancing its affinity to DNA. In the present study, we systematically investigated the interaction of full length human protein p53 with DNA in metal ion solution by atomic force microscopy (AFM). The p53–DNA complexes at various p53 concentrations were scanned by AFM and their images are used to measure the dissociation constant of p53–DNA binding by a statistical method. We found that the dissociation constant of p53 binding DNA is 328.02 nmol/L in physiological buffer conditions. The influence of magnesium ions on p53–DNA binding was studied by AFM at various ion strengths through visualization. We found that magnesium ions significantly stimulate the binding of the protein to DNA in a sequence-independent manner, different from that stimulated by zinc. Furthermore, the high concentrations of magnesium ions can promote p53 aggregation and even lead to the formation of self-assembly networks of DNA and p53 proteins. We propose an aggregation and self-assembly model based on the present observation and discuss its biological meaning

The Mixing Counterion Effect on DNA Compaction and Charge Neutralization at Low Ionic Strength

DNA compaction and charge neutralization in a mixing counterion solution involves competitive and cooperative electrostatic binding, and sometimes counterion complexation. At normal ionic strength, it has been found that the charge neutralization of DNA by the multivalent counterion is suppressed when being added extra mono- and di-valent counterions. Here, we explore the effect mixing counterion on DNA compaction and charge neutralization under the condition of low ionic strength. Being quite different from normal ionic strength, the electrophoretic mobility of DNA in multivalent counterion solution (octalysine, spermine) increases the presence of mono- and di-valent cations, such as sodium and magnesium ions. It means that the charge neutralization of DNA by the multivalent counterion is promoted rather than suppressed when introducing extra mono- and di-valent counterions into solution. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates under the same condition by single molecular magnetic tweezers. This mixing effect can be attributed to the cooperative electrostatic binding of counterions to DNA when the concentration of counterions in solution is below a critical concentration

DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution

DNA conformation is strongly dependent on the valence of counterions in solution, and a valence of at least three is needed for DNA compaction. Recently, we directly demonstrated DNA compaction and its regulation, mediated by divalent cations, by lowering the pH of a solution. In the present study, we found that the critical electrophoretic mobility of DNA is promoted to around −1.0 × 10−4 cm2 V−1 s−1 to incur DNA compaction or condensation in a tri- and tetravalent counterions solution, corresponding to an about 89% neutralized charge fraction of DNA. This is also valid for DNA compaction by divalent counterions in a low pH solution. It is notable that the critical charge neutralization of DNA for compaction is only about 1% higher than the saturated charge fraction of DNA in a mild divalent ion solution. We also found that DNA compaction by divalent cations at low pH is weakened and even decondensed with an increasing concentration of counterions

Correlations between Social Support and Emotional Well-being.

<p>Note. PA  =  Positive affect; NA  =  Negative affect.</p><p>*<i>p</i><0.05. **<i>p</i><0.01. ***<i>p</i><0.001.</p