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Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning
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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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Social-ecological perspective on the suicidal behaviour factors of early adolescents in China:a network analysis 被引量:1
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作者 Yuan Li Peiying Li +5 位作者 Mengyuan Yuan Yonghan Li Xueying Zhang Juan Chen Gengfu Wang Puyu Su 《General Psychiatry》 CSCD 2024年第1期143-150,共8页
Background In early adolescence,youth are highly prone to suicidal behaviours.Identifying modifiable risk factors during this critical phase is a priority to inform effective suicide prevention strategies.Aims To expl... Background In early adolescence,youth are highly prone to suicidal behaviours.Identifying modifiable risk factors during this critical phase is a priority to inform effective suicide prevention strategies.Aims To explore the risk and protective factors of suicidal behaviours(ie,suicidal ideation,plans and attempts)in early adolescence in China using a social-ecological perspective.Methods Using data from the cross-sectional project‘Healthy and Risky Behaviours Among Middle School Students in Anhui Province,China',stratified random cluster sampling was used to select 5724 middle school students who had completed self-report questionnaires in November 2020.Network analysis was employed to examine the correlates of suicidal ideation,plans and attempts at four levels,namely individual(sex,academic performance,serious physical llness/disability,history of self-harm,depression,impulsivity,sleep problems,resilience),family(family economic status,relationship with mother,relationship with father,family violence,childhood abuse,parental mental illness),school(relationship with teachers,relationship with classmates,school-bullying victimisation and perpetration)and social(social support,satisfaction with society).Results In total,37.9%,19.0%and 5.5%of the students reported suicidal ideation,plans and attempts in the past 6 months,respectively.The estimated network revealed that suicidal ideation,plans and attempts were collectively associated with a history of self-harm,sleep problems,childhood abuse,school bullying and victimisation.Centrality analysis indicated that the most influential nodes in the network were history of self-harm and childhood abuse.Notably,the network also showed unique correlates of suicidal ideation(sex,weight=0.60;impulsivity,weight=0.24;family violence,weight=0.17;relationship with teachers,weight=-0.03;school-bullying perpetration,weight=0.22),suicidal plans(social support,weight=-0.15)and suicidal attempts(relationship with mother,weight=-0.10;parental mental llness,weight=0.61).Conclusions This study identified the correlates of suicidal ideation,plans and attempts,and provided practical implications for suicide prevention for young adolescents in China.Firstly,this study highlighted the importance of joint interventions across multiple departments.Secondly,the common risk factors of suicidal ideation,plans and attempts were elucidated.Thirdly,this study proposed target interventions to address the unique influencing factors of suicidal ideation,plans and attempts. 展开更多
关键词 network analysis PREVENTION
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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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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 王微 杜文博 +2 位作者 李威翰 佟路 王姣娥 《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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Measuring Global Supply Chain Vulnerabilities Using Trade Network Analysis Method
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作者 Cui Xiaomin Xiong Wanting +1 位作者 Yang Panpan Xu Qiyuan 《China Economist》 2023年第1期68-86,共19页
With the trade network analysis method and bilateral country-product level trade data of 2017-2020,this paper reveals the overall characteristics and intrinsic vulnerabilities of China’s global supply chains.Our rese... With the trade network analysis method and bilateral country-product level trade data of 2017-2020,this paper reveals the overall characteristics and intrinsic vulnerabilities of China’s global supply chains.Our research finds that first,most global supply-chain-vulnerable products are from technology-intensive sectors.For advanced economies,their supply chain vulnerabilities are primarily exposed to political and economic alliances.In comparison,developing economies are more dependent on regional communities.Second,China has a significant export advantage with over 80%of highly vulnerable intermediate inputs relying on imports of high-end electrical,mechanical and chemical products from advanced economies or their multinational companies.China also relies on developing economies for the import of some resource products.Third,during the trade frictions from 2018 to 2019 and the subsequent COVID-19 pandemic,there was a significant reduction in the supply chain vulnerabilities of China and the US for critical products compared with other products,which reflects a shift in the layout of critical product supply chains to ensure not just efficiency but security.China should address supply chain vulnerabilities by bolstering supply-side weaknesses,diversifying import sources,and promoting international coordination and cooperation. 展开更多
关键词 Supply chain VULNERABILITIES TRADE network analysis EXPORT CENTRALITY variance INDEX IMPORT CENTRALITY variance INDEX
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A Spatial Supply-Demand Imbalance Between Rural Primary and Secondary Schools in Shaanxi Province Based on Road Network Analysis
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作者 Ziwei Qiang Bei Jin Shiyuan Xu 《Journal of Contemporary Educational Research》 2022年第2期17-26,共10页
It is of great significance to optimize the spatial matching of basic education facilities in rural areas and promote the equalization of urban and rural basic public services and the overall revitalization of rural a... It is of great significance to optimize the spatial matching of basic education facilities in rural areas and promote the equalization of urban and rural basic public services and the overall revitalization of rural areas.Based on the theory of spatial accessibility and spatial balance of supply and demand,this paper constructs the evaluation system of rural basic education facilities and layout rationality.In this study,we took 42 primary and secondary schools and 2089 rural areas with concentrated population in six township areas of Hancheng City as the research subjects.We used ArcGIS network analysis,population coupling model,and other methods,from the administrative scale and rural population concentration area scale for evaluation.The accessibility of basic education facilities and its coupling relationship with the spatial distribution of student population describe the spatial and geographical pattern of basic education facilities in rural areas.The results show that the accessibility of rural administrative scale and the spatial balance of supply and demand of population concentration area scale are associated with great problems,the differences between towns are obvious,and the overall level of the best performing towns is still low.On the scale of population concentration area,the overall coupling degree is too low,the"dislocation"distribution of educational facilities and student population is obvious,and the matching degree of the student population and school in different towns is significantly different,showing a more obvious"core-periphery"spatial structure characteristics centered on the eastern and southeast regions.The terrain characteristics of rural areas in Shaanxi province are prominent,and the accessibility of the road network is particularly significant.Therefore,optimizing the construction of rural roads and optimizing school layout according to local conditions will become an important solution to promote the balanced allocation of basic education resources in Shaanxi province. 展开更多
关键词 Rural basic education facilities network analysis Balanced spatial layout spatial population coupling
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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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Spatial Social Network Analysis: Program Pengembangan Usaha Agribisnis Perdesaan (PUAP) or an Exertion Development Program in Supporting the Region Revitalization Development
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作者 Bentar Priyopradono Danny Manongga Wiranto Herry Utomo 《Social Networking》 2013年第2期63-76,共14页
As the exertion development (PUAP) develop in Rejang Lebong Regency in Bengkulu province which had been started since 2008 by giving a kind of fund aid called Bantuan Langsung Masyarakat (BLM PUAP), to Gapoktan (Gabun... As the exertion development (PUAP) develop in Rejang Lebong Regency in Bengkulu province which had been started since 2008 by giving a kind of fund aid called Bantuan Langsung Masyarakat (BLM PUAP), to Gapoktan (Gabungan Kelompok Tani) or an organization of farmers such by giving some money as the capital used for 1) food plant cultiva-tion, horticulture, animal husbandry, plantation, and2) non-cultivation exertion such as;home industry of agriculture, small marketing scale and another agriculture exertion. By the approach which had been done is hoped to get the important result, on the other way the role of analysis factor (Social Network Analysis) from all undertaking stakeholders programs PUAP to be relevance steps aimed to understand the relation or connectivity from all factors in the network and also the role of factor inside the network itself be the relevance steps in arranging the strategy and work intention from the realization stage of PUAP program for the continuity of the realization program in the future (finding the good strategy) which aimed to develop the program of PUAP in Rejang Lebong Regency in Bengkulu Province, and to be a reference from doing the program as a national program in Indonesia. 展开更多
关键词 EXERTION DEVELOPMENT PROGRAM (PUAP) Social network analysis AGRICULTURE HORTICULTURE
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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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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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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 key genes involved in axon regeneration and Wallerian degeneration by weighted gene co-expression network analysis 被引量:3
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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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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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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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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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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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