Marine organisms cannot grow and reproduce without proper metabolic regulation.Within a metabolic network,problems with a given link will affect the normal life activities of the organism.Many metabolic mechanisms ass...Marine organisms cannot grow and reproduce without proper metabolic regulation.Within a metabolic network,problems with a given link will affect the normal life activities of the organism.Many metabolic mechanisms associated with behaviors of Am-phioctopus fangsiao are still unclear.Moreover,as a factor affecting the normal growth of A.fangsiao,egg protection has rarely been considered in previous behavioral studies.In this research,we analyzed the transcriptome profile of gene expression in A.fangsiao egg-unprotected larvae and egg-protected larvae,and identified 818 differentially expressed genes(DEGs).We used GO and KEGG enrichment analyses to search for metabolism-related DEGs.Protein-protein interaction networks were constructed to examine the interactions between metabolism-related genes.Twenty hub genes with multiple protein-protein interaction relationships or that were involved in multiple KEGG signaling pathways were obtained and verified by quantitative RT-PCR.We first studied the effects of egg protection on the metabolism of A.fangsiao larvae by means of protein-protein interaction networks,and the results provide va-luable gene resources for understanding the metabolism of invertebrate larvae.The data serve as a foundation for further research on the egg-protecting behavior of invertebrates.展开更多
Alpha-synuclein plays an important role in Parkinson's disease(PD).The current study of alpha-synuclein mainly concentrates at the gene level.However, it is found that the study at the protein level has special si...Alpha-synuclein plays an important role in Parkinson's disease(PD).The current study of alpha-synuclein mainly concentrates at the gene level.However, it is found that the study at the protein level has special significance.Meanwhile, there is free information on the Internet, such as databases and algorithms of protein-protein interactions(PPIs).In this paper, a novel method which integrates distributed heterogeneous data sources and algorithms to predict PPIs for alpha-synuclein in silico is proposed.The PPIs generated by the method take advantage of various experimental data, and indicate new information about PPIs for alpha-synuclein.In the end of this paper, the result illustrates that the method is practical.It is hoped that the prediction result obtained by this method can provide guidance for biological experiments of PPIs for alpha-synuclein to reveal possible mechanisms of PD.展开更多
Duplication and divergence have been widely recognized as the two domi- nant evolutionary forces in shaping biological networks, e.g., gene regulatory networks and protein-protein interaction （PPI） networks. It has ...Duplication and divergence have been widely recognized as the two domi- nant evolutionary forces in shaping biological networks, e.g., gene regulatory networks and protein-protein interaction （PPI） networks. It has been shown that the network growth models constructed on the principle of duplication and divergence can recapture the topo- logical properties of real PPI networks. However, such network models only consider the evolution processes. How to select the model parameters with the real biological experi- mental data has not been presented. Therefore, based on the real PPI network statistical data, a yeast PPI network model is constructed. The simulation results indicate that the topological characteristics of the constructed network model are well consistent with those of real PPI networks, especially on sparseness, scale-free, small-world, hierarchical modularity, and disassortativity.展开更多
Searching the maximum bicliques or bipartite subgraphs in a graph is a tough question. We proposed a new and efficient method, Searching Quasi-Bicliques (SQB) algorithm, to detect maximum quasi-bicliques from protein-...Searching the maximum bicliques or bipartite subgraphs in a graph is a tough question. We proposed a new and efficient method, Searching Quasi-Bicliques (SQB) algorithm, to detect maximum quasi-bicliques from protein-protein interaction network. As a Divide-and-Conquer method, SQB consists of three steps: first, it divides the protein-protein interaction network into a number of Distance-2-Subgraphs;second, by combining top-down and branch-and-bound methods, SQB seeks quasi-bicliques from every Distance-2-Subgraph;third, all the redundant results are removed. We successfully applied our method on the Saccharomyces cerevisiae dataset and obtained 2754 distinct quasi-bicliques.展开更多
Domain-domain interactions are important clues to inferring protein-protein interactions. Although about 8 000 domain-domain interactions are discovered so far,they are just the tip of the iceberg. Because domains are...Domain-domain interactions are important clues to inferring protein-protein interactions. Although about 8 000 domain-domain interactions are discovered so far,they are just the tip of the iceberg. Because domains are conservative and commonplace in proteins,domain-domain interactions are discovered based on pairs of domains which significantly co-exist in proteins. Meanwhile,it is realized that:( 1) domain-domain interactions may exist within the same proteins or across different proteins;( 2) only the domain-domain interactions across different proteins can mediate interactions between proteins;( 3) domains have biases to interact with other domains. And then,a novel method is put forward to construct protein-protein interaction network by using domain-domain interactions. The method is validated by experiments and compared with the state- of-art methods in the field. The experimental results suggest that the method is reasonable and effectiveness on constructing Protein-protein interactions network.展开更多
To explore the molecular mechanism of Ind-igo Naturalis in intervening chronic myelocytic leukemia （CML） under the guidance of protein-protein interaction network, the molecular docking technique and in vitro c...To explore the molecular mechanism of Ind-igo Naturalis in intervening chronic myelocytic leukemia （CML） under the guidance of protein-protein interaction network, the molecular docking technique and in vitro cell experiment were chosen. CML-related genes were obtained from the online mendelian inheritance in man database （OMIM）, then String 10. 0 was used for text mining and constructing the CML protein-protein interaction network. The interaction data were input in Cytoscape 3. 4. 0 software. Plug-in CentiScaPe 2. 1 was used for implement topology analysis. Small active substances of Indigo Naturalis were obtained from a third-party database, which were optimized by Chemoffice 8. 0 and Sybyl 8. 1, then small molecular ligand library was obtained. The molecular docking was carried out by Surflex-Dock module, the key target was received after scoring. Protein-protein interaction network of CML was constructed, which was consisted of 425 nodes （ proteins） and 2 799 sides （ interactions）. The key gene J.AK2 was got. CML is a polygenic disease and JAK2 is likely to be a key node.展开更多
Owing to intensified globalization and informatization,the structures of the urban scale hierarchy and urban networks between cities have become increasingly intertwined,resulting in different spatial effects.Therefor...Owing to intensified globalization and informatization,the structures of the urban scale hierarchy and urban networks between cities have become increasingly intertwined,resulting in different spatial effects.Therefore,this paper analyzes the spatial interaction between urban scale hierarchy and urban networks in China from 2019 to 2023,drawing on Baidu migration data and employing a spatial simultaneous equation model.The results reveal a significant positive spatial correlation between cities with higher hierarchy and those with greater network centrality.Within a static framework,we identify a positive interaction between urban scale hierarchy and urban network centrality,while their spatial cross-effects manifest as negative neighborhood interactions based on geographical distance and positive cross-scale interactions shaped by network connections.Within a dynamic framework,changes in urban scale hierarchy and urban networks are mutually reinforcing,thereby widening disparities within the urban hierarchy.Furthermore,an increase in a city’s network centrality had a dampening effect on the population growth of neighboring cities and network-connected cities.This study enhances understanding of the spatial organisation of urban systems and offers insights for coordinated regional development.展开更多
Recognizing human interactions in RGB videos is a critical task in computer vision,with applications in video surveillance.Existing deep learning-based architectures have achieved strong results,but are computationall...Recognizing human interactions in RGB videos is a critical task in computer vision,with applications in video surveillance.Existing deep learning-based architectures have achieved strong results,but are computationally intensive,sensitive to video resolution changes and often fail in crowded scenes.We propose a novel hybrid system that is computationally efficient,robust to degraded video quality and able to filter out irrelevant individuals,making it suitable for real-life use.The system leverages multi-modal handcrafted features for interaction representation and a deep learning classifier for capturing complex dependencies.Using Mask R-CNN and YOLO11-Pose,we extract grayscale silhouettes and keypoint coordinates of interacting individuals,while filtering out irrelevant individuals using a proposed algorithm.From these,we extract silhouette-based features(local ternary pattern and histogram of optical flow)and keypoint-based features(distances,angles and velocities)that capture distinct spatial and temporal information.A Bidirectional Long Short-Term Memory network(BiLSTM)then classifies the interactions.Extensive experiments on the UT Interaction,SBU Kinect Interaction and the ISR-UOL 3D social activity datasets demonstrate that our system achieves competitive accuracy.They also validate the effectiveness of the chosen features and classifier,along with the proposed system’s computational efficiency and robustness to occlusion.展开更多
Background:Triple-negative breast cancer(TNBC),characterized by its lack of traditional hormone receptors and HER2,presents a significant challenge in oncology due to its poor response to conventional therapies.Autoph...Background:Triple-negative breast cancer(TNBC),characterized by its lack of traditional hormone receptors and HER2,presents a significant challenge in oncology due to its poor response to conventional therapies.Autophagy is an important process for maintaining cellular homeostasis,and there are currently autophagy biomarkers that play an effective role in the clinical treatment of tumors.In contrast to targeting protein activity,intervention with proteinprotein interaction(PPI)can avoid unrelated crosstalk and regulate the autophagy process with minimal interference pathways.Methods:Here,we employed Naive Bayes,Decision Tree,and k-Nearest Neighbors to elucidate the complex PPI network associated with autophagy in TNBC,aiming to uncover novel therapeutic targets.Meanwhile,the candidate proteins interacting with Beclin 2 were initially screened in MDA-MB-231 cells using Beclin 2 as bait protein by immunoprecipitation-mass spectrometry assay,and the interaction relationship was verified by molecular docking and CO-IP experiments after intersection.Colony formation,cellular immunofluorescence,cell scratch and 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide(MTT)tests were used to predict the clinical therapeutic effects of manipulating candidate PPI.Results:By developing three PPI classification models and analyzing over 13,000 datasets,we identified 3733 previously unknown autophagy-related PPIs.Our network analysis revealed the central role of Beclin 2 in autophagy regulation,uncovering its interactions with 39 newly identified proteins.Notably,the CO-IP studies identified the substantial interaction between Beclin 2 and Ubiquilin 1,which was anticipated by our model and discovered in immunoprecipitation-mass spectrometry assay results.Subsequently,in vitro investigations showed that overexpressing Beclin 2 increased Ubiquilin 1,promoted autophagy-dependent cell death,and inhibited proliferation and metastasis in MDA-MB-231 cells.Conclusions:This study not only enhances our understanding of autophagy regulation in TNBC but also identifies the Beclin 2-Ubiquilin 1 axis as a promising target for precision therapy.These findings open new avenues for drug discovery and offer inspiration for more effective treatments for this aggressive cancer subtype.展开更多
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
Drug-drug interaction(DDI)refers to the interaction between two or more drugs in the body,altering their efficacy or pharmacokinetics.Fully considering and accurately predicting DDI has become an indispensable part of...Drug-drug interaction(DDI)refers to the interaction between two or more drugs in the body,altering their efficacy or pharmacokinetics.Fully considering and accurately predicting DDI has become an indispensable part of ensuring safe medication for patients.In recent years,many deep learning-based methods have been proposed to predict DDI.However,most existing computational models tend to oversimplify the fusion of drug structural and topological information,often relying on methods such as splicing or weighted summation,which fail to adequately capture the potential complementarity between structural and topological features.This loss of information may lead to models that do not fully leverage these features,thus limiting their performance in DDI prediction.To address these challenges,we propose a relation-aware cross adversarial network for predicting DDI,named RCAN-DDI,which combines a relationship-aware structure feature learning module and a topological feature learning module based on DDI networks to capture multimodal features of drugs.To explore the correlations and complementarities among different information sources,the cross-adversarial network is introduced to fully integrate features from various modalities,enhancing the predictive performance of the model.The experimental results demonstrate that the RCAN-DDI method outperforms other methods.Even in cases of labelled DDI scarcity,the method exhibits good robustness in the DDI prediction task.Furthermore,the effectiveness of the cross-adversarial module is validated through ablation experiments,demonstrating its superiority in learning multimodal complementary information.展开更多
Achieving a reduction in global greenhouse gas(GHG)emissions requires collaborative efforts from the international community;however,a comprehensive understanding of the spatiotemporal characteristics(i.e.,complex emi...Achieving a reduction in global greenhouse gas(GHG)emissions requires collaborative efforts from the international community;however,a comprehensive understanding of the spatiotemporal characteristics(i.e.,complex emission networks and driver patterns)and the mutual influence of gross domestic product(GDP)and GHG emissions remains limited at a global level in the 21st century,which is not conducive to forming a consensus in global climate change negotiations and formulating relevant policies.To fill these gaps,this study comprehensively analyzes the complex network and driver pattern of GHG emissions,as well as the corresponding mutual influence with GDP for 185 countries during 2000-2021,based on social network analysis,the logarithmic Divisia decomposition approach,and panel vector autoregression model at global and regional levels.The results indicate that significant heterogeneity and inequality exist in terms of GHG emissions among regions and countries in different geographical areas and economic income levels.Additionally,GDP per capita and GHG emission intensity are the largest positive and negative drivers,respectively,affecting the increase in global GHG emissions.Furthermore,key countries,such as Germany and Canada,that could serve as coordinating bridges to strengthen collaboration in the global emission network are identified.This study highlights the need to encourage key participants in the emission network and foster international cooperation in governance,energy technology,and economic investment to address climate change.展开更多
Under the dual background of global urbanization and climate change,challenges such as urban waterlogging,degradation of water environment,and fragmentation of biological habitats are intensifying.Advancing the transf...Under the dual background of global urbanization and climate change,challenges such as urban waterlogging,degradation of water environment,and fragmentation of biological habitats are intensifying.Advancing the transformation of blue-green infrastructure from a single function to multiple coordinated functions has emerged as a critical path for enhancing urban ecological resilience.The Catharijnesingel Canal Park in Utrecht,the Netherlands,serves as a case study to investigate the synergistic interaction of hydrological regulation and habitat network construction through the transformation of historical canals from grey to blue-green infrastructure.Initially,the implementation path of this“blue-green renaissance”is analyzed,followed by a detailed examination of the spatial realization patterns and mechanisms underlying hydrology and habitat synergy,focusing on river form remodeling,vegetation community alignment,and precise habitat design.The results indicate that the collaborative model of“hydrology and habitat”coupling not only enhances rain-flood resilience,biodiversity,and the quality of public spaces in urban areas but also serves as a reference model for high-density urban regeneration by integrating space,ecology,and efficiency.This model offers both a theoretical foundation and practical guidance for Chinese cities aiming to achieve functional integration and synergistic interaction in ecological restoration and the development of bluegreen spaces.展开更多
With the increasing importance of multimodal data in emotional expression on social media,mainstream methods for sentiment analysis have shifted from unimodal to multimodal approaches.However,the challenges of extract...With the increasing importance of multimodal data in emotional expression on social media,mainstream methods for sentiment analysis have shifted from unimodal to multimodal approaches.However,the challenges of extracting high-quality emotional features and achieving effective interaction between different modalities remain two major obstacles in multimodal sentiment analysis.To address these challenges,this paper proposes a Text-Gated Interaction Network with Inter-Sample Commonality Perception(TGICP).Specifically,we utilize a Inter-sample Commonality Perception(ICP)module to extract common features from similar samples within the same modality,and use these common features to enhance the original features of each modality,thereby obtaining a richer and more complete multimodal sentiment representation.Subsequently,in the cross-modal interaction stage,we design a Text-Gated Interaction(TGI)module,which is text-driven.By calculating the mutual information difference between the text modality and nonverbal modalities,the TGI module dynamically adjusts the influence of emotional information from the text modality on nonverbal modalities.This helps to reduce modality information asymmetry while enabling full cross-modal interaction.Experimental results show that the proposed model achieves outstanding performance on both the CMU-MOSI and CMU-MOSEI baseline multimodal sentiment analysis datasets,validating its effectiveness in emotion recognition tasks.展开更多
Computational approaches for predicting drug-target interactions(DTIs)are pivotal in advancing drug discovery.Current methodologies leveraging heterogeneous networks often fall short in fully integrating both local an...Computational approaches for predicting drug-target interactions(DTIs)are pivotal in advancing drug discovery.Current methodologies leveraging heterogeneous networks often fall short in fully integrating both local and global network information.To comprehensively consider network information,we propose DHGT-DTI,a novel deep learning-based approach for DTI prediction.Specifically,we capture the local and global structural information of the network from both neighborhood and meta-path per-spectives.In the neighborhood perspective,we employ a heterogeneous graph neural network(HGNN),which extends Graph Sample and Aggregate(GraphSAGE)to handle diverse node and edge types,effectively learning local network structures.In the meta-path perspective,we introduce a Graph Transformer with residual connections to model higher-order relationships defined by meta-paths,such as"drug-disease-drug",and use an attention mechanism to fuse information across multiple meta-paths.The learned features from these dual perspectives are synergistically integrated for DTI prediction via a matrix decomposition method.Furthermore,DHGT-DTI reconstructs not only the DTI network but also auxiliary networks to bolster prediction accuracy.Comprehensive experiments on two benchmark datasets validate the superiority of DHGT-DTI over existing baseline methods.Additionally,case studies on six drugs used to treat Parkinson's disease not only validate the practical utility of DHGT-DTI but also highlight its broader potential in accelerating drug discovery for other diseases.展开更多
Proteins carry out their functions by interacting with other proteins and small molecules, forming a complex interaction network. In this review, we briefly introduce classical graph theory based protein-protein inter...Proteins carry out their functions by interacting with other proteins and small molecules, forming a complex interaction network. In this review, we briefly introduce classical graph theory based protein-protein interaction networks. We also describe the commonly used experimental methods to construct these networks, and the insights that can be gained from these networks. We then discuss the recent transition from graph theory based networks to structure based protein-protein interaction networks and the advantages of the latter over the former, using two networks as examples. We further discuss the usefulness of structure based protein-protein interaction networks for drug discovery, with a special emphasis on drug repositioning.展开更多
Proteins usually bind together to form complexes, which play an important role in cellular activities. Many graph clustering methods have been proposed to identify protein complexes by finding dense regions in protein...Proteins usually bind together to form complexes, which play an important role in cellular activities. Many graph clustering methods have been proposed to identify protein complexes by finding dense regions in protein-protein interaction networks. We present a novel framework （CPL） that detects protein complexes by propagating labels through interactions in a network, in which labels denote complex identifiers. With proper propagation in CPL, proteins in the same complex will be assigned with the same labels. CPL does not make any strong assumptions about the topological structures of the complexes, as in previous methods. Tile CPL algorithm is tested on several publicly available yeast protein-protein interaction networks and compared with several state-of-the-art methods. The results suggest that CPL performs better than the existing methods. An analysis of the functional homogeneity based on a gene ontology analysis shows that the detected complexes of CPL are highly biologically relevant.展开更多
Plants are frequently affected by pathogen infections.To effectively defend against such infections,two major modes of innate immunity have evolved in plants;pathogen-associated molecular pattern-triggered immunity an...Plants are frequently affected by pathogen infections.To effectively defend against such infections,two major modes of innate immunity have evolved in plants;pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity.Although the molecular components as well as the corresponding pathways involved in these two processes have been identified,many aspects of the molecular mechanisms of the plant immune system remain elusive.Recently,the rapid development of omics techniques(e.g.,genomics,proteomics and transcriptomics) has provided a great opportunity to explore plant–pathogen interactions from a systems perspective and studies on protein–protein interactions(PPIs) between plants and pathogens have been carried out and characterized at the network level.In this review,we introduce experimental and computational identification methods of PPIs,popular PPI network analysis approaches,and existing bioinformatics resources/tools related to PPIs.Then,we focus on reviewing the progress in genome-wide PPI networks related to plant–pathogen interactions,including pathogen-centric PPI networks,plant-centric PPI networks and interspecies PPI networks between plants and pathogens.We anticipate genome-wide PPI network analysis will provide a clearer understanding of plant–pathogen interactions and will offer some new opportunities for crop protection and improvement.展开更多
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
基金supported by the earmarked fund for the Modern Agro-industry Technology Research System(No.CARS-49)the Natural Science Foundation of Shan-dong Province(No.ZR2019BC052)the National Natural Science Foundation of China(No.42006077).
文摘Marine organisms cannot grow and reproduce without proper metabolic regulation.Within a metabolic network,problems with a given link will affect the normal life activities of the organism.Many metabolic mechanisms associated with behaviors of Am-phioctopus fangsiao are still unclear.Moreover,as a factor affecting the normal growth of A.fangsiao,egg protection has rarely been considered in previous behavioral studies.In this research,we analyzed the transcriptome profile of gene expression in A.fangsiao egg-unprotected larvae and egg-protected larvae,and identified 818 differentially expressed genes(DEGs).We used GO and KEGG enrichment analyses to search for metabolism-related DEGs.Protein-protein interaction networks were constructed to examine the interactions between metabolism-related genes.Twenty hub genes with multiple protein-protein interaction relationships or that were involved in multiple KEGG signaling pathways were obtained and verified by quantitative RT-PCR.We first studied the effects of egg protection on the metabolism of A.fangsiao larvae by means of protein-protein interaction networks,and the results provide va-luable gene resources for understanding the metabolism of invertebrate larvae.The data serve as a foundation for further research on the egg-protecting behavior of invertebrates.
基金supported by the National Basic Research Program of China (Grant No.2006CB500702)the Shanghai Lead-ing Academic Discipline Project (Grant No.J50103)Shanghai University Systems Biology Reasearch Funding (GrantNo.SBR08001)
文摘Alpha-synuclein plays an important role in Parkinson's disease(PD).The current study of alpha-synuclein mainly concentrates at the gene level.However, it is found that the study at the protein level has special significance.Meanwhile, there is free information on the Internet, such as databases and algorithms of protein-protein interactions(PPIs).In this paper, a novel method which integrates distributed heterogeneous data sources and algorithms to predict PPIs for alpha-synuclein in silico is proposed.The PPIs generated by the method take advantage of various experimental data, and indicate new information about PPIs for alpha-synuclein.In the end of this paper, the result illustrates that the method is practical.It is hoped that the prediction result obtained by this method can provide guidance for biological experiments of PPIs for alpha-synuclein to reveal possible mechanisms of PD.
基金Project supported by the National Natural Science Foundation of China(No.11172158)
文摘Duplication and divergence have been widely recognized as the two domi- nant evolutionary forces in shaping biological networks, e.g., gene regulatory networks and protein-protein interaction （PPI） networks. It has been shown that the network growth models constructed on the principle of duplication and divergence can recapture the topo- logical properties of real PPI networks. However, such network models only consider the evolution processes. How to select the model parameters with the real biological experi- mental data has not been presented. Therefore, based on the real PPI network statistical data, a yeast PPI network model is constructed. The simulation results indicate that the topological characteristics of the constructed network model are well consistent with those of real PPI networks, especially on sparseness, scale-free, small-world, hierarchical modularity, and disassortativity.
文摘Searching the maximum bicliques or bipartite subgraphs in a graph is a tough question. We proposed a new and efficient method, Searching Quasi-Bicliques (SQB) algorithm, to detect maximum quasi-bicliques from protein-protein interaction network. As a Divide-and-Conquer method, SQB consists of three steps: first, it divides the protein-protein interaction network into a number of Distance-2-Subgraphs;second, by combining top-down and branch-and-bound methods, SQB seeks quasi-bicliques from every Distance-2-Subgraph;third, all the redundant results are removed. We successfully applied our method on the Saccharomyces cerevisiae dataset and obtained 2754 distinct quasi-bicliques.
基金Sponsored by the National Natural Science Foundation of China(Grant No.61271346,61571163,61532014,91335112 and 61402132)the Fundamental Research Funds for the Central Universities(Grant No.DB13AB02)
文摘Domain-domain interactions are important clues to inferring protein-protein interactions. Although about 8 000 domain-domain interactions are discovered so far,they are just the tip of the iceberg. Because domains are conservative and commonplace in proteins,domain-domain interactions are discovered based on pairs of domains which significantly co-exist in proteins. Meanwhile,it is realized that:( 1) domain-domain interactions may exist within the same proteins or across different proteins;( 2) only the domain-domain interactions across different proteins can mediate interactions between proteins;( 3) domains have biases to interact with other domains. And then,a novel method is put forward to construct protein-protein interaction network by using domain-domain interactions. The method is validated by experiments and compared with the state- of-art methods in the field. The experimental results suggest that the method is reasonable and effectiveness on constructing Protein-protein interactions network.
文摘To explore the molecular mechanism of Ind-igo Naturalis in intervening chronic myelocytic leukemia （CML） under the guidance of protein-protein interaction network, the molecular docking technique and in vitro cell experiment were chosen. CML-related genes were obtained from the online mendelian inheritance in man database （OMIM）, then String 10. 0 was used for text mining and constructing the CML protein-protein interaction network. The interaction data were input in Cytoscape 3. 4. 0 software. Plug-in CentiScaPe 2. 1 was used for implement topology analysis. Small active substances of Indigo Naturalis were obtained from a third-party database, which were optimized by Chemoffice 8. 0 and Sybyl 8. 1, then small molecular ligand library was obtained. The molecular docking was carried out by Surflex-Dock module, the key target was received after scoring. Protein-protein interaction network of CML was constructed, which was consisted of 425 nodes （ proteins） and 2 799 sides （ interactions）. The key gene J.AK2 was got. CML is a polygenic disease and JAK2 is likely to be a key node.
基金Under the auspices of the National Natural Science Foundation of China(No.42371222,41971167)Fundamental Scientific Research Funds of Central China Normal University(No.CCNU24ZZ120)。
文摘Owing to intensified globalization and informatization,the structures of the urban scale hierarchy and urban networks between cities have become increasingly intertwined,resulting in different spatial effects.Therefore,this paper analyzes the spatial interaction between urban scale hierarchy and urban networks in China from 2019 to 2023,drawing on Baidu migration data and employing a spatial simultaneous equation model.The results reveal a significant positive spatial correlation between cities with higher hierarchy and those with greater network centrality.Within a static framework,we identify a positive interaction between urban scale hierarchy and urban network centrality,while their spatial cross-effects manifest as negative neighborhood interactions based on geographical distance and positive cross-scale interactions shaped by network connections.Within a dynamic framework,changes in urban scale hierarchy and urban networks are mutually reinforcing,thereby widening disparities within the urban hierarchy.Furthermore,an increase in a city’s network centrality had a dampening effect on the population growth of neighboring cities and network-connected cities.This study enhances understanding of the spatial organisation of urban systems and offers insights for coordinated regional development.
基金supported and funded by Princess Nourah bint Abdulrahman University Researchers Supporting Project number(PNURSP2025R410),Princess Nourah bint Abdulrahman University,Riyadh,Saudi Arabia.
文摘Recognizing human interactions in RGB videos is a critical task in computer vision,with applications in video surveillance.Existing deep learning-based architectures have achieved strong results,but are computationally intensive,sensitive to video resolution changes and often fail in crowded scenes.We propose a novel hybrid system that is computationally efficient,robust to degraded video quality and able to filter out irrelevant individuals,making it suitable for real-life use.The system leverages multi-modal handcrafted features for interaction representation and a deep learning classifier for capturing complex dependencies.Using Mask R-CNN and YOLO11-Pose,we extract grayscale silhouettes and keypoint coordinates of interacting individuals,while filtering out irrelevant individuals using a proposed algorithm.From these,we extract silhouette-based features(local ternary pattern and histogram of optical flow)and keypoint-based features(distances,angles and velocities)that capture distinct spatial and temporal information.A Bidirectional Long Short-Term Memory network(BiLSTM)then classifies the interactions.Extensive experiments on the UT Interaction,SBU Kinect Interaction and the ISR-UOL 3D social activity datasets demonstrate that our system achieves competitive accuracy.They also validate the effectiveness of the chosen features and classifier,along with the proposed system’s computational efficiency and robustness to occlusion.
基金the National Natural Science Foundation of China(Nos.22307009,82374155,82073997,82104376)the Sichuan Science and Technology Program(Nos.2023NSFSC1108,2024NSFTD0023)+1 种基金the Postdoctoral Research Project of Sichuan Provincethe Xinglin Scholar Research Promotion Project of Chengdu University of TCM.
文摘Background:Triple-negative breast cancer(TNBC),characterized by its lack of traditional hormone receptors and HER2,presents a significant challenge in oncology due to its poor response to conventional therapies.Autophagy is an important process for maintaining cellular homeostasis,and there are currently autophagy biomarkers that play an effective role in the clinical treatment of tumors.In contrast to targeting protein activity,intervention with proteinprotein interaction(PPI)can avoid unrelated crosstalk and regulate the autophagy process with minimal interference pathways.Methods:Here,we employed Naive Bayes,Decision Tree,and k-Nearest Neighbors to elucidate the complex PPI network associated with autophagy in TNBC,aiming to uncover novel therapeutic targets.Meanwhile,the candidate proteins interacting with Beclin 2 were initially screened in MDA-MB-231 cells using Beclin 2 as bait protein by immunoprecipitation-mass spectrometry assay,and the interaction relationship was verified by molecular docking and CO-IP experiments after intersection.Colony formation,cellular immunofluorescence,cell scratch and 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide(MTT)tests were used to predict the clinical therapeutic effects of manipulating candidate PPI.Results:By developing three PPI classification models and analyzing over 13,000 datasets,we identified 3733 previously unknown autophagy-related PPIs.Our network analysis revealed the central role of Beclin 2 in autophagy regulation,uncovering its interactions with 39 newly identified proteins.Notably,the CO-IP studies identified the substantial interaction between Beclin 2 and Ubiquilin 1,which was anticipated by our model and discovered in immunoprecipitation-mass spectrometry assay results.Subsequently,in vitro investigations showed that overexpressing Beclin 2 increased Ubiquilin 1,promoted autophagy-dependent cell death,and inhibited proliferation and metastasis in MDA-MB-231 cells.Conclusions:This study not only enhances our understanding of autophagy regulation in TNBC but also identifies the Beclin 2-Ubiquilin 1 axis as a promising target for precision therapy.These findings open new avenues for drug discovery and offer inspiration for more effective treatments for this aggressive cancer subtype.
基金the National Natural Science Foundation of China,No.81360595 and No.81860790Guangxi Natural Science Foundation Program,No.KJT13066+2 种基金the Bagui Scholars Foundation Program of Guangxithe Special-term Experts Foundation Program of Guangxithe Project of Guangxi Young Teacher Fundamental Ability Promotion,No.2017KY0298
文摘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.
基金supported by the Natural Science Foundation of Shandong Province(Grant No.:ZR2023MF053)the National Natural Science Foundation of China(Grant No.:61902430).
文摘Drug-drug interaction(DDI)refers to the interaction between two or more drugs in the body,altering their efficacy or pharmacokinetics.Fully considering and accurately predicting DDI has become an indispensable part of ensuring safe medication for patients.In recent years,many deep learning-based methods have been proposed to predict DDI.However,most existing computational models tend to oversimplify the fusion of drug structural and topological information,often relying on methods such as splicing or weighted summation,which fail to adequately capture the potential complementarity between structural and topological features.This loss of information may lead to models that do not fully leverage these features,thus limiting their performance in DDI prediction.To address these challenges,we propose a relation-aware cross adversarial network for predicting DDI,named RCAN-DDI,which combines a relationship-aware structure feature learning module and a topological feature learning module based on DDI networks to capture multimodal features of drugs.To explore the correlations and complementarities among different information sources,the cross-adversarial network is introduced to fully integrate features from various modalities,enhancing the predictive performance of the model.The experimental results demonstrate that the RCAN-DDI method outperforms other methods.Even in cases of labelled DDI scarcity,the method exhibits good robustness in the DDI prediction task.Furthermore,the effectiveness of the cross-adversarial module is validated through ablation experiments,demonstrating its superiority in learning multimodal complementary information.
基金supported by the Humanities and Social Sciences Youth Foundation,Ministry of Education of China[Grant No.24YJC630248]Sichuan Office of Philosophy and Social Science,China[Grant No.SCJJ24ND299].
文摘Achieving a reduction in global greenhouse gas(GHG)emissions requires collaborative efforts from the international community;however,a comprehensive understanding of the spatiotemporal characteristics(i.e.,complex emission networks and driver patterns)and the mutual influence of gross domestic product(GDP)and GHG emissions remains limited at a global level in the 21st century,which is not conducive to forming a consensus in global climate change negotiations and formulating relevant policies.To fill these gaps,this study comprehensively analyzes the complex network and driver pattern of GHG emissions,as well as the corresponding mutual influence with GDP for 185 countries during 2000-2021,based on social network analysis,the logarithmic Divisia decomposition approach,and panel vector autoregression model at global and regional levels.The results indicate that significant heterogeneity and inequality exist in terms of GHG emissions among regions and countries in different geographical areas and economic income levels.Additionally,GDP per capita and GHG emission intensity are the largest positive and negative drivers,respectively,affecting the increase in global GHG emissions.Furthermore,key countries,such as Germany and Canada,that could serve as coordinating bridges to strengthen collaboration in the global emission network are identified.This study highlights the need to encourage key participants in the emission network and foster international cooperation in governance,energy technology,and economic investment to address climate change.
基金Sponsored by 2025 Postgraduate Teaching Reform Project of North China University of Technology。
文摘Under the dual background of global urbanization and climate change,challenges such as urban waterlogging,degradation of water environment,and fragmentation of biological habitats are intensifying.Advancing the transformation of blue-green infrastructure from a single function to multiple coordinated functions has emerged as a critical path for enhancing urban ecological resilience.The Catharijnesingel Canal Park in Utrecht,the Netherlands,serves as a case study to investigate the synergistic interaction of hydrological regulation and habitat network construction through the transformation of historical canals from grey to blue-green infrastructure.Initially,the implementation path of this“blue-green renaissance”is analyzed,followed by a detailed examination of the spatial realization patterns and mechanisms underlying hydrology and habitat synergy,focusing on river form remodeling,vegetation community alignment,and precise habitat design.The results indicate that the collaborative model of“hydrology and habitat”coupling not only enhances rain-flood resilience,biodiversity,and the quality of public spaces in urban areas but also serves as a reference model for high-density urban regeneration by integrating space,ecology,and efficiency.This model offers both a theoretical foundation and practical guidance for Chinese cities aiming to achieve functional integration and synergistic interaction in ecological restoration and the development of bluegreen spaces.
基金supported by the Natural Science Foundation of Henan under Grant 242300421220the Henan Provincial Science and Technology Research Project under Grants 252102211047 and 252102211062+3 种基金the Jiangsu Provincial Scheme Double Initiative Plan JSS-CBS20230474the XJTLU RDF-21-02-008the Science and Technology Innovation Project of Zhengzhou University of Light Industry under Grant 23XNKJTD0205the Higher Education Teaching Reform Research and Practice Project of Henan Province under Grant 2024SJGLX0126.
文摘With the increasing importance of multimodal data in emotional expression on social media,mainstream methods for sentiment analysis have shifted from unimodal to multimodal approaches.However,the challenges of extracting high-quality emotional features and achieving effective interaction between different modalities remain two major obstacles in multimodal sentiment analysis.To address these challenges,this paper proposes a Text-Gated Interaction Network with Inter-Sample Commonality Perception(TGICP).Specifically,we utilize a Inter-sample Commonality Perception(ICP)module to extract common features from similar samples within the same modality,and use these common features to enhance the original features of each modality,thereby obtaining a richer and more complete multimodal sentiment representation.Subsequently,in the cross-modal interaction stage,we design a Text-Gated Interaction(TGI)module,which is text-driven.By calculating the mutual information difference between the text modality and nonverbal modalities,the TGI module dynamically adjusts the influence of emotional information from the text modality on nonverbal modalities.This helps to reduce modality information asymmetry while enabling full cross-modal interaction.Experimental results show that the proposed model achieves outstanding performance on both the CMU-MOSI and CMU-MOSEI baseline multimodal sentiment analysis datasets,validating its effectiveness in emotion recognition tasks.
基金the National Natural Science Foundation of China(Grant Nos.:62272288,U22A2041)Fundamental Research Funds for the Central Universities,Shaanxi Normal University(Grant No.:GK202302006)the Scientific Research Fund of Hunan Provincial Education Department of China(Grant No.:22B0097).
文摘Computational approaches for predicting drug-target interactions(DTIs)are pivotal in advancing drug discovery.Current methodologies leveraging heterogeneous networks often fall short in fully integrating both local and global network information.To comprehensively consider network information,we propose DHGT-DTI,a novel deep learning-based approach for DTI prediction.Specifically,we capture the local and global structural information of the network from both neighborhood and meta-path per-spectives.In the neighborhood perspective,we employ a heterogeneous graph neural network(HGNN),which extends Graph Sample and Aggregate(GraphSAGE)to handle diverse node and edge types,effectively learning local network structures.In the meta-path perspective,we introduce a Graph Transformer with residual connections to model higher-order relationships defined by meta-paths,such as"drug-disease-drug",and use an attention mechanism to fuse information across multiple meta-paths.The learned features from these dual perspectives are synergistically integrated for DTI prediction via a matrix decomposition method.Furthermore,DHGT-DTI reconstructs not only the DTI network but also auxiliary networks to bolster prediction accuracy.Comprehensive experiments on two benchmark datasets validate the superiority of DHGT-DTI over existing baseline methods.Additionally,case studies on six drugs used to treat Parkinson's disease not only validate the practical utility of DHGT-DTI but also highlight its broader potential in accelerating drug discovery for other diseases.
基金This work was funded by grants from the National Natural Science Foundation of China （NSFC） （Grant No. 31210103916 and 91019019）, Chinese Ministry of Science and Technology （Grant No. 2011CB504206） and Chinese Academy of Sciences （CAS） （Grant Nos. KSCX2-EW-R-02 and KSCX2-EW-J-15） and stem cell leading project XDA01010303 to J.D.J.H.H.N. was supported by the Chinese Academy of Sciences Fellow- ship for Young International Scientist [Grant No. 2012Y1SB0006] and the National Natural Science Foundation of China [Grant No. 31250110524]. The authors thank Dr. Jerome Boyd-Kirkup for extensive editing and Hamna Anwar for proofreading the manu- script.
文摘Proteins carry out their functions by interacting with other proteins and small molecules, forming a complex interaction network. In this review, we briefly introduce classical graph theory based protein-protein interaction networks. We also describe the commonly used experimental methods to construct these networks, and the insights that can be gained from these networks. We then discuss the recent transition from graph theory based networks to structure based protein-protein interaction networks and the advantages of the latter over the former, using two networks as examples. We further discuss the usefulness of structure based protein-protein interaction networks for drug discovery, with a special emphasis on drug repositioning.
基金supported by the National Natural Science Foundation of China under Grant Nos.61271346,61172098,and91335112the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No.20112302110040the Fundamental Research Funds for the Central Universities of China under Grant No.HIT.KISTP.201418
文摘Proteins usually bind together to form complexes, which play an important role in cellular activities. Many graph clustering methods have been proposed to identify protein complexes by finding dense regions in protein-protein interaction networks. We present a novel framework （CPL） that detects protein complexes by propagating labels through interactions in a network, in which labels denote complex identifiers. With proper propagation in CPL, proteins in the same complex will be assigned with the same labels. CPL does not make any strong assumptions about the topological structures of the complexes, as in previous methods. Tile CPL algorithm is tested on several publicly available yeast protein-protein interaction networks and compared with several state-of-the-art methods. The results suggest that CPL performs better than the existing methods. An analysis of the functional homogeneity based on a gene ontology analysis shows that the detected complexes of CPL are highly biologically relevant.
基金supported by grants from the National Natural Science Foundation of China(31271414,31471249)
文摘Plants are frequently affected by pathogen infections.To effectively defend against such infections,two major modes of innate immunity have evolved in plants;pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity.Although the molecular components as well as the corresponding pathways involved in these two processes have been identified,many aspects of the molecular mechanisms of the plant immune system remain elusive.Recently,the rapid development of omics techniques(e.g.,genomics,proteomics and transcriptomics) has provided a great opportunity to explore plant–pathogen interactions from a systems perspective and studies on protein–protein interactions(PPIs) between plants and pathogens have been carried out and characterized at the network level.In this review,we introduce experimental and computational identification methods of PPIs,popular PPI network analysis approaches,and existing bioinformatics resources/tools related to PPIs.Then,we focus on reviewing the progress in genome-wide PPI networks related to plant–pathogen interactions,including pathogen-centric PPI networks,plant-centric PPI networks and interspecies PPI networks between plants and pathogens.We anticipate genome-wide PPI network analysis will provide a clearer understanding of plant–pathogen interactions and will offer some new opportunities for crop protection and improvement.
基金supported by grants from the National Natural Science Foundation of China (No. 91130009)Science and Technology Planning Project of Guangdong Province of China (No. 2003A3080503)
文摘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.
