CircRNAs,widely found throughout the human bodies,play a crucial role in regulating various biological processes and are closely linked to complex human diseases.Investigating potential associations between circRNAs a...CircRNAs,widely found throughout the human bodies,play a crucial role in regulating various biological processes and are closely linked to complex human diseases.Investigating potential associations between circRNAs and diseases can enhance our understanding of diseases and provide new strategies and tools for early diagnosis,treatment,and disease prevention.However,existing models have limitations in accurately capturing similarities,handling the sparse and noise attributes of association networks,and fully leveraging bioinformatical aspects from multiple viewpoints.To address these issues,this study introduces a new non-negative matrix factorization-based framework called NMFMSN.First,we incorporate circRNA sequence data and disease semantic information to compute circRNA and disease similarity,respectively.Given the sparse known associations between circRNAs and diseases,we reconstruct the network to complete more associations by imputing missing links based on neighboring circRNA and disease interactions.Finally,we integrate these two similarity networks into a non-negative matrix factorization framework to identify potential circRNA-disease associations.Upon conducting 5-fold cross-validation and leave-one-out cross-validation,the AUC values for NMFMSN reach 0.9712 and 0.9768,respectively,outperforming the currently most advanced models.Case studies on lung cancer and hepatocellular carcinoma show that NMFMSN is a good way to predict new associations between circRNAs and diseases.展开更多
An approximate approach of querying between heterogeneous ontology-basedinformation systems based on an association matrix is proposed. First, the association matrix isdefined to describe relations between concepts in...An approximate approach of querying between heterogeneous ontology-basedinformation systems based on an association matrix is proposed. First, the association matrix isdefined to describe relations between concepts in two ontologies. Then, a methodof rewriting queriesbased on the association matrix is presented to solve the ontology heterogeneity problem. Itrewrites the queries in one ontology to approximate queries in another ontology based on thesubsumption relations between concepts. The method also uses vectors to represent queries, and thencomputes the vectors with the association matrix; the disjoint relations between concepts can beconsidered by the results. It can get better approximations than the methods currently in use, whichdonot consider disjoint relations. The method can be processed by machines automatically. It issimple to implement and expected to run quite fast.展开更多
This paper introduces the definition and calculation of the association matrix between ontologies. It uses the association matrix to describe the relations between concepts in different ontologies and uses concept vec...This paper introduces the definition and calculation of the association matrix between ontologies. It uses the association matrix to describe the relations between concepts in different ontologies and uses concept vectors to represent queries; then computes the vectors with the association matrix in order to rewrite queries. This paper proposes a simple method of querying through heterogeneous Ontology using association matrix. This method is based on the correctness of approximate information filtering theory; and it is simple to be implemented and expected to run quite fast. Key words semantic Web - information retrieval - ontology - query - association matrix CLC number TP 391 Foundation item: Supported by the National Natural Science Foundation of China (60373066, 60303024), National Grand Fundamental Research 973 Program of China (2002CB312000) and National Research Foundation for the Doctoral Program of Higher Education of China (20020286004)Biography: KANG Da-zhou (1980-), male, Master candidate, research direction: Semantic Web, knowledge representation on the Web.展开更多
Aim： To compare the results of bladder tumor associated antigen （BTA TRAK）, nuclear matrix protein 22 （NMP 22） and voided urine cytology （VUC） in detecting bladder cancer. Methods： A total of 135 elderly male ...Aim： To compare the results of bladder tumor associated antigen （BTA TRAK）, nuclear matrix protein 22 （NMP 22） and voided urine cytology （VUC） in detecting bladder cancer. Methods： A total of 135 elderly male and 50 healthy volunteers enrolled in this study were classified into three groups： （i） 93 patients with bladder cancer; （ii） 42 patients with urinary benign conditions; and （iii） 50 healthy volunteers. BTA TRAK and NMP 22 kits were used to detect bladder cancer. Voided urine cytology was used to compare the sensitivity and specificity of the screening tests. Results： The sensitivity and specificity of cytology, BTA TRAK and NMP 22 were 24% and 97%, 51% and 73%, 78% and 73%, respectively. The level of NMP 22 increased with tumor grading. The BTA TRAK kit has the lowest sensitivity among the screening tests. The NMP 22 with the best sensitivity can be an adjunct to cytology for evaluating bladder cancer. Conclusion： The NMP 22 test has a better correlation with the grading of the bladder cancer than BTA TRAK. As cytology units are typically not available in hospitals or in outpatient clinics, NMP 22 might be a promising tool for screening bladder cancer.展开更多
Aiming at three-passive-sensor location system, a generalized 3-dimension （3-D） assignment model is constructed based on property information, and a multi-target programming model is proposed based on direction-find...Aiming at three-passive-sensor location system, a generalized 3-dimension （3-D） assignment model is constructed based on property information, and a multi-target programming model is proposed based on direction-finding and property fusion information. The multi-target programming model is transformed into a single target programming problem to resolve, and its data association result is compared with the results which are solved by using one kind of information only. Simulation experiments show the effectiveness of the multi-target programming algorithm with higher data association accuracy and less calculation.展开更多
Recapitulating the tumor microenvironment is a major challenge in the development of in vitro tumor model for the study of cancer biology and therapeutic treatments. 3D multicellular tumor spheroids (MCTS) have been u...Recapitulating the tumor microenvironment is a major challenge in the development of in vitro tumor model for the study of cancer biology and therapeutic treatments. 3D multicellular tumor spheroids (MCTS) have been used as reliable models of mimicking in vivo solid tumors. Macrophages and extracellular matrix (ECM), regarded as two key factors of the tumor microenvironment, play significant roles in tumor progression and drug resistance. In order to investigate their effects on tumor cell migration, a microfluidic chip-based 3D breast cancer model was developed by co-culturing monodisperse MCTS with monocytes in 3 D collagen matrix. A reversible bonding technique was employed for the fabrication of the microfluidic chip, which made it easier for MCTS formation and tailoring the MCTS co-culture conditions. When co-culturing monocytes with low invasive T47D spheroids or high invasive MD-MBA-231 spheroids, we found that T47 D cells with the stimulation of macrophage colony-stimulating factor (M-CSF) and MD-MBA-231 cells could polarize monocytes into tumor-associated macrophages (TAMs). The increased stiffness via increasing collagen concentration decreased tumor cell migration, whereas the presence of TAMs enhanced the migration ability of cells.Moreover, M-CSF-activated TAMs promoted the migration of T47 D tumor cells via the regulation of TGFβ1. Overall, this 3D co-culture microfluidic model may be useful for studying tumor progress and may offer a reliable and low-cost method for evaluation of drug efficiency.展开更多
We determine the left eigenvector of a stochastic matrix M associated to the eigenvalue 1 in the commutative and the noncommutative cases. In the commutative case, we see that the eigenvector associated to the eigenva...We determine the left eigenvector of a stochastic matrix M associated to the eigenvalue 1 in the commutative and the noncommutative cases. In the commutative case, we see that the eigenvector associated to the eigenvalue 0 is (N1,Nn) , where Ni is the i–th iprincipal minor of N=M–In , where In is the identity matrix of dimension n. In the noncommutative case, this eigenvector is (P1-1,Pn-1) , where Pi is the sum in Q《αij》 of the corresponding labels of nonempty paths starting from i and not passing through i in the complete directed graph associated to M .展开更多
Based on Input-Output Table in 2010 issued by National Bureau of Statistics of China, with the help of input-output model and with the calculation of indexes of industrial relevance degree in Chinese information techn...Based on Input-Output Table in 2010 issued by National Bureau of Statistics of China, with the help of input-output model and with the calculation of indexes of industrial relevance degree in Chinese information technology industry, the paper reveals the industrial relevance in Chinese information technology industry. The paper also selects the relevant industries which are highly associated with the development of Chinese information technology industry based on industrial relevance degree to analyze the influences of these industries on the financial situation risk fluctuation in information technology industry and to design the matrix of financial situation risk in information technology industry. Then, the paper offers countermeasures and suggestions for the development of our information technology industry.展开更多
Indirect association is a high level relationship between items and frequent item sets in data. There are many potential applications for indirect associations, such as database marketing, intelligent data analysis, w...Indirect association is a high level relationship between items and frequent item sets in data. There are many potential applications for indirect associations, such as database marketing, intelligent data analysis, web -log analysis, recommended system, etc. Existing indirect association mining algorithms are mostly based on the notion of post - processing of discovery of frequent item sets. In the mining process, all frequent item sets need to be generated first, and then they are fihered and joined to form indirect associations. We have presented an indirect association mining algorithm （NIA） based on anti -monotonicity of indirect associations whereas k candidate indirect associations can be generated directly from k - 1 candidate indirect associations, without all frequent item sets generated. We also use the frequent itempair support matrix to reduce the time and memory space needed by the algorithm. In this paper, a novel algorithm （NIA2） is introduced based on the generation of indirect association patterns between itempairs through one item mediator sets from frequent itempair support matrix. A notion of mediator set support threshold is also presented. NIA2 mines indirect association patterns directly from the dataset, without generating all frequent item sets. The frequent itempair support matrix and the notion of using tm as the support threshold for mediator sets can significantly reduce the cost of joint operations and the search process compared with existing algorithms. Results of experiments on a real - word web log dataset have proved NIA2 one order of magnitude faster than existing algorithms.展开更多
On the basis of the association theory of nuclear structure, we have studied the （t, p） reaction. Study was carried out with the distorted plane waves of triton and of proton. It has been suggested that bineutron as...On the basis of the association theory of nuclear structure, we have studied the （t, p） reaction. Study was carried out with the distorted plane waves of triton and of proton. It has been suggested that bineutron association is acceptable if the time during which the association maintains its structure, is large compared with the time when neutrons are in a dissociated form, and there is no exchange of nucleons between fragments associations. The cross section is written as a product of two factors, one is the spectroscopic factor which reflects the nature of the nuclear structure concerned and the other describes the process in which the target nucleus captures two nucleons as a cluster into an orbit which is characterized by a form factor. In the argument, that the radial wave function of two neutrons which form association captured nuclei close to each other, this leads to the formation of bineutron association on the nuclei surface. In this approach, the proton is emitted at the same point, which is captured bineutron association.展开更多
Objectives The impairment of matrix metallopro- teinase-2(MMP-2)has been associated with the development of cardiac fibrosis.Although the Chinese herb Salvia miltior-rhiza has been widely used in patients with cardiov...Objectives The impairment of matrix metallopro- teinase-2(MMP-2)has been associated with the development of cardiac fibrosis.Although the Chinese herb Salvia miltior-rhiza has been widely used in patients with cardiovascular disorders,the mechanisms involved have not been elucidated. The purpose of the present study was to determine whether the administration of cryptotanshinone,an active ingredient of Salvia miltiorrhiza,could prevent the cardiac fibrosis induced by isoprenaline and to investigate the underlying mechanisms. Methods and Results Male C57BL/6 mice were submitted to receive daily injection of 0.9%saline,3 mg/kg isoprenaline, or isoprenaline plus 20 mg/kg cryptotanshinone by gastric gavage for 2 weeks.Herein,we demonstrate that cryptotanshinone can significantly ameliorate the isoprenaline-induced cardiac fibrosis,which was associated with marked up-regulation and activation of MMP-2 in ventricular myocardium. Additionally,we demonstrate that cryptotanshinone can dose-dependently upregulate and activate MMP-2 in cultured cardiac fibroblast.Moreover,incubation with cryptotanshinone also can prevent isoprenaline-induced downregulation and inactivation of MMP-2 in cultured cardiac fibroblast. Conclusions Taken together,our data suggest that cryptotanshinone may become a novel and potent antifibrotic agent. The present findings might further our understanding of the role of MMP-2 in cardiac fibrosis and antifibrotic mechanisms of cryptotanshinone.展开更多
基金the Gansu Province Industrial Support Plan(No.2023CYZC-25)Natural Science Foundation of Gansu Province(No.23JRRA770)the National Natural Science Foundation of China(No.62162040)。
文摘CircRNAs,widely found throughout the human bodies,play a crucial role in regulating various biological processes and are closely linked to complex human diseases.Investigating potential associations between circRNAs and diseases can enhance our understanding of diseases and provide new strategies and tools for early diagnosis,treatment,and disease prevention.However,existing models have limitations in accurately capturing similarities,handling the sparse and noise attributes of association networks,and fully leveraging bioinformatical aspects from multiple viewpoints.To address these issues,this study introduces a new non-negative matrix factorization-based framework called NMFMSN.First,we incorporate circRNA sequence data and disease semantic information to compute circRNA and disease similarity,respectively.Given the sparse known associations between circRNAs and diseases,we reconstruct the network to complete more associations by imputing missing links based on neighboring circRNA and disease interactions.Finally,we integrate these two similarity networks into a non-negative matrix factorization framework to identify potential circRNA-disease associations.Upon conducting 5-fold cross-validation and leave-one-out cross-validation,the AUC values for NMFMSN reach 0.9712 and 0.9768,respectively,outperforming the currently most advanced models.Case studies on lung cancer and hepatocellular carcinoma show that NMFMSN is a good way to predict new associations between circRNAs and diseases.
文摘An approximate approach of querying between heterogeneous ontology-basedinformation systems based on an association matrix is proposed. First, the association matrix isdefined to describe relations between concepts in two ontologies. Then, a methodof rewriting queriesbased on the association matrix is presented to solve the ontology heterogeneity problem. Itrewrites the queries in one ontology to approximate queries in another ontology based on thesubsumption relations between concepts. The method also uses vectors to represent queries, and thencomputes the vectors with the association matrix; the disjoint relations between concepts can beconsidered by the results. It can get better approximations than the methods currently in use, whichdonot consider disjoint relations. The method can be processed by machines automatically. It issimple to implement and expected to run quite fast.
文摘This paper introduces the definition and calculation of the association matrix between ontologies. It uses the association matrix to describe the relations between concepts in different ontologies and uses concept vectors to represent queries; then computes the vectors with the association matrix in order to rewrite queries. This paper proposes a simple method of querying through heterogeneous Ontology using association matrix. This method is based on the correctness of approximate information filtering theory; and it is simple to be implemented and expected to run quite fast. Key words semantic Web - information retrieval - ontology - query - association matrix CLC number TP 391 Foundation item: Supported by the National Natural Science Foundation of China (60373066, 60303024), National Grand Fundamental Research 973 Program of China (2002CB312000) and National Research Foundation for the Doctoral Program of Higher Education of China (20020286004)Biography: KANG Da-zhou (1980-), male, Master candidate, research direction: Semantic Web, knowledge representation on the Web.
文摘Aim： To compare the results of bladder tumor associated antigen （BTA TRAK）, nuclear matrix protein 22 （NMP 22） and voided urine cytology （VUC） in detecting bladder cancer. Methods： A total of 135 elderly male and 50 healthy volunteers enrolled in this study were classified into three groups： （i） 93 patients with bladder cancer; （ii） 42 patients with urinary benign conditions; and （iii） 50 healthy volunteers. BTA TRAK and NMP 22 kits were used to detect bladder cancer. Voided urine cytology was used to compare the sensitivity and specificity of the screening tests. Results： The sensitivity and specificity of cytology, BTA TRAK and NMP 22 were 24% and 97%, 51% and 73%, 78% and 73%, respectively. The level of NMP 22 increased with tumor grading. The BTA TRAK kit has the lowest sensitivity among the screening tests. The NMP 22 with the best sensitivity can be an adjunct to cytology for evaluating bladder cancer. Conclusion： The NMP 22 test has a better correlation with the grading of the bladder cancer than BTA TRAK. As cytology units are typically not available in hospitals or in outpatient clinics, NMP 22 might be a promising tool for screening bladder cancer.
基金This project was supported by the National Natural Science Foundation of China (60172033) the Excellent Ph.D.PaperAuthor Foundation of China (200036 ,200237) .
文摘Aiming at three-passive-sensor location system, a generalized 3-dimension （3-D） assignment model is constructed based on property information, and a multi-target programming model is proposed based on direction-finding and property fusion information. The multi-target programming model is transformed into a single target programming problem to resolve, and its data association result is compared with the results which are solved by using one kind of information only. Simulation experiments show the effectiveness of the multi-target programming algorithm with higher data association accuracy and less calculation.
基金supported by the National Natural Science Foundation of China (Nos. 21675096 and 21475073)Youth Scientific Research Funds from Graduate School at Shenzhen, Tsinghua University (No. QN20160002)
文摘Recapitulating the tumor microenvironment is a major challenge in the development of in vitro tumor model for the study of cancer biology and therapeutic treatments. 3D multicellular tumor spheroids (MCTS) have been used as reliable models of mimicking in vivo solid tumors. Macrophages and extracellular matrix (ECM), regarded as two key factors of the tumor microenvironment, play significant roles in tumor progression and drug resistance. In order to investigate their effects on tumor cell migration, a microfluidic chip-based 3D breast cancer model was developed by co-culturing monodisperse MCTS with monocytes in 3 D collagen matrix. A reversible bonding technique was employed for the fabrication of the microfluidic chip, which made it easier for MCTS formation and tailoring the MCTS co-culture conditions. When co-culturing monocytes with low invasive T47D spheroids or high invasive MD-MBA-231 spheroids, we found that T47 D cells with the stimulation of macrophage colony-stimulating factor (M-CSF) and MD-MBA-231 cells could polarize monocytes into tumor-associated macrophages (TAMs). The increased stiffness via increasing collagen concentration decreased tumor cell migration, whereas the presence of TAMs enhanced the migration ability of cells.Moreover, M-CSF-activated TAMs promoted the migration of T47 D tumor cells via the regulation of TGFβ1. Overall, this 3D co-culture microfluidic model may be useful for studying tumor progress and may offer a reliable and low-cost method for evaluation of drug efficiency.
文摘We determine the left eigenvector of a stochastic matrix M associated to the eigenvalue 1 in the commutative and the noncommutative cases. In the commutative case, we see that the eigenvector associated to the eigenvalue 0 is (N1,Nn) , where Ni is the i–th iprincipal minor of N=M–In , where In is the identity matrix of dimension n. In the noncommutative case, this eigenvector is (P1-1,Pn-1) , where Pi is the sum in Q《αij》 of the corresponding labels of nonempty paths starting from i and not passing through i in the complete directed graph associated to M .
基金Key project of National Social Scientific Fund--"Study on Financing Early-warning and Fixation of Listed Corporations in Information Technology Industry based on the Dynamic Monitoring of Industrial Risk"(Project approval Number:15AGL008)
文摘Based on Input-Output Table in 2010 issued by National Bureau of Statistics of China, with the help of input-output model and with the calculation of indexes of industrial relevance degree in Chinese information technology industry, the paper reveals the industrial relevance in Chinese information technology industry. The paper also selects the relevant industries which are highly associated with the development of Chinese information technology industry based on industrial relevance degree to analyze the influences of these industries on the financial situation risk fluctuation in information technology industry and to design the matrix of financial situation risk in information technology industry. Then, the paper offers countermeasures and suggestions for the development of our information technology industry.
文摘Indirect association is a high level relationship between items and frequent item sets in data. There are many potential applications for indirect associations, such as database marketing, intelligent data analysis, web -log analysis, recommended system, etc. Existing indirect association mining algorithms are mostly based on the notion of post - processing of discovery of frequent item sets. In the mining process, all frequent item sets need to be generated first, and then they are fihered and joined to form indirect associations. We have presented an indirect association mining algorithm （NIA） based on anti -monotonicity of indirect associations whereas k candidate indirect associations can be generated directly from k - 1 candidate indirect associations, without all frequent item sets generated. We also use the frequent itempair support matrix to reduce the time and memory space needed by the algorithm. In this paper, a novel algorithm （NIA2） is introduced based on the generation of indirect association patterns between itempairs through one item mediator sets from frequent itempair support matrix. A notion of mediator set support threshold is also presented. NIA2 mines indirect association patterns directly from the dataset, without generating all frequent item sets. The frequent itempair support matrix and the notion of using tm as the support threshold for mediator sets can significantly reduce the cost of joint operations and the search process compared with existing algorithms. Results of experiments on a real - word web log dataset have proved NIA2 one order of magnitude faster than existing algorithms.
文摘On the basis of the association theory of nuclear structure, we have studied the （t, p） reaction. Study was carried out with the distorted plane waves of triton and of proton. It has been suggested that bineutron association is acceptable if the time during which the association maintains its structure, is large compared with the time when neutrons are in a dissociated form, and there is no exchange of nucleons between fragments associations. The cross section is written as a product of two factors, one is the spectroscopic factor which reflects the nature of the nuclear structure concerned and the other describes the process in which the target nucleus captures two nucleons as a cluster into an orbit which is characterized by a form factor. In the argument, that the radial wave function of two neutrons which form association captured nuclei close to each other, this leads to the formation of bineutron association on the nuclei surface. In this approach, the proton is emitted at the same point, which is captured bineutron association.
文摘Objectives The impairment of matrix metallopro- teinase-2(MMP-2)has been associated with the development of cardiac fibrosis.Although the Chinese herb Salvia miltior-rhiza has been widely used in patients with cardiovascular disorders,the mechanisms involved have not been elucidated. The purpose of the present study was to determine whether the administration of cryptotanshinone,an active ingredient of Salvia miltiorrhiza,could prevent the cardiac fibrosis induced by isoprenaline and to investigate the underlying mechanisms. Methods and Results Male C57BL/6 mice were submitted to receive daily injection of 0.9%saline,3 mg/kg isoprenaline, or isoprenaline plus 20 mg/kg cryptotanshinone by gastric gavage for 2 weeks.Herein,we demonstrate that cryptotanshinone can significantly ameliorate the isoprenaline-induced cardiac fibrosis,which was associated with marked up-regulation and activation of MMP-2 in ventricular myocardium. Additionally,we demonstrate that cryptotanshinone can dose-dependently upregulate and activate MMP-2 in cultured cardiac fibroblast.Moreover,incubation with cryptotanshinone also can prevent isoprenaline-induced downregulation and inactivation of MMP-2 in cultured cardiac fibroblast. Conclusions Taken together,our data suggest that cryptotanshinone may become a novel and potent antifibrotic agent. The present findings might further our understanding of the role of MMP-2 in cardiac fibrosis and antifibrotic mechanisms of cryptotanshinone.
