Objective To predict the main active ingredients,potential targets and molecular mechanisms of Yuan Zhi powder in treatment of dementia by using network pharmacology.Methods A database of chemical constituents of Yuan...Objective To predict the main active ingredients,potential targets and molecular mechanisms of Yuan Zhi powder in treatment of dementia by using network pharmacology.Methods A database of chemical constituents of Yuan Zhi powder was constructed by using databases and literatures.Potential targets were predicted by reverse molecular docking,and then a component-target network was constructed.The target network of Alzheimer's disease(AD)was mapped and analyzed to obtain the“active ingredient-AD target”network.The key targets were screened through network analysis.Finally,the rationality of the prediction was analyzed by comparing with the target reported in the literatures.Results There were180chemical constituents acting on the AD target,and the targets included three key targets(cyclooxygenase-2,muscarinic acetylcholine receptor M1,and muscarinic acetylcholine receptor M2)and an important target(acetylcholine esterase).Alzheimer's disease may be treated by regulating the activity of acetylcholine receptors and the binding toβ-amyloid protein,and its biological process may be concentrated in the acetylcholine receptor signal pathway,negative regulation of synaptic transmission and so on.Conclusion The fact that Yuan Zhi powder can treat AD is consistent with the characteristics of multi-components-multitargets-multiple pathways of traditional Chinese medicine.The important targets obtained from network analysis have a large proportion in literature research,so network analysis have some rationality.展开更多
From the comparison of correlation tensor in the theory of quantum network, the Alexander relation matrix in the theory of knot crystals and the identical inversion relations under the action of Pauli matrices, we sho...From the comparison of correlation tensor in the theory of quantum network, the Alexander relation matrix in the theory of knot crystals and the identical inversion relations under the action of Pauli matrices, we show that there is a one to one correspondence between four Bell bases and four oriented links of the linkage in knot theory.展开更多
In game theoretic context, it is assumed that the decision maker has the extraordinary skills of reasoning and calculation. This assumption is called "perfect rationality". A player with perfect rationality can solv...In game theoretic context, it is assumed that the decision maker has the extraordinary skills of reasoning and calculation. This assumption is called "perfect rationality". A player with perfect rationality can solve complex problems without making mistakes. However, recently, many studies have restricted this rationality or the structure of game. These restrictions are called "bounded rationality." The authors also focus on bounded rationality, but with learning dynamics and complex networks. A complex network covers a wide area. Currently, a wide range of studies have not only investigated network formation and the characteristics of a formed network, but also analyzed situations where a network is already provided. In addition, in an analysis using game theory, a prisoners' dilemma type game was used to investigate how a change in the network structure would affect the players' relationships Therefore, our model employs decision makers with learning dynamics and describes the interaction of decision makers as a network. The purpose of this study is to examine the behavior of the decision maker with learning dynamics and the formation of networks by the interaction of decision makers through an agent-based simulation.展开更多
The melting points of organic compounds were estimated using a combined method that includes a backpropagation neural network and quantitative structure property relationship (QSPR) parameters in quantum chemistry. ...The melting points of organic compounds were estimated using a combined method that includes a backpropagation neural network and quantitative structure property relationship (QSPR) parameters in quantum chemistry. Eleven descriptors that reflect the intermolecular forces and molecular symmetry were used as input variables. QSPR parameters were calculated using molecular modeling and PM3 semi-empirical molecular orbital theories. A total of 260 compounds were used to train the network, which was developed using MatLab. Then, the melting points of 73 other compounds were predicted and results were compared to experimental data from the literature. The study shows that the chosen artificial neural network and the quantitative structure property relationships method present an excellent alternative for the estimation of the melting point of an organic compound, with average absolute deviation of 5%.展开更多
A new back-analysis method of ground stress is proposed with comprehensive consideration of influence of topography, geology and nonlinear physical mechanical properties of rock on ground stress. This method based on ...A new back-analysis method of ground stress is proposed with comprehensive consideration of influence of topography, geology and nonlinear physical mechanical properties of rock on ground stress. This method based on non-uniform rational B-spline (NURBS) technology provides the means to build a refined three-dimensional finite element model with more accurate meshing under complex terrain and geological conditions. Meanwhile, this method is a back-analysis of ground stress with combination of multivariable linear regression model and neural network (ANN) model. Firstly, the regression model is used to fit approximately boundary loads. Regarding the regressed loads as mean value, some sets of boundary loads with the same interval are constructed according to the principle of orthogonal design, to calculate the corresponding ground stress at the observation positions using finite element method. The results (boundary loads and the corresponding ground stress) are added to the samples for ANN training. And on this basis, an ANN model is established to implement higher precise back-analysis of initial ground stress. A practical application case shows that the relative error between the inversed ground stress and observed value is mostly less than 10 %, which can meet the need of engineering design and construction requirements.展开更多
Based on the non-equilibrium thermodynamics,an internal-variable theory in thermo-viscoelasticity at finite deformation was proposed by Huang in 1999.In this theory,a modified stretch of the molecular chain was introd...Based on the non-equilibrium thermodynamics,an internal-variable theory in thermo-viscoelasticity at finite deformation was proposed by Huang in 1999.In this theory,a modified stretch of the molecular chain was introduced,and hence the molecular network model in rubber elasticity was extended to take into account the viscous and thermal effects of the material.The viscous dissipation of the material can then be described by means of these internal variables,which appear in the expression of the modified stretch.In order to give a clearer explanation on the physical implication of the internal variables,a connection between the internal-variable theory and theoretical formulation based on the multiplicative decomposition of the deformation gradient in existing literature is presented in this paper,which allows the above internal-variable theory to be more systematic.展开更多
Infinitesimal prolongation theorem is extended from sequences to nets based on κ-saturated nonstandard model. As its an application, a main property about topology of uniform convergence is proved. The proof is much ...Infinitesimal prolongation theorem is extended from sequences to nets based on κ-saturated nonstandard model. As its an application, a main property about topology of uniform convergence is proved. The proof is much simpler than it was, meanwhile the nonstandard characteristics of convergence with respect to u.c. topology is given.展开更多
Signal transduction pathways play important roles in various biological processes such as cell cycle, apoptosis, proliferation, differentiation and responses to the external stimuli. Efficient computational methods ar...Signal transduction pathways play important roles in various biological processes such as cell cycle, apoptosis, proliferation, differentiation and responses to the external stimuli. Efficient computational methods are of great demands to map signaling pathways systematically based on the interactome and microarray data in the post-genome era. This paper proposes a novel approach to infer the pathways based on the network flow well studied in the operation research. The authors define a potentiality variable for each protein to denote the extent to which it contributes to the objective pathway. And the capacity on each edge is not a constant but a function of the potentiality variables of the corresponding two proteins. The total potentiality of all proteins is given an upper bound. The approach is formulated to a linear programming model and solved by the simplex method. Experiments on the yeast sporulation data suggest this novel approach recreats successfully the backbone of the MAPK signaling pathway with a low upper bound of the total potentiality. By increasing the upper bound, the approach successfully predicts all the members of the Mitogen-activated protein kinases (MAPK) pathway responding to the pheromone. This simple but effective approach can also be used to infer the genetic information processing pathways underlying the expression quantitative trait loci (eQTL) associations, illustrated by the second example.展开更多
This paper investigates the finite-time generalized outer synchronization between two complex dynamical networks with different dynamical behaviors. The two networks can be undirected or directed, and they may also co...This paper investigates the finite-time generalized outer synchronization between two complex dynamical networks with different dynamical behaviors. The two networks can be undirected or directed, and they may also contain isolated nodes and clusters. By using suitable controllers, sufficient conditions for finite-time generalized outer synchronization are derived based on the finite-time stability theory. Finally, numerical examples are examined to illustrate the effectiveness of the analytical results. The effect of control parameters on the synchronization time is also numerically demonstrated.展开更多
With the rapid growth of the Web, the volume of information on the Web is increasing exponentially. However, information on the current Web is only understandable to humans, and this makes precise information retrieva...With the rapid growth of the Web, the volume of information on the Web is increasing exponentially. However, information on the current Web is only understandable to humans, and this makes precise information retrieval difficult. To solve this problem, the Semantic Web was proposed. We must use ontology languages that can assign data the semantics for realizing the Semantic Web. One of the representative ontology languages is the Web ontology language OWL, adopted as a recommen-dation by the World-Wide Web Consortium (W3C). OWL includes hierarchical structural information between classes or prop-erties. Therefore, an efficient OWL storage model that considers a hierarchical structure for effective information retrieval on the Semantic Web is required. In this paper we suggest an XPath-based OWL storage (XPOS) model, which includes hierarchical information between classes or properties in XPath form, and enables intuitive and effective information retrieval. Also, we show the comparative evaluation results for the performance of the XPOS model, Sesame, and the XML file system-based storage (XFSS) model, in terms of query processing and ontology updating.展开更多
基金funding support from the Major new drug creation project (2017ZX09101002-002-008)National Natural Science Foundation of China (81403171)Autonomous Program of China Academy of Chinese Medical Sciences (QZPT001 and 2014065)
文摘Objective To predict the main active ingredients,potential targets and molecular mechanisms of Yuan Zhi powder in treatment of dementia by using network pharmacology.Methods A database of chemical constituents of Yuan Zhi powder was constructed by using databases and literatures.Potential targets were predicted by reverse molecular docking,and then a component-target network was constructed.The target network of Alzheimer's disease(AD)was mapped and analyzed to obtain the“active ingredient-AD target”network.The key targets were screened through network analysis.Finally,the rationality of the prediction was analyzed by comparing with the target reported in the literatures.Results There were180chemical constituents acting on the AD target,and the targets included three key targets(cyclooxygenase-2,muscarinic acetylcholine receptor M1,and muscarinic acetylcholine receptor M2)and an important target(acetylcholine esterase).Alzheimer's disease may be treated by regulating the activity of acetylcholine receptors and the binding toβ-amyloid protein,and its biological process may be concentrated in the acetylcholine receptor signal pathway,negative regulation of synaptic transmission and so on.Conclusion The fact that Yuan Zhi powder can treat AD is consistent with the characteristics of multi-components-multitargets-multiple pathways of traditional Chinese medicine.The important targets obtained from network analysis have a large proportion in literature research,so network analysis have some rationality.
文摘From the comparison of correlation tensor in the theory of quantum network, the Alexander relation matrix in the theory of knot crystals and the identical inversion relations under the action of Pauli matrices, we show that there is a one to one correspondence between four Bell bases and four oriented links of the linkage in knot theory.
文摘In game theoretic context, it is assumed that the decision maker has the extraordinary skills of reasoning and calculation. This assumption is called "perfect rationality". A player with perfect rationality can solve complex problems without making mistakes. However, recently, many studies have restricted this rationality or the structure of game. These restrictions are called "bounded rationality." The authors also focus on bounded rationality, but with learning dynamics and complex networks. A complex network covers a wide area. Currently, a wide range of studies have not only investigated network formation and the characteristics of a formed network, but also analyzed situations where a network is already provided. In addition, in an analysis using game theory, a prisoners' dilemma type game was used to investigate how a change in the network structure would affect the players' relationships Therefore, our model employs decision makers with learning dynamics and describes the interaction of decision makers as a network. The purpose of this study is to examine the behavior of the decision maker with learning dynamics and the formation of networks by the interaction of decision makers through an agent-based simulation.
文摘The melting points of organic compounds were estimated using a combined method that includes a backpropagation neural network and quantitative structure property relationship (QSPR) parameters in quantum chemistry. Eleven descriptors that reflect the intermolecular forces and molecular symmetry were used as input variables. QSPR parameters were calculated using molecular modeling and PM3 semi-empirical molecular orbital theories. A total of 260 compounds were used to train the network, which was developed using MatLab. Then, the melting points of 73 other compounds were predicted and results were compared to experimental data from the literature. The study shows that the chosen artificial neural network and the quantitative structure property relationships method present an excellent alternative for the estimation of the melting point of an organic compound, with average absolute deviation of 5%.
基金Innovative Research Groups of the National Natural Science Foundation of China (No.51021004)National Science Foundation of China (No. 51079096)Program for New Century Excellent Talents in University (No. NCET-08-0391)
文摘A new back-analysis method of ground stress is proposed with comprehensive consideration of influence of topography, geology and nonlinear physical mechanical properties of rock on ground stress. This method based on non-uniform rational B-spline (NURBS) technology provides the means to build a refined three-dimensional finite element model with more accurate meshing under complex terrain and geological conditions. Meanwhile, this method is a back-analysis of ground stress with combination of multivariable linear regression model and neural network (ANN) model. Firstly, the regression model is used to fit approximately boundary loads. Regarding the regressed loads as mean value, some sets of boundary loads with the same interval are constructed according to the principle of orthogonal design, to calculate the corresponding ground stress at the observation positions using finite element method. The results (boundary loads and the corresponding ground stress) are added to the samples for ANN training. And on this basis, an ANN model is established to implement higher precise back-analysis of initial ground stress. A practical application case shows that the relative error between the inversed ground stress and observed value is mostly less than 10 %, which can meet the need of engineering design and construction requirements.
基金supported by the National Natural Science Foundation of China (Grant Nos. 11132003,11172033,11272007 and 10932001)the National Basic Research Program of China (Grant No. 2010CB-7321004)
文摘Based on the non-equilibrium thermodynamics,an internal-variable theory in thermo-viscoelasticity at finite deformation was proposed by Huang in 1999.In this theory,a modified stretch of the molecular chain was introduced,and hence the molecular network model in rubber elasticity was extended to take into account the viscous and thermal effects of the material.The viscous dissipation of the material can then be described by means of these internal variables,which appear in the expression of the modified stretch.In order to give a clearer explanation on the physical implication of the internal variables,a connection between the internal-variable theory and theoretical formulation based on the multiplicative decomposition of the deformation gradient in existing literature is presented in this paper,which allows the above internal-variable theory to be more systematic.
基金Supported by the Speaial Science Foundation of the Edneational Committee of Shaanxi Province(oojk207).
文摘Infinitesimal prolongation theorem is extended from sequences to nets based on κ-saturated nonstandard model. As its an application, a main property about topology of uniform convergence is proved. The proof is much simpler than it was, meanwhile the nonstandard characteristics of convergence with respect to u.c. topology is given.
基金This research is supported by the National Natural Science Foundation of China under Grant Nos. 10631070, 60873205, the grant kjcx-yw-s7 from Chinese Academy of Sciences, and 2006CB503905 from Ministry of Science and Technology of China.
文摘Signal transduction pathways play important roles in various biological processes such as cell cycle, apoptosis, proliferation, differentiation and responses to the external stimuli. Efficient computational methods are of great demands to map signaling pathways systematically based on the interactome and microarray data in the post-genome era. This paper proposes a novel approach to infer the pathways based on the network flow well studied in the operation research. The authors define a potentiality variable for each protein to denote the extent to which it contributes to the objective pathway. And the capacity on each edge is not a constant but a function of the potentiality variables of the corresponding two proteins. The total potentiality of all proteins is given an upper bound. The approach is formulated to a linear programming model and solved by the simplex method. Experiments on the yeast sporulation data suggest this novel approach recreats successfully the backbone of the MAPK signaling pathway with a low upper bound of the total potentiality. By increasing the upper bound, the approach successfully predicts all the members of the Mitogen-activated protein kinases (MAPK) pathway responding to the pheromone. This simple but effective approach can also be used to infer the genetic information processing pathways underlying the expression quantitative trait loci (eQTL) associations, illustrated by the second example.
基金Supported by the National Natural Science Foundation of China under Grant Nos.61203304,61203055 and 10901145the Fundamental Research Funds for the Central Universities under Grant Nos.2011QNA26,2010LKSX04,and 2010LKSX01
文摘This paper investigates the finite-time generalized outer synchronization between two complex dynamical networks with different dynamical behaviors. The two networks can be undirected or directed, and they may also contain isolated nodes and clusters. By using suitable controllers, sufficient conditions for finite-time generalized outer synchronization are derived based on the finite-time stability theory. Finally, numerical examples are examined to illustrate the effectiveness of the analytical results. The effect of control parameters on the synchronization time is also numerically demonstrated.
文摘With the rapid growth of the Web, the volume of information on the Web is increasing exponentially. However, information on the current Web is only understandable to humans, and this makes precise information retrieval difficult. To solve this problem, the Semantic Web was proposed. We must use ontology languages that can assign data the semantics for realizing the Semantic Web. One of the representative ontology languages is the Web ontology language OWL, adopted as a recommen-dation by the World-Wide Web Consortium (W3C). OWL includes hierarchical structural information between classes or prop-erties. Therefore, an efficient OWL storage model that considers a hierarchical structure for effective information retrieval on the Semantic Web is required. In this paper we suggest an XPath-based OWL storage (XPOS) model, which includes hierarchical information between classes or properties in XPath form, and enables intuitive and effective information retrieval. Also, we show the comparative evaluation results for the performance of the XPOS model, Sesame, and the XML file system-based storage (XFSS) model, in terms of query processing and ontology updating.