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Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning 被引量:5
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作者 Xiaolu Li Ye Yang +3 位作者 Senming Xu Yuchang Gui Jianmin Chen Jianwen Xu 《Neural Regeneration Research》 SCIE CAS CSCD 2024年第12期2723-2734,共12页
Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is s... Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022). 展开更多
关键词 bioinformatics analysis BIOMARKER CIBERSORT GEO dataset LASSO miRNA-mRNA network RNA sequencing spinal cord injury SVM-RFE weighted gene co-expression network analysis
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Network analysis of the relationships between depressive symptoms and social participation activities among Chinese older adults and its implications for nursing
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作者 Yebo Yu Hewei Min +3 位作者 Wei Pan Ping Chen Xuxi Zhang Xinying Sun 《International Journal of Nursing Sciences》 CSCD 2024年第4期465-472,I0002,共9页
Objective:Network analysis was used to explore the complex inter-relationships between social participation activities and depressive symptoms among the Chinese older population,and the differences in network structur... Objective:Network analysis was used to explore the complex inter-relationships between social participation activities and depressive symptoms among the Chinese older population,and the differences in network structures among different genders,age groups,and urban-rural residency would be compared.Methods:Based on the 2018 wave of the Chinese Longitudinal Healthy Longevity Survey(CLHLS),12,043 people aged 65 to 105 were included.The 10-item Center for Epidemiologic Studies Depression(CESD)Scale was used to assess depressive symptoms and 10 types of social participation activities were collected,including housework,tai-chi,square dancing,visiting and interacting with friends,garden work,reading newspapers or books,raising domestic animals,playing cards or mahjong,watching TV or listening to radio,and organized social activities.R 4.2.1 software was used to estimate the network model and calculate strength and bridge strength.Results:21.60%(2,601/12,043)of the participants had depressive symptoms.The total social participation score was negatively associated with depressive symptoms after adjusting for sociodemographic factors.The network of social participation and depressive symptoms showed that“D9(Inability to get going)”and“S9(Watching TV and/or listening to the radio)”had the highest strength within depressive symptoms and social participation communities,respectively,and“S1(Housework)”,“S9(Watching TV and/or listening to the radio)”,and“D5(Hopelessness)”were the most prominent bridging nodes between the two communities.Most edges linking the two communities were negative.“S5(Graden work)-D5(Hopelessness)”and“S6(Reading newspapers/books)-D4(Everything was an effort)”were the top 2 strongest negative edges.Older females had significantly denser network structures than older males.Compared to older people aged 65e80,the age group 81e105 showed higher network global strength.Conclusions:This study provides novel insights into the complex relationships between social participation and depressive symptoms.Except for doing housework,other social participation activities were found to be protective for depression levels.Different nursing strategies should be taken to prevent and alleviate depressive symptoms for different genders and older people of different ages. 展开更多
关键词 Depressive symptoms network analysis Older adults Sex characteristics Social participation
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Citation and bibliographic coupling between authors in the field of social network analysis
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作者 Daria Maltseva Vladimir Batagelj 《Journal of Data and Information Science》 CSCD 2024年第4期110-154,共45页
Purpose:We analyzed the structure of a community of authors working in the field of social network analysis(SNA)based on citation indicators:direct citation and bibliographic coupling metrics.We observed patterns at t... Purpose:We analyzed the structure of a community of authors working in the field of social network analysis(SNA)based on citation indicators:direct citation and bibliographic coupling metrics.We observed patterns at the micro,meso,and macro levels of analysis.Design/methodology/approach:We used bibliometric network analysis,including the“temporal quantities”approach proposed to study temporal networks.Using a two-mode network linking publications with authors and a one-mode network of citations between the works,we constructed and analyzed the networks of citation and bibliographic coupling among authors.We used an iterated saturation data collection approach.Findings:At the macro-level,we observed the global structural features of citations between authors,showing that 80%of authors have not more than 15 citations from other works.At the meso-level,we extracted the groups of authors citing each other and similar to each other according to their citation patterns.We have seen a division of authors in SNA into groups of social scientists and physicists,as well as into other groups of authors from different disciplines.We found some examples of brokerage between different groups that maintained the common identity of the field.At the micro-level,we extracted authors with extremely high values of received citations,who can be considered as the most prominent authors in the field.We examined the temporal properties of the most popular authors.Research limitations:The main challenge in this approach is the resolution of the author’s name(synonyms and homonyms).We faced the author disambiguation,or“multiple personalities”(Harzing,2015)problem.To remain consistent and comparable with our previously published articles,we used the same SNA data collected up to 2018.The analysis and conclusions on the activity,productivity,and visibility of the authors are relative only to the field of SNA.Practical implications:The proposed approach can be utilized for similar objectives and identifying key structures and characteristics in other disciplines.This may potentially inspire the application of network approaches in other research areas,creating more authors collaborating in the field of SNA.Originality/value:We identified and applied an innovative approach and methods to study the structure of scientific communities,which allowed us to get the findings going beyond those obtained with other methods.We used a new approach to temporal network analysis,which is an important addition to the analysis as it provides detailed information on different measures for the authors and pairs of authors over time. 展开更多
关键词 Development of scientific fields Social network analysis Bibliographic network Temporal network CITATION Bibliographic coupling
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Weighted gene co-expression network analysis reveals similarities and differences of molecular features between dilated and ischemic cardiomyopathies 被引量:1
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作者 Felix K.Biwott Ni-Ni Rao +1 位作者 Chang-Long Dong Guang-Bin Wang 《Journal of Electronic Science and Technology》 EI CAS CSCD 2023年第2期14-29,共16页
Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different c... Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different classes of cardiomyopathies remain elusive.This paper aims to describe the similarities and differences in molecular features of dilated cardiomyopathy(DCM)and ischemic cardiomyopathy(ICM).We firstly detected the co-expressed modules using the weighted gene co-expression network analysis(WGCNA).Significant modules associated with DCM/ICM were identified by the Pearson correlation coefficient(PCC)between the modules and the phenotype of DCM/ICM.The differentially expressed genes in the modules were selected to perform functional enrichment.The potential transcription factors(TFs)prediction was conducted for transcription regulation of hub genes.Apoptosis and cardiac conduction were perturbed in DCM and ICM,respectively.TFs demonstrated that the biomarkers and the transcription regulations in DCM and ICM were different,which helps make more accurate discrimination between them at molecular levels.In conclusion,comprehensive analyses of the molecular features may advance our understanding of DCM and ICM causes and progression.Thus,this understanding may promote the development of innovative diagnoses and treatments. 展开更多
关键词 Dilated cardiomyopathy(DCM) Hub genes Ischemic cardiomyopathy(ICM) Transcription factors(TFs) Weighted gene co-expression network analysis(WGCNA)
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Identification of key genes underlying clinical features of hepatocellular carcinoma based on weighted gene co‑expression network analysis and bioinformatics analysis
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作者 ZHANG Kan LONG Fu‑li +3 位作者 LI Yuan SHU Fa‑ming YAO Fan WEI Ai‑Ling 《Journal of Hainan Medical University》 2023年第2期49-55,共7页
Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagno... Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagnosis and treatment. Methods: GSE84598 chip data were downloaded from the GEO database, and module genes closely related to the clinical features of HCC were extracted by comprehensive weighted gene co‑expression network analysis. Hub genes were identified through protein interaction network analysis by the maximum clique centrality (MCC) algorithm;Finally, the expression of hub genes was validated by TCGA database and the Kaplan Meier plotter online database was used to evaluate the prognostic relationship between hub genes and HCC patients. Results: By comparing the gene expression data between HCC tissue samples and normal liver tissue samples, a total of 6 262 differentially expressed genes were obtained, of which 2 207 were upregulated and 4 055 were downregulated. Weighted gene co‑expression network analysis was applied to identify 120 genes of key modules. By intersecting with the differentially expressed genes, 115 candidate hub genes were obtained. The results of enrichment analysis showed that the candidate hub genes were closely related to cell mitosis, p53 signaling pathway and so on. Further application of the MCC algorithm to the protein interaction network of 115 candidate hub genes identified five hub genes, namely NUF2, RRM2, UBE2C, CDC20 and MAD2L1. Validation of hub genes by TCGA database revealed that all five hub genes were significantly upregulated in HCC tissues compared to normal liver tissues;Moreover, survival analysis revealed that high expression of hub genes was closely associated with poor prognosis in HCC patients. Conclusions: This study identifies five hub genes by combining multiple databases, which may provide directions for the clinical diagnosis and treatment of HCC. 展开更多
关键词 Weighted gene co‑expression network analysis Bioinformatics Hepatocellular carcinoma Maximal clique centrality algorithm
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Network Analysis of Road Traffic Crash and Rescue Operations in Federal Capital City
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作者 Mamman Saba Jibril David Sesugh Aule +1 位作者 Badiatu Danladi Garba Taye Oluwafemi Adewuyi 《International Journal of Geosciences》 CAS 2023年第1期36-51,共16页
Abuja is witnessing an upsurge of victims from Road Traffic Crash (RTC) which is mostly due to the attendant rapid increase in the volume of vehicles, traffic jams, bad driving, over speeding, insufficient road signs ... Abuja is witnessing an upsurge of victims from Road Traffic Crash (RTC) which is mostly due to the attendant rapid increase in the volume of vehicles, traffic jams, bad driving, over speeding, insufficient road signs and bad conditions of vehicles that ply the roads. The problem is compounded by a lack of early emergency response. Geographic Information System (GIS) based travel time model was applied in the street network analysis to identify RTC black spots that are outside the close reach of Federal Road Safety Commission (FRSC) rescue points/health facilities in Federal Capital City (FCC). Five minutes, Ten minutes and Fifteen minutes travel times were used as the impedance factor. Remote Sensing and GIS techniques were used to carry out network analysis. This was achieved by conducting the closest facility operation in the ArcGIS network analyst extension using the time of travel from each FRSC zebra point location to the RTC black spot zones/health facility. The results were presented on road network maps and bar graphs. The areas where quick response and medical facilities are insufficient were identified. It was concluded that the available health centres can sufficiently service RTC black spots in FCC, but the FRSC zebra points are insufficient which renders rescue operations inefficient and thereby exposes RTC victims to more danger. In order to ensure that there is sufficient coverage for response times, it was suggested that additional zebra points be created. 展开更多
关键词 network analysis Health Facilities Zebra Points RTC GIS FCC Remote Sensing
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Network Analysis of Research Project Members in Grant-in-Aid for Scientific Research in Japan
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作者 Hozumi Morohosi 《American Journal of Operations Research》 2023年第4期71-92,共22页
The researcher network that appeared in research projects funded by the Japanese government was analyzed. Several static and dynamic network analysis methods were applied to the data for 20 years to explore the fine s... The researcher network that appeared in research projects funded by the Japanese government was analyzed. Several static and dynamic network analysis methods were applied to the data for 20 years to explore the fine structure of the researcher’s network for grants. Our analysis shows that the long-term trend of researchers’ group sizes has become smaller, particularly rapidly decreasing in recent years. Some findings on researcher behavior in joining a project have also been reported. 展开更多
关键词 Scientific Research Fund network analysis Power Law
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Weighted Gene Co-expression Network Analysis of Gene Modules for the Prognosis of Esophageal Cancer 被引量:2
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作者 张丛 孙茜 《Journal of Huazhong University of Science and Technology(Medical Sciences)》 SCIE CAS 2017年第3期319-325,共7页
Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict t... Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer. 展开更多
关键词 esophageal cancer The Cancer Genome Atlas co-expression network analysis weighted gene co-expression network analysis enrichment analysis
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Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis 被引量:10
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作者 Kai Shi Zhi-Tong Bing +4 位作者 Gui-Qun Cao Ling Guo Ya-Na Cao Hai-Ou Jiang Mei-Xia Zhang 《International Journal of Ophthalmology(English edition)》 SCIE CAS 2015年第2期269-274,共6页
AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression lev... AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma. 展开更多
关键词 weighted gene co-expression network analysis microarray data gene ontology
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Identification of key genes involved in axon regeneration and Wallerian degeneration by weighted gene co-expression network analysis 被引量:4
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作者 Yan Lu Qi Shan +4 位作者 Mei Ling Xi-An Ni Su-Su Mao Bin Yu Qian-Qian Cao 《Neural Regeneration Research》 SCIE CAS CSCD 2022年第4期911-919,共9页
Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair perip... Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair peripheral nerve injury may uncover the molecular mechanisms and signal cascades underlying peripheral nerve repair and provide potential strategies for improving the low axon regeneration capacity of the central nervous system.In this study,we applied weighted gene co-expression network analysis to identify differentially expressed genes in proximal and distal sciatic nerve segments from rats with sciatic nerve injury.We identified 31 and 15 co-expression modules from the proximal and distal sciatic nerve segments,respectively.Functional enrichment analysis revealed that the differentially expressed genes in proximal modules promoted regeneration,while the differentially expressed genes in distal modules promoted neurodegeneration.Next,we constructed hub gene networks for selected modules and identified a key hub gene,Kif22,which was up-regulated in both nerve segments.In vitro experiments confirmed that Kif22 knockdown inhibited proliferation and migration of Schwann cells by modulating the activity of the extracellular signal-regulated kinase signaling pathway.Collectively,our findings provide a comparative framework of gene modules that are co-expressed in injured proximal and distal sciatic nerve segments,and identify Kif22 as a potential therapeutic target for promoting peripheral nerve injury repair via Schwann cell proliferation and migration.All animal experiments were approved by the Institutional Animal Ethics Committee of Nantong University,China(approval No.S20210322-008)on March 22,2021. 展开更多
关键词 axon regeneration extracellular signal-regulated kinase signaling pathway hub genes Kif22 peripheral nerve injury protein kinase Schwann cells Wallerian degeneration weighted gene co-expression network analysis
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A spillover network analysis of the global crude oil market:Evidence from the post-financial crisis era 被引量:3
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作者 Zhi-Yi Ouyang Zheng Qin +3 位作者 Hong Cao Tian-Yu Xie Xing-Yu Dai Qun-Wei Wang 《Petroleum Science》 SCIE CAS CSCD 2021年第4期1256-1269,共14页
The frequent occurrence of geopolitical crises in the post-financial crisis era is driving the rethinking behind whether the global crude oil market is still a highly connected"great pool".Using the spillove... The frequent occurrence of geopolitical crises in the post-financial crisis era is driving the rethinking behind whether the global crude oil market is still a highly connected"great pool".Using the spillover network model suggested by Baruník and Krehlík(2018),and the daily data of 31 global crude oil markets from 2009 to 2019,this study examines the return and volatility spillover effects and their timevarying behavior in six crude oil market segments at different timescales.The findings indicate that heterogeneity exists in the co-movements between global crude oil markets in the post-financial crisis era.In the medium term,both return and volatility spillover effects are not significant,which makes the diversified portfolio strategy useful.Prices in the Europe and Central Asian regions take the lead in return spillovers.In contrast,Asia-Pacific regional prices contribute the most in terms of volatility spillovers.Long-term volatility spillovers increase sharply when confronted with oil-related events in the postfinancial crisis era.Therefore,policymakers should take effective measures to prevent any large-scale risk transmission in the long run. 展开更多
关键词 Oil price network analysis Spillover effect Multiscale analysis Baruník and Krehlík model
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Ecological Network Analysis Quantifying the Sustainability of Regional Economies: A Case Study of Guangdong Province in China 被引量:2
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作者 LIANG Jinshe HU Ke DAI Teqi 《Chinese Geographical Science》 SCIE CSCD 2018年第1期127-136,共10页
To meet the challenge of sustainable development, sustainability must be made. Ecological network analysis(ENA) was introduced in this paper as an approach to quantitatively measure the growth, development, and sustai... To meet the challenge of sustainable development, sustainability must be made. Ecological network analysis(ENA) was introduced in this paper as an approach to quantitatively measure the growth, development, and sustainability of an economic system. The Guangdong economic networks from 1987 to 2010 were analyzed by applying the ENA approach. Firstly, a currency flow network among economic sectors was constructed to represent the Guangdong economic system by adapting the input-output(I-O) table data. Then, the network indicators from the ENA framework involving the total system throughput(TST), average mutual information(AMI), ascendency(A), redundancy(R) and development capacity(C) were calculated. Lastly, the network indicators were analyzed to acquire the overall features of Guangdong's economic operations during 1987–2010. The results are as follows: the trends of the network indicators show that the size of the Guangdong economic network grows exponentially at a high rate during 1987–2010, whereas its efficiency does not present a clear trend over its whole period. The growth is the main characteristic of the Guangdong economy during 1987–2010, with no clear evidence regarding its development. The quantitative results of the network also confirmed that the growth contributed to a great majority of the Guangdong economy during 1987–2010, whereas the development's contribution was tiny during the same period. The average value of the sustainability indicator(α) of the Guangdong economic network was 0.222 during 1987–2010, which is less than the theoretically optimal value of 0.37 for a sustainable human-influenced system. The results suggest that the Guangdong economic system needs a further autocatalysis to improve its efficiency to support the system maintaining a sustainable evolvement. 展开更多
关键词 network analysis regional economy sustainability evaluation ASCENDENCY Guangdong Province of China
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Network analysis using organizational risk analyzer 被引量:2
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作者 Chen, Xiaodong Li, Jianfeng Huang, Yanbo 《Journal of Southeast University(English Edition)》 EI CAS 2008年第S1期104-108,共5页
The tool system of the organizational risk analyzer (ORA) to study the network of East Turkistan terrorists is selected. The model of the relationships among its personnel, knowledge, resources and task entities is re... The tool system of the organizational risk analyzer (ORA) to study the network of East Turkistan terrorists is selected. The model of the relationships among its personnel, knowledge, resources and task entities is represented by the meta-matrix in ORA, with which to analyze the risks and vulnerabilities of organizational structure quantitatively, and obtain the last vulnerabilities and risks of the organization. Case study in this system shows that it should be a shortcut to destroy effectively the network of terrorists by recognizing the caucus persons of the terrorism organization for the first and eliminating them when strikes the terror organization. It is vital to ensure effective use of the resources and control the risks of terrorist attacks. 展开更多
关键词 dynamic network analysis meta-matrix organization risk
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Identification of Prognostic Genes for Colon Cancer through Gene Coexpression Network Analysis 被引量:1
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作者 Dan-wen WANG Zhang-shuo YANG +5 位作者 Jian XU Li-jie YANG Tie-cheng YANG Hua-qiao WANG Mao-hui FENG Fei SU 《Current Medical Science》 SCIE CAS 2021年第5期1012-1022,共11页
Objective:The present study was aimed to identify novel key genes,prognostic biomarkers and molecular pathways implicated in tumorigenesis of colon cancer.Methods:The microarray data GSE41328 containing 10 colon cance... Objective:The present study was aimed to identify novel key genes,prognostic biomarkers and molecular pathways implicated in tumorigenesis of colon cancer.Methods:The microarray data GSE41328 containing 10 colon cancer samples and 10 adjacent normal tissues was analyzed to identify 4763 differentially expressed genes.Meanwhile,another microarray data GSE17536 was performed for weighted gene co-expression network analysis(WGCNA).Results:In present study,12 co-expressed gene modules associated with tumor progression were identified for further studies.The red module showed the highest association with pathological stage by Pearson's correlation analysis.Functional enrichment analysis revealed that genes in red module focused on cell division,cell proliferation,cell cycle and metabolic related pathway.Then,a total of 26 key hub genes were identified,and GEPIA database was subsequently selected for validation.Holliday junction-recognizing protein(HJURP)and cell division cycle 25 homolog C(CDC25C)were identified as effective prognosis biomarkers,which were all detrimental to prognosis.Gene set enrichment analyses(GSEA)found the two hub genes were enriched in“oocyte meiosis”,“oocyte maturation that are progesterone-mediated”,“p53 signaling pathway”,and“cell cycle”.Furthermore,the immunohistochemistry and western blotting showed that HJURP was highly expressed in colon cancer tissue.Conclusion:HJURP was identified as a key gene associated with colon cancer progression and prognosis by WGCNA,which might influence the prognosis by regulating cell cycle pathways. 展开更多
关键词 colon cancer biomarkers weighted gene co-expression network analysis prognosis pathological stage
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Network analysis and spatial agglomeration of China’s high-speed rail: A dual network approach 被引量:1
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作者 Wei Wang Wen-Bo Du +2 位作者 Wei-Han Li Lu(Carol)Tong Jiao-E Wang 《Chinese Physics B》 SCIE EI CAS CSCD 2021年第1期612-622,共11页
China has the largest high-speed railway(HSR) system in the world, and it has gradually reshaped the urban network.The HSR system can be represented as different types of networks in terms of the nodes and various rel... China has the largest high-speed railway(HSR) system in the world, and it has gradually reshaped the urban network.The HSR system can be represented as different types of networks in terms of the nodes and various relationships(i.e.,linkages) between them. In this paper, we first introduce a general dual network model, including a physical network(PN)and a logical network(LN) to provide a comparative analysis for China’s high-speed rail network via complex network theory. The PN represents a layout of stations and rail tracks, and forms the basis for operating all trains. The LN is a network composed of the origin and destination stations of each high-speed train and the train flows between them. China’s high-speed railway(CHSR) has different topological structures and link strengths for PN in comparison with the LN. In the study, the community detection is used to analyze China’s high-speed rail networks and several communities are found to be similar to the layout of planned urban agglomerations in China. Furthermore, the hierarchies of urban agglomerations are different from each other according to the strength of inter-regional interaction and intra-regional interaction, which are respectively related to location and spatial development strategies. Moreover, a case study of the Yangtze River Delta shows that the hub stations have different resource divisions and are major contributors to the gap between train departure and arrival flows. 展开更多
关键词 China’s high-speed rail dual network network analysis urban agglomeration
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Global Collaboration in Artificial Intelligence:Bibliometrics and Network Analysis from 1985 to 2019 被引量:1
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作者 Haotian Hu Dongbo Wang Sanhong Deng 《Journal of Data and Information Science》 CSCD 2020年第4期86-115,共30页
Purpose:This study aims to explore the trend and status of international collaboration in the field of artificial intelligence(AI)and to understand the hot topics,core groups,and major collaboration patterns in global... Purpose:This study aims to explore the trend and status of international collaboration in the field of artificial intelligence(AI)and to understand the hot topics,core groups,and major collaboration patterns in global AI research.Design/methodology/approach:We selected 38,224 papers in the field of AI from 1985 to 2019 in the core collection database of Web of Science(WoS)and studied international collaboration from the perspectives of authors,institutions,and countries through bibliometric analysis and social network analysis.Findings:The bibliometric results show that in the field of AI,the number of published papers is increasing every year,and 84.8%of them are cooperative papers.Collaboration with more than three authors,collaboration between two countries and collaboration within institutions are the three main levels of collaboration patterns.Through social network analysis,this study found that the US,the UK,France,and Spain led global collaboration research in the field of AI at the country level,while Vietnam,Saudi Arabia,and United Arab Emirates had a high degree of international participation.Collaboration at the institution level reflects obvious regional and economic characteristics.There are the Developing Countries Institution Collaboration Group led by Iran,China,and Vietnam,as well as the Developed Countries Institution Collaboration Group led by the US,Canada,the UK.Also,the Chinese Academy of Sciences(China)plays an important,pivotal role in connecting the these institutional collaboration groups.Research limitations:First,participant contributions in international collaboration may have varied,but in our research they are viewed equally when building collaboration networks.Second,although the edge weight in the collaboration network is considered,it is only used to help reduce the network and does not reflect the strength of collaboration.Practical implications:The findings fill the current shortage of research on international collaboration in AI.They will help inform scientists and policy makers about the future of AI research.Originality/value:This work is the longest to date regarding international collaboration in the field of AI.This research explores the evolution,future trends,and major collaboration patterns of international collaboration in the field of AI over the past 35 years.It also reveals the leading countries,core groups,and characteristics of collaboration in the field of AI. 展开更多
关键词 Artificial intelligence International collaboration Collaboration pattern Bibliometric analysis Social network analysis
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Identification of Potential Therapeutic Targets of Alzheimer's Disease By Weighted Gene Co-Expression Network Analysis 被引量:1
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作者 Fan Zhang Siran Zhong +5 位作者 Siman Yang Yuting Wei Jingjing Wang Jinlan Huang Dengpan Wu Zhenguo Zhong 《Chinese Medical Sciences Journal》 CAS CSCD 2020年第4期330-341,共12页
Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughp... Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughput gene expression data using weighted co-expression network analysis(WGCNA)to explore the potential therapeutic targets.Methods The dataset of GSE36980 was obtained from the Gene Expression Omnibus(GEO)database.Normalization,quality control,filtration,and soft-threshold calculation were carried out before clustering the co-expressed genes into different modules.Furthermore,the correlation coefiidents between the modules and clinical traits were computed to identify the key modules.Gene ontology and pathway enrichment analyses were performed on the key module genes.The STRING database was used to construct the protein-protein interaction(PPI)networks,which were further analyzed by Cytoscape app(MCODE).Finally,validation of hub genes was conducted by external GEO datasets of GSE 1297 and GSE 28146.Results Co-expressed genes were clustered into 27 modules,among which 6 modules were identified as the key module relating to AD occurrence.These key modules are primarily involved in chemical synaptic transmission(G0:0007268),the tricarboxylic acid(TCA)cycle and respiratory electron transport(R-HSA-1428517).WDR47,OXCT1,C3orfl4,ATP6V1A,SLC25A14,NAPB were found as the hub genes and their expression were validated by external datasets.Conclusions Through modules co-expression network analyses and PPI network analyses,we identified the hub genes of AD,including WDR47,0XCT1,C3orfl4i ATP6V1A,SLC25A14 and NAPB.Among them,three hub genes(ATP6V1A,SLC25A14,OXCT1)might contribute to AD pathogenesis through pathway of TCA cycle. 展开更多
关键词 bioinformatics analysis Alzheimer's disease Tricarboxylic acid(TCA)cycle weighted gene co-expression network analysis OXCT1 ATP6V1A
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Mathematical Modeling in Social Network Analysis: Using TOPSIS to Find Node Influences in a Social Network 被引量:4
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作者 William P Fox Sean F. Everton 《Journal of Mathematics and System Science》 2013年第10期531-541,共11页
In a social network analysis the output provided includes many measures and metrics. For each of these measures and metric, the output provides the ability to obtain a rank ordering of the nodes in terms of these meas... In a social network analysis the output provided includes many measures and metrics. For each of these measures and metric, the output provides the ability to obtain a rank ordering of the nodes in terms of these measures. We might use this information in decision making concerning disrupting or deceiving a given network. All is fine when all the measures indicate the same node as the key or influential node. What happens when the measures indicate different key nodes? Our goal in this paper is to explore two methodologies to identify the key players or nodes in a given network. We apply TOPSIS to analyze these outputs to find the most influential nodes as a function of the decision makers' inputs as a process to consider both subjective and objectives inputs through pairwise comparison matrices. We illustrate our results using two common networks from the literature: the Kite network and the Information flow network from Knoke and Wood. We discuss some basic sensitivity analysis can may be applied to the methods. We find the use of TOPSIS as a flexible method to weight the criterion based upon the decision makers' inputs or the topology of the network. 展开更多
关键词 Social network analysis multi-attribute decision making Analytical hierarchy process (AHP) weighted criterion TOPSIS node influence
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Core acupoints of acupuncture for hyperplasia of mammary gland: a network analysis 被引量:1
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作者 Bao-Min Dou Yuan-Yuan Sun +4 位作者 Tian-Yi Zhao Qian-Nan Jia Jiang Liu Bo Chen Yi Guo 《TMR Non-Drug Therapy》 2020年第1期12-22,共11页
Backgroud:Clinical studies on acupuncture treatment of hyperplasia of mammary gland(HMG)have proved its effectiveness,but most studies have paid little attention to acupoints prescription and acupoint compatibility.Th... Backgroud:Clinical studies on acupuncture treatment of hyperplasia of mammary gland(HMG)have proved its effectiveness,but most studies have paid little attention to acupoints prescription and acupoint compatibility.The clinical prescription is not identical,the curative effect also has the difference.Therefore,through data mining and network analysis,this study explored the core acupoints and the compatibility law of acupoints in acupuncture treatment of HMG.Methods:To search and select qualified literature according to inclusion and exclusion criteria for relevant clinical research literature on acupuncture treatment of HMG in CNKI,VIP database,WanFang database and PubMed,etc.Then extract relevant information and establish a database.Using the method of statistical and complex network analysis,this paper studies the core acupoints and the law of acupoint compatibility.Results:A total of 104 Chinese literatures and 0 English literatures were included and 106 acupuncture prescriptions were extracted.The core acupoints in the treatment of HMG are Danzhong(CV 17),Wuyi(ST 15),Zusanli(ST 36),Jianjing(GB 21).Danzhong(CV 17)and Zusanli(ST 36),Danzhong(CV 17)and Wuyi(ST 15),Jianjing(GB 21)and Tianzong(SI 11),Jianjing(GB 21)and Wuyi(ST 15)have the highest correlation degree.The method of acupoint matching mainly consists of local-remote acupoints,upper-lower acupoints and front-rear acupoints.Conclusion:The results of a network analysis substantially accord with the general rules of acupuncture theories in traditional Chinese medicine,able to reflect the points-selection principles and features in acupuncture treatment of HMG and provide evidence for the acupoints selection in the treatment of HMG in acupuncture clinic. 展开更多
关键词 Hyperplasia of mammary glands(HMG) Acupoints compatibility Complex network analysis Traditional Chinese medicine
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A comparative study of information diffusion in weblogs and microblogs based on social network analysis 被引量:2
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作者 Yang ZHANG Wanyang LING 《Chinese Journal of Library and Information Science》 2012年第4期51-66,共16页
Purpose: This paper intends to explore a quantitative method for investigating the characteristics of information diffusion through social media like weblogs and microblogs.By using the social network analysis methods... Purpose: This paper intends to explore a quantitative method for investigating the characteristics of information diffusion through social media like weblogs and microblogs.By using the social network analysis methods,we attempt to analyze the different characteristics of information diffusion in weblogs and microblogs as well as the possible reasons of these differences.Design/methodology/approach: Using the social network analysis methods,this paper carries out an empirical study by taking the Chinese weblogs and microblogs in the field of Library and Information Science(LIS) as the research sample and employing measures such as network density,core/peripheral structure and centrality.Findings: Firstly,both bloggers and microbloggers maintain weak ties,and both of their social networks display a small-world effect. Secondly,compared with weblog users,microblog users are more interconnected,more equal and more capable of developing relationships with people outside their own social networks. Thirdly,the microblogging social network is more conducive to information diffusion than the blogging network,because of their differences in functions and the information flow mechanism. Finally,the communication mode emerged with microblogging,with the characteristics of micro-content,multi-channel information dissemination,dense and decentralized social network and content aggregation,will be one of the trends in the development of the information exchange platform in the future.Research limitations: The sample size needs to be increased so that samples are more representative. Errors may exist during the data collection. Moreover,the individual-level characteristics of the samples as well as the types of information exchanged need to be further studied.Practical implications: This preliminary study explores the characteristics of information diffusion in the network environment and verifies the feasibility of conducting a quantitative analysis of information diffusion through social media. In addition,it provides insight into the characteristics of information diffusion in weblogs and microblogs and the possible reasons of these differences.Originality/value: We have analyzed the characteristics of information diffusion in weblogs and microblogs by using the social network analysis methods. This research will be useful for a quantitative analysis of the underlying mechanisms of information flow through social media in the network environment. 展开更多
关键词 WEBLOG Microblog Information diffusion Social network analysis(SNA) Library and information science(LIS
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