Maize （Zea mays） is the most widely grown grain crop in the world, playing important roles in agriculture and industry. However, the functions of maize genes remain largely unknown. High-quality genome- wide transcr...Maize （Zea mays） is the most widely grown grain crop in the world, playing important roles in agriculture and industry. However, the functions of maize genes remain largely unknown. High-quality genome- wide transcriptome datasets provide important biological knowledge which has been widely and suc- cessfully used in plants not only by measuring gene expression levels but also by enabling co-expression analysis for predicting gene functions and modules related to agronomic traits. Recently, thousands of maize transcriptomic data are available across different inbred lines, development stages, tissues, and treatments, or even across different tissue sections and cell lines. Here, we integrated 701 transcriptomic and 108 epigenomic data and studied the different conditional networks with multi-dimensional omics levels. We constructed a searchable, integrative, one-stop online platform, the maize conditional co- expression network （MCENet） platform. MCENet provides 10 global/conditional co-expression net- works, 5 network accessional analysis toolkits （i.e., Network Search, Network Remodel, Module Finder, Network Comparison, and Dynamic Expression View） and multiple network functional support toolkits （e.g., motif and module enrichment analysis）. We hope that our database might help plant research communities to identify maize functional genes or modules that regulate important agronomic traits.展开更多
AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression lev...AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.展开更多
Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is s...Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).展开更多
The ripening process of grape is an important stage during grape growth and development. During this process, color of grape skin is the most obvious change. The molecular mechanism for the ripening of grape(a non-cli...The ripening process of grape is an important stage during grape growth and development. During this process, color of grape skin is the most obvious change. The molecular mechanism for the ripening of grape(a non-climacteric fruit, which ripens without ethylene and respiration bursts) is still unclear. Although numerous studies have been done on the changes in the contents of metabolites during grape ripening, the differentially expressed genes at veraison and maturity stages have not been systematically analyzed. In this study, 1 524 genes that are significantly differentially expressed in grape(Pinot Noir) skin at veraison and maturity stages were identified, and a co-expression network of these genes was built. Some of the eight co-expression modules we identified may be closely related to the synthesis or metabolism of anthocyanins, sugar acids, and other flavor substances. The transcription factor families WRKY, b ZIP, HSF and WOX may play an important role in the regulation of anthocyanin synthesis or metabolism. The results provide a foundation for further study of the molecular mechanism of grape ripening.展开更多
Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict t...Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.展开更多
Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair perip...Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair peripheral nerve injury may uncover the molecular mechanisms and signal cascades underlying peripheral nerve repair and provide potential strategies for improving the low axon regeneration capacity of the central nervous system.In this study,we applied weighted gene co-expression network analysis to identify differentially expressed genes in proximal and distal sciatic nerve segments from rats with sciatic nerve injury.We identified 31 and 15 co-expression modules from the proximal and distal sciatic nerve segments,respectively.Functional enrichment analysis revealed that the differentially expressed genes in proximal modules promoted regeneration,while the differentially expressed genes in distal modules promoted neurodegeneration.Next,we constructed hub gene networks for selected modules and identified a key hub gene,Kif22,which was up-regulated in both nerve segments.In vitro experiments confirmed that Kif22 knockdown inhibited proliferation and migration of Schwann cells by modulating the activity of the extracellular signal-regulated kinase signaling pathway.Collectively,our findings provide a comparative framework of gene modules that are co-expressed in injured proximal and distal sciatic nerve segments,and identify Kif22 as a potential therapeutic target for promoting peripheral nerve injury repair via Schwann cell proliferation and migration.All animal experiments were approved by the Institutional Animal Ethics Committee of Nantong University,China(approval No.S20210322-008)on March 22,2021.展开更多
Testis specific protein Y-encoded（TSPY） is a Y-located proto-oncogene predominantly expressed in normal male germ cells and various types of germ cell tumor. Significantly, TSPY is frequently expressed in somatic ca...Testis specific protein Y-encoded（TSPY） is a Y-located proto-oncogene predominantly expressed in normal male germ cells and various types of germ cell tumor. Significantly, TSPY is frequently expressed in somatic cancers including liver cancer but not in adjacent normal tissues, suggesting that ectopic TSPY expression could be associated with oncogenesis in non-germ cell cancers. Various studies demonstrated that TSPY expression promotes growth and proliferation in cancer cells; however, its relationship to other oncogenic events in TSPY-positive cancers remains unknown. The present study seeks to correlate TSPY expression with other molecular features in clinical cancer samples, by analyses of RNA-seq transcriptome and DNA methylation data in the Cancer Genome Atlas（TCGA） database. A total of 53 genes,including oncogenic lineage protein 28 homolog B（LIN28B） gene and RNA-binding motif protein Y-linked（RBMY） gene, are identified to be consistently co-expressed with TSPY, and have been collectively designated as the TSPY co-expression network（TCN）. TCN genes were simultaneously activated in subsets of liver hepatocellular carcinoma（30%） and lung adenocarcinoma（10%） regardless of pathological stage, but only minimally in other cancer types. Further analysis revealed that the DNA methylation level was globally lower in the TCN-active than TCN-silent cancers. The specific expression and methylation patterns of TCN genes suggest that they could be useful as biomarkers for the diagnosis,prognosis and clinical management of cancers, especially those for liver and lung cancers, associated with TSPY co-expression network genes.展开更多
Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughp...Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughput gene expression data using weighted co-expression network analysis(WGCNA)to explore the potential therapeutic targets.Methods The dataset of GSE36980 was obtained from the Gene Expression Omnibus(GEO)database.Normalization,quality control,filtration,and soft-threshold calculation were carried out before clustering the co-expressed genes into different modules.Furthermore,the correlation coefiidents between the modules and clinical traits were computed to identify the key modules.Gene ontology and pathway enrichment analyses were performed on the key module genes.The STRING database was used to construct the protein-protein interaction(PPI)networks,which were further analyzed by Cytoscape app(MCODE).Finally,validation of hub genes was conducted by external GEO datasets of GSE 1297 and GSE 28146.Results Co-expressed genes were clustered into 27 modules,among which 6 modules were identified as the key module relating to AD occurrence.These key modules are primarily involved in chemical synaptic transmission(G0:0007268),the tricarboxylic acid(TCA)cycle and respiratory electron transport(R-HSA-1428517).WDR47,OXCT1,C3orfl4,ATP6V1A,SLC25A14,NAPB were found as the hub genes and their expression were validated by external datasets.Conclusions Through modules co-expression network analyses and PPI network analyses,we identified the hub genes of AD,including WDR47,0XCT1,C3orfl4i ATP6V1A,SLC25A14 and NAPB.Among them,three hub genes(ATP6V1A,SLC25A14,OXCT1)might contribute to AD pathogenesis through pathway of TCA cycle.展开更多
Primary biliary cholangitis(PBC) is an autoimmune disease involving dysregulation of a broad array of homeostatic and metabolic processes. Although considerable single-nucleotide polymorphisms have been unveiled, a la...Primary biliary cholangitis(PBC) is an autoimmune disease involving dysregulation of a broad array of homeostatic and metabolic processes. Although considerable single-nucleotide polymorphisms have been unveiled, a large fraction of risk factors remains enigmatic. Candidate genes with rare mutations that tend to confer more deleterious effects need to be identified. To help pinpoint cellular and developmental mechanisms beyond common noncoding variants, we integrate whole exome sequencing with integrative network analysis to investigate genes harboring de novo mutations. Prominent convergence has been revealed on a network of disease-specific co-expression comprised of 55 genes associated with homeostasis and metabolism. The transcription factor gene MEF2 D and the DNA repair gene PARP2 are highlighted as hub genes and identified to be up-and down-regulated, respectively, in peripheral blood data set. Enrichment analysis demonstrates that altered expression of MEF2 D and PARP2 may trigger a series of molecular and cellular processes with pivotal roles in PBC pathophysiology. Our study identifies genes with de novo mutations in PBC and suggests that a subset of genes in homeostasis and metabolism tend to act in synergy through converging on co-expression network, providing novel insights into the etiology of PBC and expanding the pool of molecular candidates for discovering clinically actionable biomarkers.展开更多
In underground mining,the belt is a critical component,as its state directly affects the safe and stable operation of the conveyor.Most of the existing non-contact detection methods based on machine vision can only de...In underground mining,the belt is a critical component,as its state directly affects the safe and stable operation of the conveyor.Most of the existing non-contact detection methods based on machine vision can only detect a single type of damage and they require pre-processing operations.This tends to cause a large amount of calculation and low detection precision.To solve these problems,in the work described in this paper a belt tear detection method based on a multi-class conditional deep convolutional generative adversarial network(CDCGAN)was designed.In the traditional DCGAN,the image generated by the generator has a certain degree of randomness.Here,a small number of labeled belt images are taken as conditions and added them to the generator and discriminator,so the generator can generate images with the characteristics of belt damage under the aforementioned conditions.Moreover,because the discriminator cannot identify multiple types of damage,the multi-class softmax function is used as the output function of the discriminator to output a vector of class probabilities,and it can accurately classify cracks,scratches,and tears.To avoid the features learned incompletely,skiplayer connection is adopted in the generator and discriminator.This not only can minimize the loss of features,but also improves the convergence speed.Compared with other algorithms,experimental results show that the loss value of the generator and discriminator is the least.Moreover,its convergence speed is faster,and the mean average precision of the proposed algorithm is up to 96.2%,which is at least 6%higher than that of other algorithms.展开更多
In dense pedestrian tracking,frequent object occlusions and close distances between objects cause difficulty when accurately estimating object trajectories.In this study,a conditional random field tracking model is es...In dense pedestrian tracking,frequent object occlusions and close distances between objects cause difficulty when accurately estimating object trajectories.In this study,a conditional random field tracking model is established by using a visual long short term memory network in the three-dimensional(3D)space and the motion estimations jointly performed on object trajectory segments.Object visual field information is added to the long short term memory network to improve the accuracy of the motion related object pair selection and motion estimation.To address the uncertainty of the length and interval of trajectory segments,a multimode long short term memory network is proposed for the object motion estimation.The tracking performance is evaluated using the PETS2009 dataset.The experimental results show that the proposed method achieves better performance than the tracking methods based on the independent motion estimation.展开更多
Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different c...Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different classes of cardiomyopathies remain elusive.This paper aims to describe the similarities and differences in molecular features of dilated cardiomyopathy(DCM)and ischemic cardiomyopathy(ICM).We firstly detected the co-expressed modules using the weighted gene co-expression network analysis(WGCNA).Significant modules associated with DCM/ICM were identified by the Pearson correlation coefficient(PCC)between the modules and the phenotype of DCM/ICM.The differentially expressed genes in the modules were selected to perform functional enrichment.The potential transcription factors(TFs)prediction was conducted for transcription regulation of hub genes.Apoptosis and cardiac conduction were perturbed in DCM and ICM,respectively.TFs demonstrated that the biomarkers and the transcription regulations in DCM and ICM were different,which helps make more accurate discrimination between them at molecular levels.In conclusion,comprehensive analyses of the molecular features may advance our understanding of DCM and ICM causes and progression.Thus,this understanding may promote the development of innovative diagnoses and treatments.展开更多
The impacts of lateral boundary conditions(LBCs)provided by numerical models and data-driven networks on convective-scale ensemble forecasts are investigated in this study.Four experiments are conducted on the Hangzho...The impacts of lateral boundary conditions(LBCs)provided by numerical models and data-driven networks on convective-scale ensemble forecasts are investigated in this study.Four experiments are conducted on the Hangzhou RDP(19th Hangzhou Asian Games Research Development Project on Convective-scale Ensemble Prediction and Application)testbed,with the LBCs respectively sourced from National Centers for Environmental Prediction(NCEP)Global Forecast System(GFS)forecasts with 33 vertical levels(Exp_GFS),Pangu forecasts with 13 vertical levels(Exp_Pangu),Fuxi forecasts with 13 vertical levels(Exp_Fuxi),and NCEP GFS forecasts with the vertical levels reduced to 13(the same as those of Exp_Pangu and Exp_Fuxi)(Exp_GFSRDV).In general,Exp_Pangu performs comparably to Exp_GFS,while Exp_Fuxi shows slightly inferior performance compared to Exp_Pangu,possibly due to its less accurate large-scale predictions.Therefore,the ability of using data-driven networks to efficiently provide LBCs for convective-scale ensemble forecasts has been demonstrated.Moreover,Exp_GFSRDV has the worst convective-scale forecasts among the four experiments,which indicates the potential improvement of using data-driven networks for LBCs by increasing the vertical levels of the networks.However,the ensemble spread of the four experiments barely increases with lead time.Thus,each experiment has insufficient ensemble spread to present realistic forecast uncertainties,which will be investigated in a future study.展开更多
Physics informed neural networks(PINNs)are a deep learning approach designed to solve partial differential equations(PDEs).Accurately learning the initial conditions is crucial when employing PINNs to solve PDEs.Howev...Physics informed neural networks(PINNs)are a deep learning approach designed to solve partial differential equations(PDEs).Accurately learning the initial conditions is crucial when employing PINNs to solve PDEs.However,simply adjusting weights and imposing hard constraints may not always lead to better learning of the initial conditions;sometimes it even makes it difficult for the neural networks to converge.To enhance the accuracy of PINNs in learning the initial conditions,this paper proposes a novel strategy named causally enhanced initial conditions(CEICs).This strategy works by embedding a new loss in the loss function:the loss is constructed by the derivative of the initial condition and the derivative of the neural network at the initial condition.Furthermore,to respect the causality in learning the derivative,a novel causality coefficient is introduced for the training when selecting multiple derivatives.Additionally,because CEICs can provide more accurate pseudo-labels in the first subdomain,they are compatible with the temporal-marching strategy.Experimental results demonstrate that CEICs outperform hard constraints and improve the overall accuracy of pre-training PINNs.For the 1D-Korteweg–de Vries,reaction and convection equations,the CEIC method proposed in this paper reduces the relative error by at least 60%compared to the previous methods.展开更多
As a crucial storage and buffering apparatus for balancing the production and consumption of byproduct gases in industrial processes, accurate prediction of gas tank levels is essential for optimizing energy system sc...As a crucial storage and buffering apparatus for balancing the production and consumption of byproduct gases in industrial processes, accurate prediction of gas tank levels is essential for optimizing energy system scheduling. Considering that the continuous switching of the pressure and valve status(mechanism knowledge) would bring about multiple working conditions of the equipment, a multi-condition time sequential network ensembled method is proposed. In order to especially consider the time dependence of different conditions, a centralwise condition sequential network is developed, where the network branches are specially designed based on the condition switching sequences. A branch combination transfer learning strategy is developed to tackle the sample imbalance problem of different condition data. Since the condition or status data are real-time information that cannot be recognized during the prediction process, a pre-trained and ensemble learning approach is further proposed to fuse the outputs of the multi-condition networks and realize a transient-state involved prediction. The performance of the proposed method is validated on practical energy data coming from a domestic steel plant, comparing with the state-of-the-art algorithms. The results show that the proposed method can maintain a high prediction accuracy under different condition switching cases, which would provide effective guidance for the optimal scheduling of the industrial energy systems.展开更多
The goal of this research is to develop mine-scale discrete fracture network(DFN)models in which the influence of the spatial heterogeneity of fracture distributions may be investigated on the rock wedge stability of ...The goal of this research is to develop mine-scale discrete fracture network(DFN)models in which the influence of the spatial heterogeneity of fracture distributions may be investigated on the rock wedge stability of an open pit slope.For this purpose,spatially conditioned DFN models were developed for the pit walls at Tasiast mine using comprehensive structural data from the mine.Using Sequential Gaussian Simulation(SGS),volumetric fracture intensities(P32)were modeled across the entire mine site in the form of 3D block models.The simulated P32 block models were used as the input constraints for conditional DFN fracture generation,where the DFN grid dimension is the same as the SGS 3D blocks.The spatially constrained DFN models were further calibrated using aerial fracture intensities(P21)data from the pit walls,obtained by a survey of the pit walls using an unmanned aerial vehicle(UAV)and measured traces of joints from 3D point cloud data.The final DFN model is expected to honor the fracture intensities gathered through different means with optimal model accuracy.Finally,bench-scale and interramp scale rock wedge slope stability analyses were conducted using the calibrated conditional DFN models.This work proves the significance of conditioned DFN models in rock wedge stability analysis.Such models provide detailed information regarding rock wedge stability so that site monitoring and prevention plans can be conducted with higher efficiency.展开更多
Zinc(Zn)malnutrition is a major public health issue.Genetic biofortification of Zn in rice grain can alleviate global Zn malnutrition.Therefore,elucidating the genetic mechanisms regulating Zn deprivation response in ...Zinc(Zn)malnutrition is a major public health issue.Genetic biofortification of Zn in rice grain can alleviate global Zn malnutrition.Therefore,elucidating the genetic mechanisms regulating Zn deprivation response in rice is essential to identify elite genes useful for breeding high grain Zn rice varieties.Here,a meta-analysis of previous RNA-Seq studies involving Zn deficient conditions was conducted using the weighted gene co-expression network analysis(WGCNA)and other in silico prediction tools to identify modules(denoting cluster of genes with related expression pattern)of co-expressed genes,modular genes which are conserved differentially expressed genes(DEGs)across independent RNA-Seq studies,and the molecular pathways of the conserved modular DEGs.WGCNA identified 16 modules of co-expressed genes.Twenty-eight and five modular DEGs were conserved in leaf and crown,and root tissues across two independent RNA-Seq studies.Functional enrichment analysis showed that 24 of the 28 conserved modular DEGs from leaf and crown tissues significantly up-regulated 2 Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways and 15 Gene Ontology(GO)terms,including the substrate-specific transmembrane transporter and the small molecule metabolic process.Further,the well-studied transcription factors(OsWOX11 and OsbHLH120),protein kinase(OsCDPK20 and OsMPK17),and miRNAs(OSA-MIR397A and OSA-MIR397B)were predicted to target some of the identified conserved modular DEGs.Out of the 24 conserved and up-regulated modular DEGs,19 were yet to be experimentally validated as Zn deficiency responsive genes.Findings from this study provide a comprehensive insight on the molecular mechanisms of Zn deficiency response and may facilitate gene and pathway prioritization for improving Zn use efficiency and Zn biofortification in rice.展开更多
BACKGROUND Psoriasis is a chronic inflammatory skin disease,the pathogenesis of which is more complicated and often requires long-term treatment.In particular,moderate to severe psoriasis usually requires systemic tre...BACKGROUND Psoriasis is a chronic inflammatory skin disease,the pathogenesis of which is more complicated and often requires long-term treatment.In particular,moderate to severe psoriasis usually requires systemic treatment.Psoriasis is also associated with many diseases,such as cardiometabolic diseases,malignant tumors,infections,and mood disorders.Psoriasis can appear at any age,and lead to a substantial burden for individuals and society.At present,psoriasis is still a treatable,but incurable,disease.Previous studies have found that micro RNAs(mi RNAs)play an important regulatory role in the progression of various diseases.Currently,mi RNAs studies in psoriasis and dermatology are relatively new.Therefore,the identification of key mi RNAs in psoriasis is helpful to elucidate the molecular mechanism of psoriasis.AIM To identify key molecular markers and signaling pathways to provide potential basis for the treatment and management of psoriasis.METHODS The mi RNA and m RNA data were obtained from the Gene Expression Omnibus database.Then,differentially expressed m RNAs(DEm RNAs)and differentially expressed mi RNAs(DEmi RNAs)were screened out by limma R package.Subsequently,DEm RNAs were analyzed for Gene Ontology and Kyoto Encyclopedia of Genes and Genomics functional enrichment.The“WGCNA”R package was used to analyze the co-expression network of all mi RNAs.In addition,we constructed mi RNA-m RNA regulatory networks based on identified hub mi RNAs.Finally,in vitro validation was performed.All experimental procedures were approved by the ethics committee of Chinese PLA General Hospital(S2021-012-01).RESULTS A total of 639 DEm RNAs and 84 DEmi RNAs were identified.DEm RNAs screening criteria were adjusted P(adj.P)value<0.01 and|log Fold Change|(|log FC|)>1.DEmi RNAs screening criteria were adj.P value<0.01 and|logFC|>1.5.KEGG functional analysis demonstrated that DEm RNAs were significantly enriched in immune-related biological functions,for example,tolllike receptor signaling pathway,cytokine-cytokine receptor interaction,and chemokine signaling pathway.In weighted gene co-expression network analysis,turquoise module was the hub module.Moreover,10 hub mi RNAs were identified.Among these 10 hub mi RNAs,only 8 hub mi RNAs predicted the corresponding target m RNAs.97 negatively regulated mi RNA-m RNA pairs were involved in the mi RNA-m RNA regulatory network,for example,hsa-mi R-21-5 pclaudin 8(CLDN8),hsa-mi R-30 a-3 p-interleukin-1 B(IL-1 B),and hsa-mi R-181 a-5 p/hsa-mi R-30 c-2-3 p-C-X-C motif chemokine ligand 9(CXCL9).Real-time polymerase chain reaction results showed that IL-1 B and CXCL9 were up-regulated and CLDN8 was down-regulated in psoriasis with statistically significant differences.CONCLUSION The identification of potential key molecular markers and signaling pathways provides potential research directions for further understanding the molecular mechanisms of psoriasis.This may also provide new research ideas for the prevention and treatment of psoriasis in the future.展开更多
Summary:Renal cancer is a common genitourinary malignance,of which clear cell renal cell carcinoma(ccRCC)has high aggressiveness and leads to most cancer-related deaths.Identification of sensitive and reliable biomark...Summary:Renal cancer is a common genitourinary malignance,of which clear cell renal cell carcinoma(ccRCC)has high aggressiveness and leads to most cancer-related deaths.Identification of sensitive and reliable biomarkers for predicting tumorigenesis and progression has great significance in guiding the diagnosis and treatment of ccRCC.Here,we identified 2397 common difTerentially expressed genes(DEGs)using paired normal and tumor ccRCC tissues from GSE53757 and The Cancer Genome Atlas(TCGA).Then,we performed weighted gene co-expression network analysis and protein-protein interaction network analysis,17 candidate hub genes were identified.These candidate hub genes were further validated in GSE36895 and Oncomine database and 14 real hub genes were identified.All the hub genes were up-regulated and significantly positively correlated with pathological stage and histologic grade of ccRCC.Survival analysis showed that the higher expression level of each hub gene tended to predict a worse clinical outcome.ROC analysis showed that all the hub genes can accurately distinguish between tumor and normal samples,and between early stage and advanced stage ccRCC.Moreover,all the hub genes were positively associated with distant metastasis,lymph node infiltration,tumor recurrence and the expression of MKi67,suggesting these genes might promote tumor proliferation,invasion and metastasis.Furthermore,the functional annotation demonstrated that most genes were enriched in cell-cycle related biological function.In summary,our study identified 14 potential biomarkers for predicting tumorigenesis and progression,which might contribute to early diagnosis,prognosis prediction and therapeutic intervention.展开更多
Structural damage in heterogeneousmaterials typically originates frommicrostructures where stress concentration occurs.Therefore,evaluating the magnitude and location of localized stress distributions within microstru...Structural damage in heterogeneousmaterials typically originates frommicrostructures where stress concentration occurs.Therefore,evaluating the magnitude and location of localized stress distributions within microstructures under external loading is crucial.Repeating unit cells(RUCs)are commonly used to represent microstructural details and homogenize the effective response of composites.This work develops a machine learning-based micromechanics tool to accurately predict the stress distributions of extracted RUCs.The locally exact homogenization theory efficiently generates the microstructural stresses of RUCs with a wide range of parameters,including volume fraction,fiber/matrix property ratio,fiber shapes,and loading direction.Subsequently,the conditional generative adversarial network(cGAN)is employed and constructed as a surrogate model to establish the statistical correlation between these parameters and the corresponding localized stresses.The stresses predicted by cGAN are validated against the remaining true data not used for training,showing good agreement.This work demonstrates that the cGAN-based micromechanics tool effectively captures the local responses of composite RUCs.It can be used for predicting potential crack initiations starting from microstructures and evaluating the effective behavior of periodic composites.展开更多
基金supported by the National Natural Science Foundation of China (Nos. 31771467, 31571360 and 31371291)
文摘Maize （Zea mays） is the most widely grown grain crop in the world, playing important roles in agriculture and industry. However, the functions of maize genes remain largely unknown. High-quality genome- wide transcriptome datasets provide important biological knowledge which has been widely and suc- cessfully used in plants not only by measuring gene expression levels but also by enabling co-expression analysis for predicting gene functions and modules related to agronomic traits. Recently, thousands of maize transcriptomic data are available across different inbred lines, development stages, tissues, and treatments, or even across different tissue sections and cell lines. Here, we integrated 701 transcriptomic and 108 epigenomic data and studied the different conditional networks with multi-dimensional omics levels. We constructed a searchable, integrative, one-stop online platform, the maize conditional co- expression network （MCENet） platform. MCENet provides 10 global/conditional co-expression net- works, 5 network accessional analysis toolkits （i.e., Network Search, Network Remodel, Module Finder, Network Comparison, and Dynamic Expression View） and multiple network functional support toolkits （e.g., motif and module enrichment analysis）. We hope that our database might help plant research communities to identify maize functional genes or modules that regulate important agronomic traits.
基金Supported by the National Natural Science Foundation of China(No.81271019No.61463046)Gansu Province Science Foundation for Youths(No.145RJYA282)
文摘AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.
基金supported by the Notional Natural Science Foundation of China,No.81960417 (to JX)Guangxi Key Research and Development Program,No.GuiKeA B20159027 (to JX)the Natural Science Foundation of Guangxi Zhuang Autonomous Region,No.2022GXNSFBA035545 (to YG)。
文摘Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).
基金Supported by Major Agricultural Application Technology Innovation Project of Shandong Province"Development of Landmark Wines and Integrated Application of Key Technologies in Shandong Province"Major Agricultural Application Technology Innovation Project of Shandong Province"Research and Application of Precision Control of Maturation and Product Innovation of Featured Brewing Grape"Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences(CXGC2016D01)
文摘The ripening process of grape is an important stage during grape growth and development. During this process, color of grape skin is the most obvious change. The molecular mechanism for the ripening of grape(a non-climacteric fruit, which ripens without ethylene and respiration bursts) is still unclear. Although numerous studies have been done on the changes in the contents of metabolites during grape ripening, the differentially expressed genes at veraison and maturity stages have not been systematically analyzed. In this study, 1 524 genes that are significantly differentially expressed in grape(Pinot Noir) skin at veraison and maturity stages were identified, and a co-expression network of these genes was built. Some of the eight co-expression modules we identified may be closely related to the synthesis or metabolism of anthocyanins, sugar acids, and other flavor substances. The transcription factor families WRKY, b ZIP, HSF and WOX may play an important role in the regulation of anthocyanin synthesis or metabolism. The results provide a foundation for further study of the molecular mechanism of grape ripening.
文摘Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.
基金supported by the National Major Project of Research and Development of China,No.2017YFA0104701(to BY)the National Natural Science Foundation of China,No.32000725(to QQC)+1 种基金the Natural Science Foundation of Jiangsu Province of China,No.BK20200973(to QQC)the Jiangsu Provincial University Innovation Training Key Project of China,No.202010304021Z(to ML)。
文摘Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair peripheral nerve injury may uncover the molecular mechanisms and signal cascades underlying peripheral nerve repair and provide potential strategies for improving the low axon regeneration capacity of the central nervous system.In this study,we applied weighted gene co-expression network analysis to identify differentially expressed genes in proximal and distal sciatic nerve segments from rats with sciatic nerve injury.We identified 31 and 15 co-expression modules from the proximal and distal sciatic nerve segments,respectively.Functional enrichment analysis revealed that the differentially expressed genes in proximal modules promoted regeneration,while the differentially expressed genes in distal modules promoted neurodegeneration.Next,we constructed hub gene networks for selected modules and identified a key hub gene,Kif22,which was up-regulated in both nerve segments.In vitro experiments confirmed that Kif22 knockdown inhibited proliferation and migration of Schwann cells by modulating the activity of the extracellular signal-regulated kinase signaling pathway.Collectively,our findings provide a comparative framework of gene modules that are co-expressed in injured proximal and distal sciatic nerve segments,and identify Kif22 as a potential therapeutic target for promoting peripheral nerve injury repair via Schwann cell proliferation and migration.All animal experiments were approved by the Institutional Animal Ethics Committee of Nantong University,China(approval No.S20210322-008)on March 22,2021.
基金partially supported by a Merit-Reviewed grant from the Department of Veterans Affairsa Peer-Reviewed Cancer Research Program grant from the Department of Defense (W81XWH-16-1-0488) to Y-FCL
文摘Testis specific protein Y-encoded（TSPY） is a Y-located proto-oncogene predominantly expressed in normal male germ cells and various types of germ cell tumor. Significantly, TSPY is frequently expressed in somatic cancers including liver cancer but not in adjacent normal tissues, suggesting that ectopic TSPY expression could be associated with oncogenesis in non-germ cell cancers. Various studies demonstrated that TSPY expression promotes growth and proliferation in cancer cells; however, its relationship to other oncogenic events in TSPY-positive cancers remains unknown. The present study seeks to correlate TSPY expression with other molecular features in clinical cancer samples, by analyses of RNA-seq transcriptome and DNA methylation data in the Cancer Genome Atlas（TCGA） database. A total of 53 genes,including oncogenic lineage protein 28 homolog B（LIN28B） gene and RNA-binding motif protein Y-linked（RBMY） gene, are identified to be consistently co-expressed with TSPY, and have been collectively designated as the TSPY co-expression network（TCN）. TCN genes were simultaneously activated in subsets of liver hepatocellular carcinoma（30%） and lung adenocarcinoma（10%） regardless of pathological stage, but only minimally in other cancer types. Further analysis revealed that the DNA methylation level was globally lower in the TCN-active than TCN-silent cancers. The specific expression and methylation patterns of TCN genes suggest that they could be useful as biomarkers for the diagnosis,prognosis and clinical management of cancers, especially those for liver and lung cancers, associated with TSPY co-expression network genes.
基金Fund supported by the National Natural Science Foundation of China(81460598 and 81660644)the Natural Science Foundation of Jiangsu Province(BK20170267)Guangxi Special Fund for the First-Class Discipline Construction Project(05019038).
文摘Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughput gene expression data using weighted co-expression network analysis(WGCNA)to explore the potential therapeutic targets.Methods The dataset of GSE36980 was obtained from the Gene Expression Omnibus(GEO)database.Normalization,quality control,filtration,and soft-threshold calculation were carried out before clustering the co-expressed genes into different modules.Furthermore,the correlation coefiidents between the modules and clinical traits were computed to identify the key modules.Gene ontology and pathway enrichment analyses were performed on the key module genes.The STRING database was used to construct the protein-protein interaction(PPI)networks,which were further analyzed by Cytoscape app(MCODE).Finally,validation of hub genes was conducted by external GEO datasets of GSE 1297 and GSE 28146.Results Co-expressed genes were clustered into 27 modules,among which 6 modules were identified as the key module relating to AD occurrence.These key modules are primarily involved in chemical synaptic transmission(G0:0007268),the tricarboxylic acid(TCA)cycle and respiratory electron transport(R-HSA-1428517).WDR47,OXCT1,C3orfl4,ATP6V1A,SLC25A14,NAPB were found as the hub genes and their expression were validated by external datasets.Conclusions Through modules co-expression network analyses and PPI network analyses,we identified the hub genes of AD,including WDR47,0XCT1,C3orfl4i ATP6V1A,SLC25A14 and NAPB.Among them,three hub genes(ATP6V1A,SLC25A14,OXCT1)might contribute to AD pathogenesis through pathway of TCA cycle.
基金supported in part by grants from the National Natural Science Foundation of China (81870397 to X.D.L.81620108002, 81771732, 81830016 to X.M+2 种基金and 81570469 to R.Q.T.)by grants from Jiangsu provincial research fund (BE2017713 to X.D.L and BL2018657 to Y.T.)a grant from National Key R&D Program of China (2016YFC0900400)。
文摘Primary biliary cholangitis(PBC) is an autoimmune disease involving dysregulation of a broad array of homeostatic and metabolic processes. Although considerable single-nucleotide polymorphisms have been unveiled, a large fraction of risk factors remains enigmatic. Candidate genes with rare mutations that tend to confer more deleterious effects need to be identified. To help pinpoint cellular and developmental mechanisms beyond common noncoding variants, we integrate whole exome sequencing with integrative network analysis to investigate genes harboring de novo mutations. Prominent convergence has been revealed on a network of disease-specific co-expression comprised of 55 genes associated with homeostasis and metabolism. The transcription factor gene MEF2 D and the DNA repair gene PARP2 are highlighted as hub genes and identified to be up-and down-regulated, respectively, in peripheral blood data set. Enrichment analysis demonstrates that altered expression of MEF2 D and PARP2 may trigger a series of molecular and cellular processes with pivotal roles in PBC pathophysiology. Our study identifies genes with de novo mutations in PBC and suggests that a subset of genes in homeostasis and metabolism tend to act in synergy through converging on co-expression network, providing novel insights into the etiology of PBC and expanding the pool of molecular candidates for discovering clinically actionable biomarkers.
基金This work was supported by the Shanxi Province Applied Basic Research Project,China(Grant No.201901D111100).Xiaoli Hao received the grant,and the URL of the sponsors’website is http://kjt.shanxi.gov.cn/.
文摘In underground mining,the belt is a critical component,as its state directly affects the safe and stable operation of the conveyor.Most of the existing non-contact detection methods based on machine vision can only detect a single type of damage and they require pre-processing operations.This tends to cause a large amount of calculation and low detection precision.To solve these problems,in the work described in this paper a belt tear detection method based on a multi-class conditional deep convolutional generative adversarial network(CDCGAN)was designed.In the traditional DCGAN,the image generated by the generator has a certain degree of randomness.Here,a small number of labeled belt images are taken as conditions and added them to the generator and discriminator,so the generator can generate images with the characteristics of belt damage under the aforementioned conditions.Moreover,because the discriminator cannot identify multiple types of damage,the multi-class softmax function is used as the output function of the discriminator to output a vector of class probabilities,and it can accurately classify cracks,scratches,and tears.To avoid the features learned incompletely,skiplayer connection is adopted in the generator and discriminator.This not only can minimize the loss of features,but also improves the convergence speed.Compared with other algorithms,experimental results show that the loss value of the generator and discriminator is the least.Moreover,its convergence speed is faster,and the mean average precision of the proposed algorithm is up to 96.2%,which is at least 6%higher than that of other algorithms.
文摘In dense pedestrian tracking,frequent object occlusions and close distances between objects cause difficulty when accurately estimating object trajectories.In this study,a conditional random field tracking model is established by using a visual long short term memory network in the three-dimensional(3D)space and the motion estimations jointly performed on object trajectory segments.Object visual field information is added to the long short term memory network to improve the accuracy of the motion related object pair selection and motion estimation.To address the uncertainty of the length and interval of trajectory segments,a multimode long short term memory network is proposed for the object motion estimation.The tracking performance is evaluated using the PETS2009 dataset.The experimental results show that the proposed method achieves better performance than the tracking methods based on the independent motion estimation.
基金supported by the National Natural Science Foundation of China under Grants No.61720106004 and No.61872405the Key R&D Project of Sichuan Province,China under Grants No.20ZDYF2772 and No.2020YFS0243.
文摘Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different classes of cardiomyopathies remain elusive.This paper aims to describe the similarities and differences in molecular features of dilated cardiomyopathy(DCM)and ischemic cardiomyopathy(ICM).We firstly detected the co-expressed modules using the weighted gene co-expression network analysis(WGCNA).Significant modules associated with DCM/ICM were identified by the Pearson correlation coefficient(PCC)between the modules and the phenotype of DCM/ICM.The differentially expressed genes in the modules were selected to perform functional enrichment.The potential transcription factors(TFs)prediction was conducted for transcription regulation of hub genes.Apoptosis and cardiac conduction were perturbed in DCM and ICM,respectively.TFs demonstrated that the biomarkers and the transcription regulations in DCM and ICM were different,which helps make more accurate discrimination between them at molecular levels.In conclusion,comprehensive analyses of the molecular features may advance our understanding of DCM and ICM causes and progression.Thus,this understanding may promote the development of innovative diagnoses and treatments.
基金supported by the Strategic Research and Consulting Project of the Chinese Academy of Engineering[grant number 2024-XBZD-14]the National Natural Science Foundation of China[grant numbers 42192553 and 41922036]the Fundamental Research Funds for the Central Universities–Cemac“GeoX”Interdisciplinary Program[grant number 020714380207]。
文摘The impacts of lateral boundary conditions(LBCs)provided by numerical models and data-driven networks on convective-scale ensemble forecasts are investigated in this study.Four experiments are conducted on the Hangzhou RDP(19th Hangzhou Asian Games Research Development Project on Convective-scale Ensemble Prediction and Application)testbed,with the LBCs respectively sourced from National Centers for Environmental Prediction(NCEP)Global Forecast System(GFS)forecasts with 33 vertical levels(Exp_GFS),Pangu forecasts with 13 vertical levels(Exp_Pangu),Fuxi forecasts with 13 vertical levels(Exp_Fuxi),and NCEP GFS forecasts with the vertical levels reduced to 13(the same as those of Exp_Pangu and Exp_Fuxi)(Exp_GFSRDV).In general,Exp_Pangu performs comparably to Exp_GFS,while Exp_Fuxi shows slightly inferior performance compared to Exp_Pangu,possibly due to its less accurate large-scale predictions.Therefore,the ability of using data-driven networks to efficiently provide LBCs for convective-scale ensemble forecasts has been demonstrated.Moreover,Exp_GFSRDV has the worst convective-scale forecasts among the four experiments,which indicates the potential improvement of using data-driven networks for LBCs by increasing the vertical levels of the networks.However,the ensemble spread of the four experiments barely increases with lead time.Thus,each experiment has insufficient ensemble spread to present realistic forecast uncertainties,which will be investigated in a future study.
基金supported by the National Natural Science Foundation of China(Grant Nos.1217211 and 12372244).
文摘Physics informed neural networks(PINNs)are a deep learning approach designed to solve partial differential equations(PDEs).Accurately learning the initial conditions is crucial when employing PINNs to solve PDEs.However,simply adjusting weights and imposing hard constraints may not always lead to better learning of the initial conditions;sometimes it even makes it difficult for the neural networks to converge.To enhance the accuracy of PINNs in learning the initial conditions,this paper proposes a novel strategy named causally enhanced initial conditions(CEICs).This strategy works by embedding a new loss in the loss function:the loss is constructed by the derivative of the initial condition and the derivative of the neural network at the initial condition.Furthermore,to respect the causality in learning the derivative,a novel causality coefficient is introduced for the training when selecting multiple derivatives.Additionally,because CEICs can provide more accurate pseudo-labels in the first subdomain,they are compatible with the temporal-marching strategy.Experimental results demonstrate that CEICs outperform hard constraints and improve the overall accuracy of pre-training PINNs.For the 1D-Korteweg–de Vries,reaction and convection equations,the CEIC method proposed in this paper reduces the relative error by at least 60%compared to the previous methods.
基金supported by the National Natural Sciences Foundation of China(62125302,62203087)Liaoning Revitalization Talents Program(XLYC2002087)+1 种基金Sci-Tech Talent Innovation Support Program of Dalian(2022RG03)Young Elite Scientist Sponsorship Program by China Association for Science and Technology(YESS20220018)
文摘As a crucial storage and buffering apparatus for balancing the production and consumption of byproduct gases in industrial processes, accurate prediction of gas tank levels is essential for optimizing energy system scheduling. Considering that the continuous switching of the pressure and valve status(mechanism knowledge) would bring about multiple working conditions of the equipment, a multi-condition time sequential network ensembled method is proposed. In order to especially consider the time dependence of different conditions, a centralwise condition sequential network is developed, where the network branches are specially designed based on the condition switching sequences. A branch combination transfer learning strategy is developed to tackle the sample imbalance problem of different condition data. Since the condition or status data are real-time information that cannot be recognized during the prediction process, a pre-trained and ensemble learning approach is further proposed to fuse the outputs of the multi-condition networks and realize a transient-state involved prediction. The performance of the proposed method is validated on practical energy data coming from a domestic steel plant, comparing with the state-of-the-art algorithms. The results show that the proposed method can maintain a high prediction accuracy under different condition switching cases, which would provide effective guidance for the optimal scheduling of the industrial energy systems.
基金Kinross Gold and MITACS for their financial support(Grant No.FR42880).
文摘The goal of this research is to develop mine-scale discrete fracture network(DFN)models in which the influence of the spatial heterogeneity of fracture distributions may be investigated on the rock wedge stability of an open pit slope.For this purpose,spatially conditioned DFN models were developed for the pit walls at Tasiast mine using comprehensive structural data from the mine.Using Sequential Gaussian Simulation(SGS),volumetric fracture intensities(P32)were modeled across the entire mine site in the form of 3D block models.The simulated P32 block models were used as the input constraints for conditional DFN fracture generation,where the DFN grid dimension is the same as the SGS 3D blocks.The spatially constrained DFN models were further calibrated using aerial fracture intensities(P21)data from the pit walls,obtained by a survey of the pit walls using an unmanned aerial vehicle(UAV)and measured traces of joints from 3D point cloud data.The final DFN model is expected to honor the fracture intensities gathered through different means with optimal model accuracy.Finally,bench-scale and interramp scale rock wedge slope stability analyses were conducted using the calibrated conditional DFN models.This work proves the significance of conditioned DFN models in rock wedge stability analysis.Such models provide detailed information regarding rock wedge stability so that site monitoring and prevention plans can be conducted with higher efficiency.
基金financially supported by the Chinese Academy of Agricultural Sciences-Agricultural Science and Technology Innovation Programthe Shenzhen Science and Technology Program (Grant No. JCYJ20200109150650397)
文摘Zinc(Zn)malnutrition is a major public health issue.Genetic biofortification of Zn in rice grain can alleviate global Zn malnutrition.Therefore,elucidating the genetic mechanisms regulating Zn deprivation response in rice is essential to identify elite genes useful for breeding high grain Zn rice varieties.Here,a meta-analysis of previous RNA-Seq studies involving Zn deficient conditions was conducted using the weighted gene co-expression network analysis(WGCNA)and other in silico prediction tools to identify modules(denoting cluster of genes with related expression pattern)of co-expressed genes,modular genes which are conserved differentially expressed genes(DEGs)across independent RNA-Seq studies,and the molecular pathways of the conserved modular DEGs.WGCNA identified 16 modules of co-expressed genes.Twenty-eight and five modular DEGs were conserved in leaf and crown,and root tissues across two independent RNA-Seq studies.Functional enrichment analysis showed that 24 of the 28 conserved modular DEGs from leaf and crown tissues significantly up-regulated 2 Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways and 15 Gene Ontology(GO)terms,including the substrate-specific transmembrane transporter and the small molecule metabolic process.Further,the well-studied transcription factors(OsWOX11 and OsbHLH120),protein kinase(OsCDPK20 and OsMPK17),and miRNAs(OSA-MIR397A and OSA-MIR397B)were predicted to target some of the identified conserved modular DEGs.Out of the 24 conserved and up-regulated modular DEGs,19 were yet to be experimentally validated as Zn deficiency responsive genes.Findings from this study provide a comprehensive insight on the molecular mechanisms of Zn deficiency response and may facilitate gene and pathway prioritization for improving Zn use efficiency and Zn biofortification in rice.
文摘BACKGROUND Psoriasis is a chronic inflammatory skin disease,the pathogenesis of which is more complicated and often requires long-term treatment.In particular,moderate to severe psoriasis usually requires systemic treatment.Psoriasis is also associated with many diseases,such as cardiometabolic diseases,malignant tumors,infections,and mood disorders.Psoriasis can appear at any age,and lead to a substantial burden for individuals and society.At present,psoriasis is still a treatable,but incurable,disease.Previous studies have found that micro RNAs(mi RNAs)play an important regulatory role in the progression of various diseases.Currently,mi RNAs studies in psoriasis and dermatology are relatively new.Therefore,the identification of key mi RNAs in psoriasis is helpful to elucidate the molecular mechanism of psoriasis.AIM To identify key molecular markers and signaling pathways to provide potential basis for the treatment and management of psoriasis.METHODS The mi RNA and m RNA data were obtained from the Gene Expression Omnibus database.Then,differentially expressed m RNAs(DEm RNAs)and differentially expressed mi RNAs(DEmi RNAs)were screened out by limma R package.Subsequently,DEm RNAs were analyzed for Gene Ontology and Kyoto Encyclopedia of Genes and Genomics functional enrichment.The“WGCNA”R package was used to analyze the co-expression network of all mi RNAs.In addition,we constructed mi RNA-m RNA regulatory networks based on identified hub mi RNAs.Finally,in vitro validation was performed.All experimental procedures were approved by the ethics committee of Chinese PLA General Hospital(S2021-012-01).RESULTS A total of 639 DEm RNAs and 84 DEmi RNAs were identified.DEm RNAs screening criteria were adjusted P(adj.P)value<0.01 and|log Fold Change|(|log FC|)>1.DEmi RNAs screening criteria were adj.P value<0.01 and|logFC|>1.5.KEGG functional analysis demonstrated that DEm RNAs were significantly enriched in immune-related biological functions,for example,tolllike receptor signaling pathway,cytokine-cytokine receptor interaction,and chemokine signaling pathway.In weighted gene co-expression network analysis,turquoise module was the hub module.Moreover,10 hub mi RNAs were identified.Among these 10 hub mi RNAs,only 8 hub mi RNAs predicted the corresponding target m RNAs.97 negatively regulated mi RNA-m RNA pairs were involved in the mi RNA-m RNA regulatory network,for example,hsa-mi R-21-5 pclaudin 8(CLDN8),hsa-mi R-30 a-3 p-interleukin-1 B(IL-1 B),and hsa-mi R-181 a-5 p/hsa-mi R-30 c-2-3 p-C-X-C motif chemokine ligand 9(CXCL9).Real-time polymerase chain reaction results showed that IL-1 B and CXCL9 were up-regulated and CLDN8 was down-regulated in psoriasis with statistically significant differences.CONCLUSION The identification of potential key molecular markers and signaling pathways provides potential research directions for further understanding the molecular mechanisms of psoriasis.This may also provide new research ideas for the prevention and treatment of psoriasis in the future.
基金This work was supported by grants from the National Natural Science Foundation of China(No.81270354)Natural Science for Youth Foundation(No.81300213).
文摘Summary:Renal cancer is a common genitourinary malignance,of which clear cell renal cell carcinoma(ccRCC)has high aggressiveness and leads to most cancer-related deaths.Identification of sensitive and reliable biomarkers for predicting tumorigenesis and progression has great significance in guiding the diagnosis and treatment of ccRCC.Here,we identified 2397 common difTerentially expressed genes(DEGs)using paired normal and tumor ccRCC tissues from GSE53757 and The Cancer Genome Atlas(TCGA).Then,we performed weighted gene co-expression network analysis and protein-protein interaction network analysis,17 candidate hub genes were identified.These candidate hub genes were further validated in GSE36895 and Oncomine database and 14 real hub genes were identified.All the hub genes were up-regulated and significantly positively correlated with pathological stage and histologic grade of ccRCC.Survival analysis showed that the higher expression level of each hub gene tended to predict a worse clinical outcome.ROC analysis showed that all the hub genes can accurately distinguish between tumor and normal samples,and between early stage and advanced stage ccRCC.Moreover,all the hub genes were positively associated with distant metastasis,lymph node infiltration,tumor recurrence and the expression of MKi67,suggesting these genes might promote tumor proliferation,invasion and metastasis.Furthermore,the functional annotation demonstrated that most genes were enriched in cell-cycle related biological function.In summary,our study identified 14 potential biomarkers for predicting tumorigenesis and progression,which might contribute to early diagnosis,prognosis prediction and therapeutic intervention.
基金the support from the National Key R&D Program of China underGrant(Grant No.2020YFA0711700)the National Natural Science Foundation of China(Grant Nos.52122801,11925206,51978609,U22A20254,and U23A20659)G.W.is supported by the National Natural Science Foundation of China(Nos.12002303,12192210 and 12192214).
文摘Structural damage in heterogeneousmaterials typically originates frommicrostructures where stress concentration occurs.Therefore,evaluating the magnitude and location of localized stress distributions within microstructures under external loading is crucial.Repeating unit cells(RUCs)are commonly used to represent microstructural details and homogenize the effective response of composites.This work develops a machine learning-based micromechanics tool to accurately predict the stress distributions of extracted RUCs.The locally exact homogenization theory efficiently generates the microstructural stresses of RUCs with a wide range of parameters,including volume fraction,fiber/matrix property ratio,fiber shapes,and loading direction.Subsequently,the conditional generative adversarial network(cGAN)is employed and constructed as a surrogate model to establish the statistical correlation between these parameters and the corresponding localized stresses.The stresses predicted by cGAN are validated against the remaining true data not used for training,showing good agreement.This work demonstrates that the cGAN-based micromechanics tool effectively captures the local responses of composite RUCs.It can be used for predicting potential crack initiations starting from microstructures and evaluating the effective behavior of periodic composites.
