Based on the successive iteration in the Taylor series expansion method, a three-point explicit compact difference scheme with arbitrary order of accuracy is derived in this paper. Numerical characteristics of the sch...Based on the successive iteration in the Taylor series expansion method, a three-point explicit compact difference scheme with arbitrary order of accuracy is derived in this paper. Numerical characteristics of the scheme are studied by the Fourier analysisl Unlike the conventional compact difference schemes which need to solve the equation to obtain the unknown derivatives in each node, the proposed scheme is explicit and can achieve arbitrary order of accuracy in space. Application examples for the convectiondiffusion problem with a sharp front gradient and the typical lid-driven cavity flow are given. It is found that the proposed compact scheme is not only simple to implement and economical to use, but also is effective to simulate the convection-dominated problem and obtain high-order accurate solution in coarse grid systems.展开更多
The explicit compact difference scheme, proposed in Three-point explicit compact difference scheme with arbitrary order of accuracy and its application in CFD by Lin et al., published in Applied Mathematics and Mechan...The explicit compact difference scheme, proposed in Three-point explicit compact difference scheme with arbitrary order of accuracy and its application in CFD by Lin et al., published in Applied Mathematics and Mechanics （English Edition）, 2007, 28（7）, 943-953, has the same performance as the conventional finite difference schemes. It is just another expression of the conventional finite difference schemes. The proposed expression does not have the advantages of a compact difference scheme. Nonetheless, we can more easily obtain and implement compared with the conventional expression in which the coefficients can only be obtained by solving equations, especially for higher accurate schemes.展开更多
目的:基于网络药理学和分子对接技术,探讨经验方归元膏的活性成分防治慢性疲劳综合征(CFS)的潜在机制。方法:从TCMSP数据库、BATMAN数据库筛选归元膏的化学成分和靶点,通过GeneCards、OMIM、DisGenet数据库检索收集CFS靶点,将归元膏作...目的:基于网络药理学和分子对接技术,探讨经验方归元膏的活性成分防治慢性疲劳综合征(CFS)的潜在机制。方法:从TCMSP数据库、BATMAN数据库筛选归元膏的化学成分和靶点,通过GeneCards、OMIM、DisGenet数据库检索收集CFS靶点,将归元膏作用靶点和疾病靶点取交集,使用Cytoscape Version 3.9.1制做药物和疾病靶点韦恩图,运用STRING数据库构建蛋白质与蛋白质相互作用的PPI网络作用图,并通过Cytoscape3.8.2软件中的插件CytoNCA筛选关键靶点,并将交集靶点导入David数据库,利用微生信程序进行基因本体(GO)和京都和基因组百科全书(KEGG)富集分析,并通过Cytoscape3.8.2构建归元膏药物–有效成分–靶点和归元膏药物–成分–靶点–通路网络,最后用AutoDock vinna软件进行分子对接验证。结果:检索出归元膏活性成分有111个,其中quercetin,isoflavanone,poriferasta-7,22E-dien-3beta-ol,hancinol,orchinol等为归元膏防治CFS的关键成分,CFS相关靶点507个,其中IL-6 (白细胞介素-6),TNF (肿瘤坏死因子),STAT3 (信号转导及转录激活因子3),JUN,BCL2 (B细胞淋巴瘤/白血病-2),HIF1A (缺氧诱导因子1α亚单位),AKT1 (AKT丝氨酸/苏氨酸激酶1),CASP3 (caspase-3),MMP9 (基质金属蛋白酶9),NFKB1 (核因子kappa B亚基1)为防治CFS的关键靶点,GO富集分析示生物学过程方面可能通过对凋亡过程的负调控、细胞增殖的正调控、蛋白质磷酸化的正调控、内皮细胞增殖的正调控等,分子功能主要包括酶结合、受体结合、蛋白酶结合等;细胞功能主要包含线粒体、蛋白质复合物、细胞内膜结合的细胞器等。KEGG富集分析一共得到186条信号通路,主要与PI3K-Akt通路、卡波西肉瘤相关疱疹病毒感染、丝裂原活化蛋白激酶信号通路等有关。分子对接结果表明归元膏中的核心作用靶点和主要活性成分具备稳定性的结合活性。结论:归元膏将quercetin、poriferasta-7,22E-dien-3beta-ol、orchinol、isoflavanone等关键活性成分与IL6、TNF、STAT3、JUN、BCL2、HIF1A、AKT1和CASP3等靶点结合,通过对PI3K/Akt、MAPK、NF-κB等多条信号通路的调控,调节了CFS患者的免疫反应、细胞凋亡、代谢紊乱等多个生物学过程。通过激活抗凋亡通路、抑制促炎因子的产生和调节能量代谢,验证了该方多靶点多线路的调控,发挥了多靶点、多通路的协同作用,显著改善了CFS的症状。Objective: Based on network pharmacology and molecular docking technology, this study explores the potential mechanisms of active ingredients in the empirical formula Guiyuan Ointment for the prevention and treatment of chronic fatigue syndrome (CFS). Methods: Chemical components and targets of Guiyuan Ointment were screened from the TCMSP database and BATMAN database. CFS targets were collected through GeneCards, OMIM, and DisGenet databases. The intersection of Guiyuan Ointment’s action targets and disease targets was taken. Cytoscape Version 3.9.1 was used to create a Venn diagram of drug and disease targets. The STRING database was employed to construct a protein-protein interaction (PPI) network diagram, and key targets were screened using the CytoNCA plugin in Cytoscape 3.8.2 software. The intersection targets were imported into the David database, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using the microbioinformatics program. Cytoscape 3.8.2 was used to construct the Guiyuan Ointment drug-effective component-target and drug-component-target-pathway networks. Finally, molecular docking validation was conducted using AutoDock Vina software. Results: A total of 111 active components of Guiyuan Ointment were retrieved, among which quercetin, isoflavanone, poriferasta-7,22E-dien-3beta-ol, hancinol, and orchinol are key components for the prevention and treatment of CFS by Guiyuan Ointment. There are 507 CFS-related targets, with IL-6 (interleukin-6), TNF (tumor necrosis factor), STAT3 (signal transducer and activator of transcription 3), JUN, BCL2 (B-cell lymphoma/leukemia-2), HIF1A (hypoxia-inducible factor 1α subunit), AKT1 (AKT serine/threonine kinase 1), CASP3 (caspase-3), MMP9 (matrix metallopeptidase 9), and NFKB1 (nuclear factor kappa B subunit 1) being key targets for the prevention and treatment of CFS. GO enrichment analysis showed that in terms of biological processes, it may involve negative regulation of apoptosis, positive regulation of cell proliferation, positive regulation of protein phosphorylation, and positive regulation of endothelial cell proliferation, etc. The main molecular functions include enzyme binding, receptor binding, and protease binding, etc. The main cellular functions involve mitochondria, protein complexes, and cell organelles bound to the intracellular membrane, etc. KEGG enrichment analysis yielded a total of 186 signaling pathways, mainly related to the PI3K-Akt pathway, Kaposi’s sarcoma-associated herpesvirus infection, and mitogen-activated protein kinase signaling pathway, etc. The molecular docking results indicated that the core action targets and main active components in Guiyuan Ointment have stable binding activity. Conclusion: Guiyuan Ointment combines key active components such as quercetin, poriferasta-7,22E-dien-3beta-ol, orchinol, and isoflavanone with targets like IL6, TNF, STAT3, JUN, BCL2, HIF1A, AKT1, and CASP3. By regulating multiple signaling pathways such as PI3K/Akt, MAPK, and NF-κB, it modulates various biological processes in CFS patients, including immune response, cell apoptosis, and metabolic disorders. Through activating anti-apoptotic pathways, inhibiting the production of pro-inflammatory factors, and regulating energy metabolism, it verifies the multi-target and multi-pathway regulation of this formula, exerting synergistic effects on multiple targets and pathways, and significantly improving the symptoms of CFS.展开更多
基金Project supported by the National Natural Science Foundation of China(No.50479053)
文摘Based on the successive iteration in the Taylor series expansion method, a three-point explicit compact difference scheme with arbitrary order of accuracy is derived in this paper. Numerical characteristics of the scheme are studied by the Fourier analysisl Unlike the conventional compact difference schemes which need to solve the equation to obtain the unknown derivatives in each node, the proposed scheme is explicit and can achieve arbitrary order of accuracy in space. Application examples for the convectiondiffusion problem with a sharp front gradient and the typical lid-driven cavity flow are given. It is found that the proposed compact scheme is not only simple to implement and economical to use, but also is effective to simulate the convection-dominated problem and obtain high-order accurate solution in coarse grid systems.
基金Supported by the National Natural Science Foundation of China (Nos.50876114 and 10602043)the Program for New Century Excellent Talents in University,and the Scientific Research Key Project Fund of Ministry of Education (No.106142)
文摘The explicit compact difference scheme, proposed in Three-point explicit compact difference scheme with arbitrary order of accuracy and its application in CFD by Lin et al., published in Applied Mathematics and Mechanics （English Edition）, 2007, 28（7）, 943-953, has the same performance as the conventional finite difference schemes. It is just another expression of the conventional finite difference schemes. The proposed expression does not have the advantages of a compact difference scheme. Nonetheless, we can more easily obtain and implement compared with the conventional expression in which the coefficients can only be obtained by solving equations, especially for higher accurate schemes.
文摘目的:基于网络药理学和分子对接技术,探讨经验方归元膏的活性成分防治慢性疲劳综合征(CFS)的潜在机制。方法:从TCMSP数据库、BATMAN数据库筛选归元膏的化学成分和靶点,通过GeneCards、OMIM、DisGenet数据库检索收集CFS靶点,将归元膏作用靶点和疾病靶点取交集,使用Cytoscape Version 3.9.1制做药物和疾病靶点韦恩图,运用STRING数据库构建蛋白质与蛋白质相互作用的PPI网络作用图,并通过Cytoscape3.8.2软件中的插件CytoNCA筛选关键靶点,并将交集靶点导入David数据库,利用微生信程序进行基因本体(GO)和京都和基因组百科全书(KEGG)富集分析,并通过Cytoscape3.8.2构建归元膏药物–有效成分–靶点和归元膏药物–成分–靶点–通路网络,最后用AutoDock vinna软件进行分子对接验证。结果:检索出归元膏活性成分有111个,其中quercetin,isoflavanone,poriferasta-7,22E-dien-3beta-ol,hancinol,orchinol等为归元膏防治CFS的关键成分,CFS相关靶点507个,其中IL-6 (白细胞介素-6),TNF (肿瘤坏死因子),STAT3 (信号转导及转录激活因子3),JUN,BCL2 (B细胞淋巴瘤/白血病-2),HIF1A (缺氧诱导因子1α亚单位),AKT1 (AKT丝氨酸/苏氨酸激酶1),CASP3 (caspase-3),MMP9 (基质金属蛋白酶9),NFKB1 (核因子kappa B亚基1)为防治CFS的关键靶点,GO富集分析示生物学过程方面可能通过对凋亡过程的负调控、细胞增殖的正调控、蛋白质磷酸化的正调控、内皮细胞增殖的正调控等,分子功能主要包括酶结合、受体结合、蛋白酶结合等;细胞功能主要包含线粒体、蛋白质复合物、细胞内膜结合的细胞器等。KEGG富集分析一共得到186条信号通路,主要与PI3K-Akt通路、卡波西肉瘤相关疱疹病毒感染、丝裂原活化蛋白激酶信号通路等有关。分子对接结果表明归元膏中的核心作用靶点和主要活性成分具备稳定性的结合活性。结论:归元膏将quercetin、poriferasta-7,22E-dien-3beta-ol、orchinol、isoflavanone等关键活性成分与IL6、TNF、STAT3、JUN、BCL2、HIF1A、AKT1和CASP3等靶点结合,通过对PI3K/Akt、MAPK、NF-κB等多条信号通路的调控,调节了CFS患者的免疫反应、细胞凋亡、代谢紊乱等多个生物学过程。通过激活抗凋亡通路、抑制促炎因子的产生和调节能量代谢,验证了该方多靶点多线路的调控,发挥了多靶点、多通路的协同作用,显著改善了CFS的症状。Objective: Based on network pharmacology and molecular docking technology, this study explores the potential mechanisms of active ingredients in the empirical formula Guiyuan Ointment for the prevention and treatment of chronic fatigue syndrome (CFS). Methods: Chemical components and targets of Guiyuan Ointment were screened from the TCMSP database and BATMAN database. CFS targets were collected through GeneCards, OMIM, and DisGenet databases. The intersection of Guiyuan Ointment’s action targets and disease targets was taken. Cytoscape Version 3.9.1 was used to create a Venn diagram of drug and disease targets. The STRING database was employed to construct a protein-protein interaction (PPI) network diagram, and key targets were screened using the CytoNCA plugin in Cytoscape 3.8.2 software. The intersection targets were imported into the David database, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using the microbioinformatics program. Cytoscape 3.8.2 was used to construct the Guiyuan Ointment drug-effective component-target and drug-component-target-pathway networks. Finally, molecular docking validation was conducted using AutoDock Vina software. Results: A total of 111 active components of Guiyuan Ointment were retrieved, among which quercetin, isoflavanone, poriferasta-7,22E-dien-3beta-ol, hancinol, and orchinol are key components for the prevention and treatment of CFS by Guiyuan Ointment. There are 507 CFS-related targets, with IL-6 (interleukin-6), TNF (tumor necrosis factor), STAT3 (signal transducer and activator of transcription 3), JUN, BCL2 (B-cell lymphoma/leukemia-2), HIF1A (hypoxia-inducible factor 1α subunit), AKT1 (AKT serine/threonine kinase 1), CASP3 (caspase-3), MMP9 (matrix metallopeptidase 9), and NFKB1 (nuclear factor kappa B subunit 1) being key targets for the prevention and treatment of CFS. GO enrichment analysis showed that in terms of biological processes, it may involve negative regulation of apoptosis, positive regulation of cell proliferation, positive regulation of protein phosphorylation, and positive regulation of endothelial cell proliferation, etc. The main molecular functions include enzyme binding, receptor binding, and protease binding, etc. The main cellular functions involve mitochondria, protein complexes, and cell organelles bound to the intracellular membrane, etc. KEGG enrichment analysis yielded a total of 186 signaling pathways, mainly related to the PI3K-Akt pathway, Kaposi’s sarcoma-associated herpesvirus infection, and mitogen-activated protein kinase signaling pathway, etc. The molecular docking results indicated that the core action targets and main active components in Guiyuan Ointment have stable binding activity. Conclusion: Guiyuan Ointment combines key active components such as quercetin, poriferasta-7,22E-dien-3beta-ol, orchinol, and isoflavanone with targets like IL6, TNF, STAT3, JUN, BCL2, HIF1A, AKT1, and CASP3. By regulating multiple signaling pathways such as PI3K/Akt, MAPK, and NF-κB, it modulates various biological processes in CFS patients, including immune response, cell apoptosis, and metabolic disorders. Through activating anti-apoptotic pathways, inhibiting the production of pro-inflammatory factors, and regulating energy metabolism, it verifies the multi-target and multi-pathway regulation of this formula, exerting synergistic effects on multiple targets and pathways, and significantly improving the symptoms of CFS.
