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Ecological network analysis reveals complex responses of tree species life stage interactions to stand variables
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作者 Hengchao Zou Huayong Zhang Tousheng Huang 《Journal of Forestry Research》 SCIE EI CAS CSCD 2024年第1期29-43,共15页
Tree interactions are essential for the structure,dynamics,and function of forest ecosystems,but variations in the architecture of life-stage interaction networks(LSINs)across forests is unclear.Here,we constructed 16... Tree interactions are essential for the structure,dynamics,and function of forest ecosystems,but variations in the architecture of life-stage interaction networks(LSINs)across forests is unclear.Here,we constructed 16 LSINs in the mountainous forests of northwest Hebei,China based on crown overlap from four mixed forests with two dominant tree species.Our results show that LSINs decrease the complexity of stand densities and basal areas due to the interaction cluster differentiation.In addition,we found that mature trees and saplings play different roles,the first acting as“hub”life stages with high connectivity and the second,as“bridges”controlling information flow with high centrality.Across the forests,life stages with higher importance showed better parameter stability within LSINs.These results reveal that the structure of tree interactions among life stages is highly related to stand variables.Our efforts contribute to the understanding of LSIN complexity and provide a basis for further research on tree interactions in complex forest communities. 展开更多
关键词 Tree interactions Life stages interaction networks Ecological complexity
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Impact of different interaction behavior on epidemic spreading in time-dependent social networks
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作者 黄帅 陈杰 +2 位作者 李梦玉 徐元昊 胡茂彬 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第3期190-195,共6页
We investigate the impact of pairwise and group interactions on the spread of epidemics through an activity-driven model based on time-dependent networks.The effects of pairwise/group interaction proportion and pairwi... We investigate the impact of pairwise and group interactions on the spread of epidemics through an activity-driven model based on time-dependent networks.The effects of pairwise/group interaction proportion and pairwise/group interaction intensity are explored by extensive simulation and theoretical analysis.It is demonstrated that altering the group interaction proportion can either hinder or enhance the spread of epidemics,depending on the relative social intensity of group and pairwise interactions.As the group interaction proportion decreases,the impact of reducing group social intensity diminishes.The ratio of group and pairwise social intensity can affect the effect of group interaction proportion on the scale of infection.A weak heterogeneous activity distribution can raise the epidemic threshold,and reduce the scale of infection.These results benefit the design of epidemic control strategy. 展开更多
关键词 epidemic transmission complex network time-dependent networks social interaction
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Opinion consensus incorporating higher-order interactions in individual-collective networks
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作者 叶顺 涂俐兰 +2 位作者 王先甲 胡佳 王薏潮 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第7期105-115,共11页
In the current information society, the dissemination mechanisms and evolution laws of individual or collective opinions and their behaviors are the research hot topics in the field of opinion dynamics. First, in this... In the current information society, the dissemination mechanisms and evolution laws of individual or collective opinions and their behaviors are the research hot topics in the field of opinion dynamics. First, in this paper, a two-layer network consisting of an individual-opinion layer and a collective-opinion layer is constructed, and a dissemination model of opinions incorporating higher-order interactions(i.e. OIHOI dissemination model) is proposed. Furthermore, the dynamic equations of opinion dissemination for both individuals and groups are presented. Using Lyapunov's first method,two equilibrium points, including the negative consensus point and positive consensus point, and the dynamic equations obtained for opinion dissemination, are analyzed theoretically. In addition, for individual opinions and collective opinions,some conditions for reaching negative consensus and positive consensus as well as the theoretical expression for the dissemination threshold are put forward. Numerical simulations are carried to verify the feasibility and effectiveness of the proposed theoretical results, as well as the influence of the intra-structure, inter-connections, and higher-order interactions on the dissemination and evolution of individual opinions. The main results are as follows.(i) When the intra-structure of the collective-opinion layer meets certain characteristics, then a negative or positive consensus is easier to reach for individuals.(ii) Both negative consensus and positive consensus perform best in mixed type of inter-connections in the two-layer network.(iii) Higher-order interactions can quickly eliminate differences in individual opinions, thereby enabling individuals to reach consensus faster. 展开更多
关键词 two-layer social networks individual and collective opinions higher-order interactions CONSENSUS Lyapunov's first method
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Expression Pattern, Interaction Network, and Functional Analysis of the Arabidopsis Botrytis Susceptible1 Interactor
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作者 Jianzhong Huang Hongbin Zhang +4 位作者 Zhuojun Li Xiuying Guan Xiaoju Zhong Peng Jia Kai Chen 《Journal of Biomedical Science and Engineering》 2024年第10期171-178,共8页
E3 ubiquitin ligases are participated in numerous processes, regulating the response to biotic and abiotic stresses. Botrytis susceptible1 interactor (BOI) is a RING (Really Interesting New Gene)-type E3 ligase that m... E3 ubiquitin ligases are participated in numerous processes, regulating the response to biotic and abiotic stresses. Botrytis susceptible1 interactor (BOI) is a RING (Really Interesting New Gene)-type E3 ligase that mediates the ubiquitination of BOS1 (Botrytis susceptible1), a transcription factor involved in stress and pathogen responses. Although BOI is an E3 ligase, there are reports to show that BOI interacts with target proteins such as DELLAs or CONSTANS to repress gibberellin responses and flowering without the degradation of the target proteins. In this article, we utilize diversified methods to comprehensively analyze the expression pattern, interaction network and function of BOI gene. Firstly, 1800 bp upstream region of BOI gene from Arabidopsis thaliana (Arabidopsis) genome was isolated, and fused GUS reporter gene. The resulting expression cassette was introduced into wild-type Arabidopsis through Agrobacterium-mediated transformation. The result demonstrated that BOI gene was expressed predominantly in leaves, siliques, young roots, and flowering tissues, indicating that BOI gene may be involved in multiple processes in plant growth and development in Arabidopsis. Besides, eight candidate interacting proteins were obtained from the Arabidopsis cDNA library via yeast two-hybrid technology, including EXO70E2 (AT5G61010), WRKY7 (AT4G24240), WRKY11 (AT4G31550), WRKY17 (AT2G24570), UBP20 (AT4G17895), L5 (AT1G12290), SAUR9 (AT4G36110) and TCP21 (AT5G08330). Functional analysis of these candidate interacting proteins manifested that they related to multiple pathways, including biological and abiotic stress, programmed cell death, protein degradation, material metabolism and transcriptional regulation. In addition, the results of the transient assay proclaimed that BOI protein affects the protein stability of EXO70E2 and L5 through its E3 ubiquitin ligase activity. Our results provide novel clues for a better understanding of molecular mechanisms underlying BOI-mediated regulations. 展开更多
关键词 E3 Ubiquitin Ligases Expression Pattern interaction network ARABIDOPSIS
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Viral-host molecular interactions and metabolic modulation:Strategies to inhibit flaviviruses pathogenesis
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作者 Zeeshan Ahmad Khan Mukesh Kumar Yadav +3 位作者 Dong-Woo Lim Hojun Kim Jing-Hua Wang AbuZar Ansari 《World Journal of Virology》 2024年第4期41-50,共10页
Flaviviruses,which include globally impactful pathogens,such as West Nile virus,yellow fever virus,Zika virus,Japanese encephalitis virus,and dengue virus,contribute significantly to human infections.Despite the ongoi... Flaviviruses,which include globally impactful pathogens,such as West Nile virus,yellow fever virus,Zika virus,Japanese encephalitis virus,and dengue virus,contribute significantly to human infections.Despite the ongoing emergence and resurgence of flavivirus-mediated pathogenesis,the absence of specific therapeutic options remains a challenge in the prevention and treatment of flaviviral infections.Through the intricate processes of fusion,transcription,replication,and maturation,the complex interplay of viral and host metabolic interactions affects pathophysiology.Crucial interactions involve metabolic molecules,such as amino acids,glucose,fatty acids,and nucleotides,each playing a pivotal role in the replication and maturation of flaviviruses.These viral-host metabolic molecular interactions hijack and modulate the molecular mechanisms of host metabolism.A comprehensive understanding of these intricate metabolic pathways offers valuable insights,potentially unveiling novel targets for therapeutic interventions against flaviviral pathogenesis.This review emphasizes promising avenues for the development of therapeutic agents that target specific metabolic molecules,such as amino acids,glucose,fatty acids,and nucleotides,which interact with flavivirus replication and are closely linked to the modulation of host metabolism.The clinical limitations of current drugs have prompted the development of new inhibitory strategies for flaviviruses based on an understanding of the molecular interactions between the virus and the host. 展开更多
关键词 FLAVIVIRUS Nonstructural proteins virus-host interaction Metabolism Inhibitors Vaccines
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Human Interaction Recognition in Surveillance Videos Using Hybrid Deep Learning and Machine Learning Models
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作者 Vesal Khean Chomyong Kim +5 位作者 Sunjoo Ryu Awais Khan Min Kyung Hong Eun Young Kim Joungmin Kim Yunyoung Nam 《Computers, Materials & Continua》 SCIE EI 2024年第10期773-787,共15页
Human Interaction Recognition(HIR)was one of the challenging issues in computer vision research due to the involvement of multiple individuals and their mutual interactions within video frames generated from their mov... Human Interaction Recognition(HIR)was one of the challenging issues in computer vision research due to the involvement of multiple individuals and their mutual interactions within video frames generated from their movements.HIR requires more sophisticated analysis than Human Action Recognition(HAR)since HAR focuses solely on individual activities like walking or running,while HIR involves the interactions between people.This research aims to develop a robust system for recognizing five common human interactions,such as hugging,kicking,pushing,pointing,and no interaction,from video sequences using multiple cameras.In this study,a hybrid Deep Learning(DL)and Machine Learning(ML)model was employed to improve classification accuracy and generalizability.The dataset was collected in an indoor environment with four-channel cameras capturing the five types of interactions among 13 participants.The data was processed using a DL model with a fine-tuned ResNet(Residual Networks)architecture based on 2D Convolutional Neural Network(CNN)layers for feature extraction.Subsequently,machine learning models were trained and utilized for interaction classification using six commonly used ML algorithms,including SVM,KNN,RF,DT,NB,and XGBoost.The results demonstrate a high accuracy of 95.45%in classifying human interactions.The hybrid approach enabled effective learning,resulting in highly accurate performance across different interaction types.Future work will explore more complex scenarios involving multiple individuals based on the application of this architecture. 展开更多
关键词 Convolutional neural network deep learning human interaction recognition ResNet skeleton joint key points human pose estimation hybrid deep learning and machine learning
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Disease networks. Uncovering disease-disease relationships through the incomplete interactome
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作者 Jorg Menche 《四川生理科学杂志》 2024年第1期199-199,共1页
According to the disease module hypothesis,the cellular components associated with a disease segregate in the same neighborhood of the human interactome,the map of biologically relevant molecular interactions.Yet,give... According to the disease module hypothesis,the cellular components associated with a disease segregate in the same neighborhood of the human interactome,the map of biologically relevant molecular interactions.Yet,given the incompleteness of the interactome and the limited knowledge of disease-associated genes,it is not obvious if the available data have sufficient coverage to map out modules associated with each disease. 展开更多
关键词 INCOMPLETE interactions. networks.
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LncRNAs exert indispensable roles in orchestrating the interaction among diverse noncoding RNAs and enrich the regulatory network of plant growth and its adaptive environmental stress response
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作者 Lingling Zhang Tao Lin +3 位作者 Guoning Zhu Bin Wu Chunjiao Zhang Hongliang Zhu 《Horticulture Research》 SCIE CSCD 2023年第12期304-315,共12页
With the advent of advanced sequencing technologies,non-coding RNAs(ncRNAs)are increasingly pivotal and play highly regulated roles in the modulation of diverse aspects of plant growth and stress response.This include... With the advent of advanced sequencing technologies,non-coding RNAs(ncRNAs)are increasingly pivotal and play highly regulated roles in the modulation of diverse aspects of plant growth and stress response.This includes a spectrum of ncRNA classes,ranging from small RNAs to long non-coding RNAs(lncRNAs).Notably,among these,lncRNAs emerge as significant and intricate components within the broader ncRNA regulatory networks.Here,we categorize ncRNAs based on their length and structure into small RNAs,medium-sized ncRNAs,lncRNAs,and circle RNAs.Furthermore,the review delves into the detailed biosynthesis and origin of these ncRNAs.Subsequently,we emphasize the diverse regulatory mechanisms employed by lncRNAs that are located at various gene regions of coding genes,embodying promoters,5’UTRs,introns,exons,and 3’UTR regions.Furthermore,we elucidate these regulatory modes through one or two concrete examples.Besides,lncRNAs have emerged as novel central components that participate in phase separation processes.Moreover,we illustrate the coordinated regulatory mechanisms among lncRNAs,miRNAs,and siRNAs with a particular emphasis on the central role of lncRNAs in serving as sponges,precursors,spliceosome,stabilization,scaffolds,or interaction factors to bridge interactions with other ncRNAs.The review also sheds light on the intriguing possibility that some ncRNAs may encode functional micropeptides.Therefore,the review underscores the emergent roles of ncRNAs as potent regulatory factors that significantly enrich the regulatory network governing plant growth,development,and responses to environmental stimuli.There are yet-to-be-discovered roles of ncRNAs waiting for us to explore. 展开更多
关键词 interaction STRESS network
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Analysis of Commuting Modal Shift in Consideration of Social Interaction of Consciousness for Environment
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作者 Masashi Okushima 《Journal of Traffic and Transportation Engineering》 2024年第2期63-80,共18页
It is the matter for achievement of the low carbon transport system that the excessive use of private vehicles can be controlled appropriately.Not only improvement of service level of modes except private vehicle,but ... It is the matter for achievement of the low carbon transport system that the excessive use of private vehicles can be controlled appropriately.Not only improvement of service level of modes except private vehicle,but also consciousness for environmental problem of individual trip maker is important for eco-commuting promotion.On the other hand,consciousness for environment would be changed by influence of other person.Accordingly,it is aimed in the study that the structure of decision-making process for modal shift to the eco-commuting mode in the local city is described considering environmental consciousness and social interaction.For the purpose,the consciousness for the environment problem and the travel behavior of the commuter at the suburban area in the local city are investigated by the questionnaire survey.The covariance structure about the eco-consciousness is analyzed with the database of the questionnaire survey by structural equation modeling.As the result,it can be confirmed with the structural equation model that the individual environmental consciousness is strongly related with the intention of self-sacrifice and is influenced with the local interaction of the individual connections.On the other hand,the intention of modal shift for the commuting mode is analyzed with the database of the questionnaire survey.It can be found out that the environmental consciousness is not statistically significant for commuting mode choice with the present poor level of service of public transport.However,the intention of self-sacrifice for the prevention of the global warming is statistically confirmed as the factor of modal shift with the operation of eco-commuting bus service with the RP/SP integrated estimation method.As the result,the multi-agent simulation system with social interaction model for eco consciousness is developed to measure the effect of the eco-commuting promotion.For the purpose,the carbon dioxide emission is estimated based on traffic demand and road network condition in the traffic environment model.On the other hand,the relation between agents is defined based on the small world network.The proposed multi-agent simulation is applied to measure the effect of the eco-commuting promotion such as improvement of level of service on the public transport or education of eco-consciousness.The effect of the promotion plan can be observed with the proposed multi-agent system.Finally,it can be concluded that the proposed multi-agent simulation with social interaction for eco-consciousness is useful for planning of eco-commuting promotion. 展开更多
关键词 Greenhouse gas emission modal shift structural equation model RP/SP combined estimation multi-agent simulation local interaction small world network consciousness for environment commuting shuttle bus local city
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Lateral interaction by Laplacian‐based graph smoothing for deep neural networks
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作者 Jianhui Chen Zuoren Wang Cheng‐Lin Liu 《CAAI Transactions on Intelligence Technology》 SCIE EI 2023年第4期1590-1607,共18页
Lateral interaction in the biological brain is a key mechanism that underlies higher cognitive functions.Linear self‐organising map(SOM)introduces lateral interaction in a general form in which signals of any modalit... Lateral interaction in the biological brain is a key mechanism that underlies higher cognitive functions.Linear self‐organising map(SOM)introduces lateral interaction in a general form in which signals of any modality can be used.Some approaches directly incorporate SOM learning rules into neural networks,but incur complex operations and poor extendibility.The efficient way to implement lateral interaction in deep neural networks is not well established.The use of Laplacian Matrix‐based Smoothing(LS)regularisation is proposed for implementing lateral interaction in a concise form.The authors’derivation and experiments show that lateral interaction implemented by SOM model is a special case of LS‐regulated k‐means,and they both show the topology‐preserving capability.The authors also verify that LS‐regularisation can be used in conjunction with the end‐to‐end training paradigm in deep auto‐encoders.Additionally,the benefits of LS‐regularisation in relaxing the requirement of parameter initialisation in various models and improving the classification performance of prototype classifiers are evaluated.Furthermore,the topologically ordered structure introduced by LS‐regularisation in feature extractor can improve the generalisation performance on classification tasks.Overall,LS‐regularisation is an effective and efficient way to implement lateral interaction and can be easily extended to different models. 展开更多
关键词 artificial neural networks biologically plausible Laplacian‐based graph smoothing lateral interaction machine learning
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Drug–Target Interaction Prediction Model Using Optimal Recurrent Neural Network
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作者 G.Kavipriya D.Manjula 《Intelligent Automation & Soft Computing》 SCIE 2023年第2期1675-1689,共15页
Drug-target interactions prediction(DTIP)remains an important requirement in thefield of drug discovery and human medicine.The identification of interaction among the drug compound and target protein plays an essential ... Drug-target interactions prediction(DTIP)remains an important requirement in thefield of drug discovery and human medicine.The identification of interaction among the drug compound and target protein plays an essential pro-cess in the drug discovery process.It is a lengthier and complex process for pre-dicting the drug target interaction(DTI)utilizing experimental approaches.To resolve these issues,computational intelligence based DTIP techniques were developed to offer an efficient predictive model with low cost.The recently devel-oped deep learning(DL)models can be employed for the design of effective pre-dictive approaches for DTIP.With this motivation,this paper presents a new drug target interaction prediction using optimal recurrent neural network(DTIP-ORNN)technique.The goal of the DTIP-ORNN technique is to predict the DTIs in a semi-supervised way,i.e.,inclusion of both labelled and unlabelled instances.Initially,the DTIP-ORNN technique performs data preparation process and also includes class labelling process,where the target interactions from the database are used to determine thefinal label of the unlabelled instances.Besides,drug-to-drug(D-D)and target-to-target(T-T)interactions are used for the weight initia-tion of the RNN based bidirectional long short term memory(BiLSTM)model which is then utilized to the prediction of DTIs.Since hyperparameters signifi-cantly affect the prediction performance of the BiLSTM technique,the Adam optimizer is used which mainly helps to improve the DTI prediction outcomes.In order to ensure the enhanced predictive outcomes of the DTIP-ORNN techni-que,a series of simulations are implemented on four benchmark datasets.The comparative result analysis shows the promising performance of the DTIP-ORNN method on the recent approaches. 展开更多
关键词 Drug target interaction deep learning recurrent neural network parameter tuning semi-supervised learning
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Construction of gene/protein interaction networks and enrichment pathway analysis for paroxysmal nocturnal hemoglobinuria and aplastic anemia
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作者 Gong-Xi Liu Zheng-Di Sun +2 位作者 Chao Zhou Jun-Yu Wei Jing Zhuang 《Medical Theory and Hypothesis》 2023年第2期19-26,共8页
Background:To develop a protein-protein interaction network of Paroxysmal nocturnal hemoglobinuria(PNH)and Aplastic anemia(AA)based on genetic genes and to predict pathways underlying the molecular complexes in the ne... Background:To develop a protein-protein interaction network of Paroxysmal nocturnal hemoglobinuria(PNH)and Aplastic anemia(AA)based on genetic genes and to predict pathways underlying the molecular complexes in the network.Methods:In this research,the PNH and AA-related genes were screened through Online Mendelian Inheritance in Man(OMIM).The plugins and Cytoscape were used to search literature and build a protein-protein interaction network.Results:The protein-protein interaction network contains two molecular complexes that are five higher than the correlation integral values.The target genes of this study were obtained:CD59,STAT3,TERC,TNF,AKT1,C5AR1,EPO,IL6,IL10 and so on.We also found that many factors regulate biological behaviors:neutrophils,macrophages,vascular endothelial growth factor,immunoglobulin,interleukin,cytokine receptor,interleukin-6 receptor,tumor necrosis factor,and so on.This research provides a bioinformatics foundation for further explaining the mechanism of common development of both.Conclusion:This indicates that the PNH and AA is a complex process regulated by many cellular pathways and multiple genes. 展开更多
关键词 protein interaction networks paroxysmal nocturnal hemoglobinuria Online Mendelian Inheritance in Man database aplastic anemia biological pathways
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Integrated network analysis of transcriptomic and protein-protein interaction data in taurine-treated hepatic stellate cells 被引量:6
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作者 Xing-Qiu Liang Jian Liang +2 位作者 Xiao-Fang Zhao Xin-Yuan Wang Xin Deng 《World Journal of Gastroenterology》 SCIE CAS 2019年第9期1067-1079,共13页
BACKGROUND Studies show that the antifibrotic mechanism of taurine may involve its inhibition of the activation and proliferation of hepatic stellate cells(HSCs). Since the molecular mechanism of taurine-mediated anti... BACKGROUND Studies show that the antifibrotic mechanism of taurine may involve its inhibition of the activation and proliferation of hepatic stellate cells(HSCs). Since the molecular mechanism of taurine-mediated antifibrotic activity has not been fully unveiled and is little studied, it is imperative to use "omics" methods to systematically investigate the molecular mechanism by which taurine inhibits liver fibrosis.AIM To establish a network including transcriptomic and protein-protein interaction data to elucidate the molecular mechanism of taurine-induced HSC apoptosis.METHODS We used microarrays, bioinformatics, protein-protein interaction(PPI) network,and sub-modules to investigate taurine-induced changes in gene expression in human HSCs(LX-2). Subsequently, all of the differentially expressed genes(DEGs) were subjected to gene ontology function and Kyoto encyclopedia of genes and genomes pathway enrichment analysis. Furthermore, the interactions of DEGs were explored in a human PPI network, and sub-modules of the DEGs interaction network were analyzed using Cytoscape software.RESULTS A total of 635 DEGs were identified in taurine-treated HSCs when compared with the controls. Of these, 304 genes were statistically significantly up-regulated, and 331 down-regulated. Most of these DEGs were mainly located on the membrane and extracellular region, and are involved in the biological processes of signal transduction, cell proliferation, positive regulation of extracellular regulated protein kinases 1(ERK1) and ERK2 cascade, extrinsic apoptotic signaling pathway and so on. Fifteen significantly enriched pathways with DEGs were identified, including mitogen-activated protein kinase(MAPK) signaling pathway, peroxisome proliferators-activated receptor signaling pathway,estrogen signaling pathway, Th1 and Th2 cell differentiation, cyclic adenosine monophosphate signaling pathway and so on. By integrating the transcriptomics and human PPI data, nine critical genes, including MMP2, MMP9, MMP21,TIMP3, KLF10, CX3CR1, TGFB1, VEGFB, and EGF, were identified in the PPI network analysis.CONCLUSION Taurine promotes the apoptosis of HSCs via up-regulating TGFB1 and then activating the p38 MAPK-JNK-Caspase9/8/3 pathway. These findings enhance the understanding of the molecular mechanism of taurine-induced HSC apoptosis and provide references for liver disorder therapy. 展开更多
关键词 TAURINE Hepatic stellate cells DIFFERENTIALLY EXPRESSED genes Liver FIBROGENESIS TRANSCRIPTOMIC PROTEIN-PROTEIN interaction network
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Protein interaction network related to Helicobacter pylori infection response 被引量:8
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作者 Kyu Kwang Kim Han Bok Kim 《World Journal of Gastroenterology》 SCIE CAS CSCD 2009年第36期4518-4528,共11页
AIM:To understand the complex reaction of gastric inflammation induced by Helicobacter pylori(H pylori) in a systematic manner using a protein interaction network. METHODS:The expression of genes significantly changed... AIM:To understand the complex reaction of gastric inflammation induced by Helicobacter pylori(H pylori) in a systematic manner using a protein interaction network. METHODS:The expression of genes significantly changed on microarray during H pylori infection was scanned from the web literary database and translated into proteins.A network of protein interactions was constructed by searching the primary interactions of selected proteins.The constructed network was mathematically analyzed and its biological function was examined.In addition,the nodes on the network were checked to determine if they had any further functional importance or relation to other proteins by extending them. RESULTS:The scale-free network showing the relationship between inflammation and carcinogenesis was constructed.Mathematical analysis showed hub and bottleneck proteins,and these proteins were mostly related to immune response.The network contained pathways and proteins related to H pylori infection,such as the JAK-STAT pathway triggered by interleukins.Activation of nuclear factor (NF)-κB,TLR4,and other proteins known to function as core proteins of immune response were also found. These immune-related proteins interacted on the network with pathways and proteins related to the cell cycle,cell maintenance and proliferation,andtranscription regulators such as BRCA1,FOS,REL,and zinc finger proteins.The extension of nodes showed interactions of the immune proteins with cancer- related proteins.One extended network,the core network,a summarized form of the extended network, and cell pathway model were constructed. CONCLUSION:Immune-related proteins activated by H pylori infection interact with proto-oncogene proteins.The hub and bottleneck proteins are potential drug targets for gastric inflammation and cancer. 展开更多
关键词 Gastric cancer Helicobacter pylori INFLAMMATION PATHWAY Protein interaction network
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Protein-protein interactions: Methods, databases, and applications in virus-host study 被引量:3
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作者 Qurat ul Ain Farooq Zeeshan Shaukat +1 位作者 Sara Aiman Chun-Hua Li 《World Journal of Virology》 2021年第6期288-300,共13页
Almost all the cellular processes in a living system are controlled by proteins:They regulate gene expression,catalyze chemical reactions,transport small molecules across membranes,and transmit signal across membranes... Almost all the cellular processes in a living system are controlled by proteins:They regulate gene expression,catalyze chemical reactions,transport small molecules across membranes,and transmit signal across membranes.Even,a viral infection is often initiated through virus-host protein interactions.Protein-protein interactions(PPIs)are the physical contacts between two or more proteins and they represent complex biological functions.Nowadays,PPIs have been used to construct PPI networks to study complex pathways for revealing the functions of unknown proteins.Scientists have used PPIs to find the molecular basis of certain diseases and also some potential drug targets.In this review,we will discuss how PPI networks are essential to understand the molecular basis of virus-host relationships and several databases which are dedicated to virus-host interaction studies.Here,we present a short but comprehensive review on PPIs,including the experimental and computational methods of finding PPIs,the databases dedicated to virus-host PPIs,and the associated various applications in protein interaction networks of some lethal viruses with their hosts. 展开更多
关键词 Protein-protein interactions Experimental and computational methods Protein-protein interaction networks Protein-protein interaction databases Disease pathways Protein-protein interaction applications
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Spatial Interaction Network Analysis of Crude Oil Trade Relations between Countries along the Belt and Road 被引量:2
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作者 Qixin WANG Kun QIN +4 位作者 Donghai LIU Gang XU Yanqing XU Yang ZHOU Rui XIAO 《Journal of Geodesy and Geoinformation Science》 2022年第2期60-74,共15页
Based on the theories and methods of complex network,crude oil trade flows between countries along the Belt and Road(B&R,hereafter)are inserted into the Geo-space of B&R and form a spatial interaction network ... Based on the theories and methods of complex network,crude oil trade flows between countries along the Belt and Road(B&R,hereafter)are inserted into the Geo-space of B&R and form a spatial interaction network which takes the countries as nodes and takes the trade relations as edges.The networked mining and evolution analysis can provide important references for the research on trade relations among the B&R countries and the formulation of trade policy.This paper researches and discusses the construction,statistical analysis,top networks and stability of the crude oil trade network between the B&R countries from 2001 to 2020 from the perspectives of Geo-Computation for Social Sciences(GCSS)and spatial interaction.Firstly,evolutions of out-degree,in-degree,out-strength and in-strength of the top 10 countries in the crude oil trade network are computed and analyzed.Secondly,the top network method is used to explore the evolution characteristics of hierarchical structures.And finally,the sequential evolution characteristics of the crude oil trade network stability are analyzed utilizing the network stability measure method based on the trade relationship autocorrelation function.The analysis results show that Russia has the largest out-degree and out-strength,and China has the largest in-degree and in-strength.The crude oil trade volume of the top 10 import and export networks between 2001—2020 accounts for over 90%of the total trade volume of the crude oil trade network,and the proportion remains relatively stable.However,the stability of the network showed strong fluctuations in 2009,2012 and 2014,which may be closely related to major international events in these years,which could furtherly be used to build a correlation model between network volatility and major events.This paper explores how to construct and analyze the spatial interaction network of crude oil trade and can provide references for trade relations research and trade policy formulation of B&R countries. 展开更多
关键词 spatial interaction network Geo-Computation for Social Sciences(GCSS) the Belt and Road Initiative(BRI) trade relation network stability
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Dynamic protein-protein interaction subnetworks of lung cancer in cases with smoking history 被引量:2
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作者 Wei Yu Li-Ran He +3 位作者 Yan-Chao Zhao Man-Him Chan Meng Zhang Miao He 《Chinese Journal of Cancer》 SCIE CAS CSCD 2013年第2期84-90,共7页
Smoking is the primary cause of lung cancer and is linked to 85% of lung cancer cases.However,how lung cancer develops in patients with smoking history remains unclear.Systems approaches that combine human protein-pro... Smoking is the primary cause of lung cancer and is linked to 85% of lung cancer cases.However,how lung cancer develops in patients with smoking history remains unclear.Systems approaches that combine human protein-protein interaction (PPI) networks and gene expression data are superior to traditional methods.We performed these systems to determine the role that smoking plays in lung cancer development and used the support vector machine (SVM) model to predict PPIs.By defining expression variance (EV),we found 520 dynamic proteins (EV>0.4) using data from the Human Protein Reference Database and Gene Expression Omnibus Database,and built 7 dynamic PPI subnetworks of lung cancer in patients with smoking history.We also determined the primary functions of each subnetwork:signal transduction,apoptosis,and cell migration and adhesion for subnetwork A;cell-sustained angiogenesis for subnetwork B;apoptosis for subnetwork C;and,finally,signal transduction and cell replication and proliferation for subnetworks D-G.The probability distribution of the degree of dynamic protein and static protein differed,clearly showing that the dynamic proteins were not the core proteins which widely connected with their neighbor proteins.There were high correlations among the dynamic proteins,suggesting that the dynamic proteins tend to form specific dynamic modules.We also found that the dynamic proteins were only correlated with the expression of selected proteins but not all neighbor proteins when cancer occurred. 展开更多
关键词 蛋白质相互作用 肺癌 子网 吸烟 病例 基因表达数据 人类蛋白质 细胞凋亡
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Drivers for Inter-city Innovation Networks Across Chinese Cities:Modelling Physical Versus Intangible Effects
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作者 GAO Yujie SCHERNGELL Thomas NEULÄNDTNER Martina 《Chinese Geographical Science》 SCIE CSCD 2024年第4期706-721,共16页
Cross-region innovation is widely recognized as an important source of the long-term regional innovation capacity.In the recent past,a growing number of studies has investigated the network structure and mechanisms of... Cross-region innovation is widely recognized as an important source of the long-term regional innovation capacity.In the recent past,a growing number of studies has investigated the network structure and mechanisms of cross-region innovation collaboration in various contexts.However,existing research mainly focuses on physical effects,such as geographical distance and high-speed railway connections.These studies ignore the intangible drivers in a changing environment,the more digitalized economy and the increasingly solidified innovation network structure.Thus,the focus of this study is on estimating determinants of innovation networks,especially on intangible drivers,which have been largely neglected so far.Using city-level data of Chinese patents(excluding Hong Kong,Macao,and Taiwan Province of China),we trace innovation networks across Chinese cities over a long period of time.By integrating a measure on Information and Communications Technology(ICT)development gap and network structural effects into the general proximity framework,this paper explores the changing mechanisms of Chinese innovation networks from a new perspective.The results show that the structure of cross-region innovation networks has changed in China.As mechanisms behind this development,the results confirm the increasingly important role of intangible drivers in Chinese inter-city innovation collaboration when controlling for effects of physical proximity,such as geographical distance.Since digitalization and coordinated development are the mainstream trends in China and other developing countries,these countries'inter-city innovation collaboration patterns will witness dramatic changes under the influence of intangible drivers. 展开更多
关键词 inter-city innovation network co-patents information and communications technology development network structural effect spatial interaction model China
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Virtual Assembly Collision Detection Algorithm Using Backpropagation Neural Network
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作者 Baowei Wang Wen You 《Computers, Materials & Continua》 SCIE EI 2024年第10期1085-1100,共16页
As computer graphics technology continues to advance,Collision Detection(CD)has emerged as a critical element in fields such as virtual reality,computer graphics,and interactive simulations.CD is indispensable for ens... As computer graphics technology continues to advance,Collision Detection(CD)has emerged as a critical element in fields such as virtual reality,computer graphics,and interactive simulations.CD is indispensable for ensuring the fidelity of physical interactions and the realism of virtual environments,particularly within complex scenarios like virtual assembly,where both high precision and real-time responsiveness are imperative.Despite ongoing developments,current CD techniques often fall short in meeting these stringent requirements,resulting in inefficiencies and inaccuracies that impede the overall performance of virtual assembly systems.To address these limitations,this study introduces a novel algorithm that leverages the capabilities of a Backpropagation Neural Network(BPNN)to optimize the structural composition of the Hybrid Bounding Volume Tree(HBVT).Through this optimization,the research proposes a refined Hybrid Hierarchical Bounding Box(HHBB)framework,which is specifically designed to enhance the computational efficiency and precision of CD processes.The HHBB framework strategically reduces the complexity of collision detection computations,thereby enabling more rapid and accurate responses to collision events.Extensive experimental validation within virtual assembly environments reveals that the proposed algorithm markedly improves the performance of CD,particularly in handling complex models.The optimized HBVT architecture not only accelerates the speed of collision detection but also significantly diminishes error rates,presenting a robust and scalable solution for real-time applications in intricate virtual systems.These findings suggest that the proposed approach offers a substantial advancement in CD technology,with broad implications for its application in virtual reality,computer graphics,and related fields. 展开更多
关键词 Collision detection virtual assembly backpropagation neural network real-time interactivity
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Stackelberg Game for Wireless Powered and Backscattering Enabled Sensor Networks
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作者 Lyu Bin Cao Yi +2 位作者 Wang Shuai Guo Haiyan Hao Chengyao 《China Communications》 SCIE CSCD 2024年第3期189-204,共16页
This paper investigates a wireless powered and backscattering enabled sensor network based on the non-linear energy harvesting model, where the power beacon(PB) delivers energy signals to wireless sensors to enable th... This paper investigates a wireless powered and backscattering enabled sensor network based on the non-linear energy harvesting model, where the power beacon(PB) delivers energy signals to wireless sensors to enable their passive backscattering and active transmission to the access point(AP). We propose an efficient time scheduling scheme for network performance enhancement, based on which each sensor can always harvest energy from the PB over the entire block except its time slots allocated for passive and active information delivery. Considering the PB and wireless sensors are from two selfish service providers, we use the Stackelberg game to model the energy interaction among them. To address the non-convexity of the leader-level problem, we propose to decompose the original problem into two subproblems and solve them iteratively in an alternating manner. Specifically, the successive convex approximation, semi-definite relaxation(SDR) and variable substitution techniques are applied to find a nearoptimal solution. To evaluate the performance loss caused by the interaction between two providers, we further investigate the social welfare maximization problem. Numerical results demonstrate that compared to the benchmark schemes, the proposed scheme can achieve up to 35.4% and 38.7% utility gain for the leader and the follower, respectively. 展开更多
关键词 backscatter communication energy interaction stackelberg game wireless powered sensor network
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