The ontology model of a certain domatin is an effective approach for the intercommunion between people form the different domains,the communication and interoperation among agents,and the share and reuse of the softwa...The ontology model of a certain domatin is an effective approach for the intercommunion between people form the different domains,the communication and interoperation among agents,and the share and reuse of the software.But the lack of formal analysis tools for domain modeling results in taking liberties with conceptualization.This paper discusses how to introduce the ontological notions from philosophy into Knowledge Engineering in order to supply a set of formal analysis tools for conceptualization analysis.This method can definitely record the hypothesis and analysis criterions through ontology huilding,and clarify the hiberarchy of concepts.展开更多
Domain-specific ontologies are greatly useful in knowledge acquisition,sharing and analysis. In this paper, botany-specific ontology for acquiring and analyzing botanicalknowledge is presented. The ontology is represe...Domain-specific ontologies are greatly useful in knowledge acquisition,sharing and analysis. In this paper, botany-specific ontology for acquiring and analyzing botanicalknowledge is presented. The ontology is represented in a set of well-defined categories, and eachconcept is viewed as an instance of certain category. The authors also introduce botany-specificaxioms, an integral part of the ontology, for checking and reasoning with the acquired knowledge.Consistency, completeness and redundancy of the axioms are discussed.展开更多
According to the information of 231 cultural and creative industry parks on the Internet literature, this research classified and studied the park elements from the text using the method of semantic Ontotogy analysis...According to the information of 231 cultural and creative industry parks on the Internet literature, this research classified and studied the park elements from the text using the method of semantic Ontotogy analysis. The paper analyzes the cultural and creative industry park in the performance of type, constitution elements of geosraphical attributes, character- istics, etc. Through analysis, we found that ＂location＂, ＂form＂ and ＂rhetoric＂ are frequently mentioned in the park names. As the parks prefer to combine cultural relics with their own characters for hishlighting influence and specialties, the park locations also have certain restrictions （e.g., ＂historic sites＂, ＂ancient cities＂）. Furthermore, cultural and creative industry parks cover a wide range of contents （e.g., ＂digital industry＂, ＂ecological landscape＂）. The boundaries of the park type and content are not very clear in present China. And, the parks lack of overall planning and often have an imperfect industrial chain and other issues. Therefore, on developing cultural and creative industry parks, the overall planning and perfect industrial chain need to be focused on.展开更多
BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely ...BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely related to its occurrence and development. Our previous results showed that the high expression of LC3 was positively correlated with PNI in the patients with pancreatic cancer. In this study, we further searched for differential genes involved in autophagy of pancreatic cancer by gene expression profiling and analyzed their biological functions in pancreatic cancer, which provides a theoretical basis for elucidating the pathophysiological mechanism of autophagy in pancreatic cancer and PNI.AIM To identify differentially expressed genes involved in pancreatic cancer autophagy and explore the pathogenesis at the molecular level.METHODS Two sets of gene expression profiles of pancreatic cancer/normal tissue(GSE16515 and GSE15471) were collected from the Gene Expression Omnibus.Significance analysis of microarrays algorithm was used to screen differentially expressed genes related to pancreatic cancer. Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis were used to analyze the functional enrichment of the differentially expressed genes. Protein interaction data containing only differentially expressed genes was downloaded from String database and screened. Module mining was carried out by Cytoscape software and ClusterOne plug-in. The interaction relationship between the modules was analyzed and the pivot nodes between the functional modules were determined according to the information of the functional modules and the data of reliable protein interaction network.RESULTS Based on the above two data sets of pancreatic tissue total gene expression, 6098 and 12928 differentially expressed genes were obtained by analysis of genes with higher phenotypic correlation. After extracting the intersection of the two differential gene sets, 4870 genes were determined. GO a展开更多
Bone marrow-derived mesenchymal stem cells differentiate into neurons under the induction of Schwann cells. However, key microRNAs and related pathways for differentiation remain unclear. This study screened and ident...Bone marrow-derived mesenchymal stem cells differentiate into neurons under the induction of Schwann cells. However, key microRNAs and related pathways for differentiation remain unclear. This study screened and identified differentially expressed microRNAs in bone marrow- derived mesenchymal stem cells induced by Schwann cell-conditioned medium, and explored targets and related pathways involved in their differentiation into neuronal-like cells. Primary bone marrow-derived mesenchymal stem cells were isolated from femoral and tibial bones, while primary Schwann cells were isolated from bilateral saphenous nerves. Bone marrow-derived mesenchymal stem cells were cultured in unconditioned (control group) and Schwann cell-conditioned medium (bone marrow-derived mesenchymal stem cell + Schwann cell group). Neuronal differentiation of bone marrow-derived mesenchymal stem cells induced by Schwann cell-conditioned medium was observed by time-lapse imaging. Upon induction, the morphology of bone marrow-derived mesencaymal stem cells changed into a neural shape with neurites. Results of quantitative reverse transcription-polymerase chain reaction revealed that nestin mRNA expression was upregulated from 1 to 3 days and downregulated from 3 to 7 days in the bone marrow-derived mesenchymal stem cell + Schwann cell group. Compared with the control group, microtubule-associated protein 2 mRNA expression gradually increased from 1 to 7 days in the bone marrow-derived mesenchymal stem cell + Schwann cell group. After 7 days of induction, microRNA analysis iden:ified 83 significantly differentially expressed microRNAs between the two groups. Gene Ontology analysis indicated enrichment of microRNA target genes for neuronal projection development, regulation of axonogenesis, and positive regulation of cell proliferation. Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that Hippo, Wnt, transforming growth factor-beta, and Hedgehog signaling pathv/ays were potentially associated with neural differentiation of b展开更多
To determine the molecular mechanism of cerebral ischemia/reperfusion injury, we examined the micro RNA（mi RNA） expression profile in rat cortex after focal cerebral ischemia/reperfusion injury using mi RNA microarr...To determine the molecular mechanism of cerebral ischemia/reperfusion injury, we examined the micro RNA（mi RNA） expression profile in rat cortex after focal cerebral ischemia/reperfusion injury using mi RNA microarrays and bioinformatic tools to systematically analyze Gene Ontology（GO） function classifications, as well as the signaling pathways of genes targeted by these differentially expressed mi RNAs. Our results show significantly changed mi RNA expression profiles in the reperfusion period after focal cerebral ischemia, with a total of 15 mi RNAs up-regulated and 44 mi RNAs down-regulated. Target genes of these differentially expressed mi RNAs were mainly involved in metabolic and cellular processes, which were identified as hub nodes of a mi RNA-GO-network. The most correlated pathways included D-glutamine and D-glutamate metabolism, the renin-angiotensin system, peroxisomes, the PPAR signaling pathway, SNARE interactions in vesicular transport, and the calcium signaling pathway. Our study suggests that mi RNAs play an important role in the pathological process of cerebral ischemia/reperfusion injury. Understanding mi RNA expression and function may shed light on the molecular mechanism of cerebral ischemia/reperfusion injury.展开更多
文摘The ontology model of a certain domatin is an effective approach for the intercommunion between people form the different domains,the communication and interoperation among agents,and the share and reuse of the software.But the lack of formal analysis tools for domain modeling results in taking liberties with conceptualization.This paper discusses how to introduce the ontological notions from philosophy into Knowledge Engineering in order to supply a set of formal analysis tools for conceptualization analysis.This method can definitely record the hypothesis and analysis criterions through ontology huilding,and clarify the hiberarchy of concepts.
文摘Domain-specific ontologies are greatly useful in knowledge acquisition,sharing and analysis. In this paper, botany-specific ontology for acquiring and analyzing botanicalknowledge is presented. The ontology is represented in a set of well-defined categories, and eachconcept is viewed as an instance of certain category. The authors also introduce botany-specificaxioms, an integral part of the ontology, for checking and reasoning with the acquired knowledge.Consistency, completeness and redundancy of the axioms are discussed.
文摘According to the information of 231 cultural and creative industry parks on the Internet literature, this research classified and studied the park elements from the text using the method of semantic Ontotogy analysis. The paper analyzes the cultural and creative industry park in the performance of type, constitution elements of geosraphical attributes, character- istics, etc. Through analysis, we found that ＂location＂, ＂form＂ and ＂rhetoric＂ are frequently mentioned in the park names. As the parks prefer to combine cultural relics with their own characters for hishlighting influence and specialties, the park locations also have certain restrictions （e.g., ＂historic sites＂, ＂ancient cities＂）. Furthermore, cultural and creative industry parks cover a wide range of contents （e.g., ＂digital industry＂, ＂ecological landscape＂）. The boundaries of the park type and content are not very clear in present China. And, the parks lack of overall planning and often have an imperfect industrial chain and other issues. Therefore, on developing cultural and creative industry parks, the overall planning and perfect industrial chain need to be focused on.
基金Supported by the National Natural Science Foundation of China,No.U1504815 and No.U1504808
文摘BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1 A/1 B-light chain 3(LC3) and perineural invasion(PNI) are closely related to its occurrence and development. Our previous results showed that the high expression of LC3 was positively correlated with PNI in the patients with pancreatic cancer. In this study, we further searched for differential genes involved in autophagy of pancreatic cancer by gene expression profiling and analyzed their biological functions in pancreatic cancer, which provides a theoretical basis for elucidating the pathophysiological mechanism of autophagy in pancreatic cancer and PNI.AIM To identify differentially expressed genes involved in pancreatic cancer autophagy and explore the pathogenesis at the molecular level.METHODS Two sets of gene expression profiles of pancreatic cancer/normal tissue(GSE16515 and GSE15471) were collected from the Gene Expression Omnibus.Significance analysis of microarrays algorithm was used to screen differentially expressed genes related to pancreatic cancer. Gene Ontology(GO) analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis were used to analyze the functional enrichment of the differentially expressed genes. Protein interaction data containing only differentially expressed genes was downloaded from String database and screened. Module mining was carried out by Cytoscape software and ClusterOne plug-in. The interaction relationship between the modules was analyzed and the pivot nodes between the functional modules were determined according to the information of the functional modules and the data of reliable protein interaction network.RESULTS Based on the above two data sets of pancreatic tissue total gene expression, 6098 and 12928 differentially expressed genes were obtained by analysis of genes with higher phenotypic correlation. After extracting the intersection of the two differential gene sets, 4870 genes were determined. GO a
基金supported by the National Natural Science Foundation of China,No.81330042,81620108018(both to SQF),and 81702147(to ZJW)
文摘Bone marrow-derived mesenchymal stem cells differentiate into neurons under the induction of Schwann cells. However, key microRNAs and related pathways for differentiation remain unclear. This study screened and identified differentially expressed microRNAs in bone marrow- derived mesenchymal stem cells induced by Schwann cell-conditioned medium, and explored targets and related pathways involved in their differentiation into neuronal-like cells. Primary bone marrow-derived mesenchymal stem cells were isolated from femoral and tibial bones, while primary Schwann cells were isolated from bilateral saphenous nerves. Bone marrow-derived mesenchymal stem cells were cultured in unconditioned (control group) and Schwann cell-conditioned medium (bone marrow-derived mesenchymal stem cell + Schwann cell group). Neuronal differentiation of bone marrow-derived mesenchymal stem cells induced by Schwann cell-conditioned medium was observed by time-lapse imaging. Upon induction, the morphology of bone marrow-derived mesencaymal stem cells changed into a neural shape with neurites. Results of quantitative reverse transcription-polymerase chain reaction revealed that nestin mRNA expression was upregulated from 1 to 3 days and downregulated from 3 to 7 days in the bone marrow-derived mesenchymal stem cell + Schwann cell group. Compared with the control group, microtubule-associated protein 2 mRNA expression gradually increased from 1 to 7 days in the bone marrow-derived mesenchymal stem cell + Schwann cell group. After 7 days of induction, microRNA analysis iden:ified 83 significantly differentially expressed microRNAs between the two groups. Gene Ontology analysis indicated enrichment of microRNA target genes for neuronal projection development, regulation of axonogenesis, and positive regulation of cell proliferation. Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that Hippo, Wnt, transforming growth factor-beta, and Hedgehog signaling pathv/ays were potentially associated with neural differentiation of b
基金supported by grants from the National Natural Science Foundation of ChinaNo.81271358+1 种基金Yunnan Science Foundation of ChinaNo.2013FZ199
文摘To determine the molecular mechanism of cerebral ischemia/reperfusion injury, we examined the micro RNA（mi RNA） expression profile in rat cortex after focal cerebral ischemia/reperfusion injury using mi RNA microarrays and bioinformatic tools to systematically analyze Gene Ontology（GO） function classifications, as well as the signaling pathways of genes targeted by these differentially expressed mi RNAs. Our results show significantly changed mi RNA expression profiles in the reperfusion period after focal cerebral ischemia, with a total of 15 mi RNAs up-regulated and 44 mi RNAs down-regulated. Target genes of these differentially expressed mi RNAs were mainly involved in metabolic and cellular processes, which were identified as hub nodes of a mi RNA-GO-network. The most correlated pathways included D-glutamine and D-glutamate metabolism, the renin-angiotensin system, peroxisomes, the PPAR signaling pathway, SNARE interactions in vesicular transport, and the calcium signaling pathway. Our study suggests that mi RNAs play an important role in the pathological process of cerebral ischemia/reperfusion injury. Understanding mi RNA expression and function may shed light on the molecular mechanism of cerebral ischemia/reperfusion injury.
