Objective:To use the gene chip of pseudomonas aeruginosa as a research sample and to explore it at an omics level,aiming at elucidating the co-expression network characteristics of the virulence genes exoS and exoU of...Objective:To use the gene chip of pseudomonas aeruginosa as a research sample and to explore it at an omics level,aiming at elucidating the co-expression network characteristics of the virulence genes exoS and exoU of pseudomonas aeruginosa in the lower respiratory tract from the perspective of molecular biology and identifying its key regulatory genes.Methods:From March 2016 to May 2018,312 patients infected with pseudomonas aeruginosa in the lower respiratory tract who were admitted to Department of Respiratory Medicine of Baogang Hospital and given follow-up treatments in the hospital were selected as subjects by use of cluster sampling.Alveolar lavage fluid and sputum collected from those patients were used as biological specimens.The genes of pseudomonas aeruginosa were detected with the help of oligonucleotide probes to make a pre-processing of chip data.A total of 8 common antibiotics(ceftazidime,gentamicin,piperacillin,amikacin,ciprofloxacin,levofloxacin,doripenem and ticarcillin)against Gram-negative bacteria were selected to determine the drug resistance of biological specimens.MCODE algorithm was used to construct a co-expression network model of the drug-resistance genes focused on exoS/exoU.Results:The expression level of exoS/exoU in the drug-resistance group was significantly higher than that in the non-resistance group(p<0.05).The top 5 differentially expressed genes in the alveolar lavage fluid specimens from the drug-resistance group were RAC1,ITGB1,ITGB5,CRK and IGF1R in the order from high to low.In the sputum specimens,the top 5 differentially expressed genes were RAC1,CRK,IGF1R,ITGB1 and ITGB5.In the alveolar lavage fluid specimens,only RAC1 had a positive correlation with the expression of exoS and exoU(p<0.05).In the sputum specimens,RAC1,ITGB1,ITGB5,CRK and IGF1R were positively correlated with the expression of exoS and exoU(p<0.05).The genes included in the co-expression network contained exoS,exoU,RAC1,ITGB1,ITGB5,CRK,CAMK2D,RHOA,FLNA,IGF1R,TGFBR2 and FOS.Among them,RAC1 had a highest score in the aspect of regulatory ability(72.00)and the largest number of regulatory genes(6);followed by ITGB1,ITGB5 and CRK genes.Conclusions:The high expression of exoS and exoU in the sputum specimens suggests that pseudomonas aeruginosa has a higher probability to get resistant to antibiotics;RAC1,ITGB1,ITGB5 and CRK genes may be the key genes that can regulate the expression of exoS and exoU.展开更多
In order to search for intensity fluctuations on the HCN(1-0) and HCO+(1-0) line pro- files, which could arise due to possible small-scale inhomogeneous structure, long-term observations of high-mass star-forming...In order to search for intensity fluctuations on the HCN(1-0) and HCO+(1-0) line pro- files, which could arise due to possible small-scale inhomogeneous structure, long-term observations of high-mass star-forming cores S140 and S199 were carried out. The data were processed by the Fourier filtering method. Line temperature fluctuations that exceed the noise level were detected. Assuming the cores consist of a large number of randomly moving small thermal fragments, the total number of frag- ments is - 4 × 106 for the region with linear size - 0.1 pc in S140 and - 106 for the region with linear size - 0.3 pc in S 199. Physical parameters of fragments in S 140 were obtained from detailed modeling of the HCN emission in the framework of the clumpy cloud model.展开更多
Data governance is a subject that is becoming increasingly important in business and government. In fact, good governance data allows improved interactions between employees of one or more organizations. Data quality ...Data governance is a subject that is becoming increasingly important in business and government. In fact, good governance data allows improved interactions between employees of one or more organizations. Data quality represents a great challenge because the cost of non-quality can be very high. Therefore the use of data quality becomes an absolute necessity within an organization. To improve the data quality in a Big-Data source, our purpose, in this paper, is to add semantics to data and help user to recognize the Big-Data schema. The originality of this approach lies in the semantic aspect it offers. It detects issues in data and proposes a data schema by applying a semantic data profiling.展开更多
BACKGROUND The objectives of this study were to identify hub genes and biological pathways involved in lung adenocarcinoma(LUAD)via bioinformatics analysis,and investigate potential therapeutic targets.AIM To determin...BACKGROUND The objectives of this study were to identify hub genes and biological pathways involved in lung adenocarcinoma(LUAD)via bioinformatics analysis,and investigate potential therapeutic targets.AIM To determine reliable prognostic biomarkers for early diagnosis and treatment of LUAD.METHODS To identify potential therapeutic targets for LUAD,two microarray datasets derived from the Gene Expression Omnibus(GEO)database were analyzed,GSE3116959 and GSE118370.Differentially expressed genes(DEGs)in LUAD and normal tissues were identified using the GEO2R tool.The Hiplot database was then used to generate a volcanic map of the DEGs.Weighted gene co-expression network analysis was conducted to cluster the genes in GSE116959 and GSE-118370 into different modules,and identify immune genes shared between them.A protein-protein interaction network was established using the Search Tool for the Retrieval of Interacting Genes database,then the CytoNCA and CytoHubba components of Cytoscape software were used to visualize the genes.Hub genes with high scores and co-expression were identified,and the Database for Annotation,Visualization and Integrated Discovery was used to perform enrichment analysis of these genes.The diagnostic and prognostic values of the hub genes were calculated using receiver operating characteristic curves and Kaplan-Meier survival analysis,and gene-set enrichment analysis was conducted.The University of Alabama at Birmingham Cancer data analysis portal was used to analyze relationships between the hub genes and normal specimens,as well as their expression during tumor progression.Lastly,validation of protein expression was conducted on the identified hub genes via the Human Protein Atlas database.RESULTS Three hub genes with high connectivity were identified;cellular retinoic acid binding protein 2(CRABP2),matrix metallopeptidase 12(MMP12),and DNA topoisomerase II alpha(TOP2A).High expression of these genes was associated with a poor LUAD prognosis,and the genes exhibited high diagnostic value.CONCLUSION Expression levels of CRABP2,MMP12,and TOP2A in LUAD were higher than those in normal lung tissue.This observation has diagnostic value,and is linked to poor LUAD prognosis.These genes may be biomarkers and therapeutic targets in LUAD,but further research is warranted to investigate their usefulness in these respects.展开更多
Programmed cell death protein 1(PD-1)/programmed cell death ligand 1(PD-L1)blockade is an important therapeutic strategy for melanoma,despite its low clinical response.It is important to identify genes and pathways th...Programmed cell death protein 1(PD-1)/programmed cell death ligand 1(PD-L1)blockade is an important therapeutic strategy for melanoma,despite its low clinical response.It is important to identify genes and pathways that may reflect the clinical outcomes of this therapy in patients.We analyzed clinical dataset GSE96619,which contains clinical information from five melanoma patients before and after anti-PD-1 therapy(five pairs of data).We identified 704 DEGs using these five pairs of data,and then the number of DEGs was narrowed down to 286 in patients who responded to treatment.Next,we performed KEGG pathway enrichment and constructed a DEG-associated protein-protein interaction network.Smooth muscle actin 2(ACTA2)and tyrosine kinase growth factor receptor(KDR)were identified as the hub genes,which were significantly downregulated in the tumor tissue of the two patients who re-sponded to treatment.To confirm our analysis,we demonstrated similar expression tendency to the clinical data for the two hub genes in a B16F10 subcutaneous xeno-graft model.This study demonstrates that ACTA2 and KDR are valuable responsive markers for PD-1/PD-L1 blockade therapy.展开更多
A physical method,based on the simplification of surface radiation terms in remote sensing equations, has been suggested to retrieve the surface temperature,vertical temperature profile and surface emissivity from the...A physical method,based on the simplification of surface radiation terms in remote sensing equations, has been suggested to retrieve the surface temperature,vertical temperature profile and surface emissivity from the first eight channel observations of TIROS-N/HIRS2.Analyses of several examples indicate that this method can obtain much more accurate temperatures in the lower atmosphere than a statistical technique, and that the surface temperature and emissivity retrieved are also reasonable.展开更多
文摘Objective:To use the gene chip of pseudomonas aeruginosa as a research sample and to explore it at an omics level,aiming at elucidating the co-expression network characteristics of the virulence genes exoS and exoU of pseudomonas aeruginosa in the lower respiratory tract from the perspective of molecular biology and identifying its key regulatory genes.Methods:From March 2016 to May 2018,312 patients infected with pseudomonas aeruginosa in the lower respiratory tract who were admitted to Department of Respiratory Medicine of Baogang Hospital and given follow-up treatments in the hospital were selected as subjects by use of cluster sampling.Alveolar lavage fluid and sputum collected from those patients were used as biological specimens.The genes of pseudomonas aeruginosa were detected with the help of oligonucleotide probes to make a pre-processing of chip data.A total of 8 common antibiotics(ceftazidime,gentamicin,piperacillin,amikacin,ciprofloxacin,levofloxacin,doripenem and ticarcillin)against Gram-negative bacteria were selected to determine the drug resistance of biological specimens.MCODE algorithm was used to construct a co-expression network model of the drug-resistance genes focused on exoS/exoU.Results:The expression level of exoS/exoU in the drug-resistance group was significantly higher than that in the non-resistance group(p<0.05).The top 5 differentially expressed genes in the alveolar lavage fluid specimens from the drug-resistance group were RAC1,ITGB1,ITGB5,CRK and IGF1R in the order from high to low.In the sputum specimens,the top 5 differentially expressed genes were RAC1,CRK,IGF1R,ITGB1 and ITGB5.In the alveolar lavage fluid specimens,only RAC1 had a positive correlation with the expression of exoS and exoU(p<0.05).In the sputum specimens,RAC1,ITGB1,ITGB5,CRK and IGF1R were positively correlated with the expression of exoS and exoU(p<0.05).The genes included in the co-expression network contained exoS,exoU,RAC1,ITGB1,ITGB5,CRK,CAMK2D,RHOA,FLNA,IGF1R,TGFBR2 and FOS.Among them,RAC1 had a highest score in the aspect of regulatory ability(72.00)and the largest number of regulatory genes(6);followed by ITGB1,ITGB5 and CRK genes.Conclusions:The high expression of exoS and exoU in the sputum specimens suggests that pseudomonas aeruginosa has a higher probability to get resistant to antibiotics;RAC1,ITGB1,ITGB5 and CRK genes may be the key genes that can regulate the expression of exoS and exoU.
基金support of the RFBR grants(projects 15–02–06098,16–02–00761 and18–02–00660)support of the Russian Science Foundation grant(project 17–12–01256)
文摘In order to search for intensity fluctuations on the HCN(1-0) and HCO+(1-0) line pro- files, which could arise due to possible small-scale inhomogeneous structure, long-term observations of high-mass star-forming cores S140 and S199 were carried out. The data were processed by the Fourier filtering method. Line temperature fluctuations that exceed the noise level were detected. Assuming the cores consist of a large number of randomly moving small thermal fragments, the total number of frag- ments is - 4 × 106 for the region with linear size - 0.1 pc in S140 and - 106 for the region with linear size - 0.3 pc in S 199. Physical parameters of fragments in S 140 were obtained from detailed modeling of the HCN emission in the framework of the clumpy cloud model.
文摘Data governance is a subject that is becoming increasingly important in business and government. In fact, good governance data allows improved interactions between employees of one or more organizations. Data quality represents a great challenge because the cost of non-quality can be very high. Therefore the use of data quality becomes an absolute necessity within an organization. To improve the data quality in a Big-Data source, our purpose, in this paper, is to add semantics to data and help user to recognize the Big-Data schema. The originality of this approach lies in the semantic aspect it offers. It detects issues in data and proposes a data schema by applying a semantic data profiling.
文摘BACKGROUND The objectives of this study were to identify hub genes and biological pathways involved in lung adenocarcinoma(LUAD)via bioinformatics analysis,and investigate potential therapeutic targets.AIM To determine reliable prognostic biomarkers for early diagnosis and treatment of LUAD.METHODS To identify potential therapeutic targets for LUAD,two microarray datasets derived from the Gene Expression Omnibus(GEO)database were analyzed,GSE3116959 and GSE118370.Differentially expressed genes(DEGs)in LUAD and normal tissues were identified using the GEO2R tool.The Hiplot database was then used to generate a volcanic map of the DEGs.Weighted gene co-expression network analysis was conducted to cluster the genes in GSE116959 and GSE-118370 into different modules,and identify immune genes shared between them.A protein-protein interaction network was established using the Search Tool for the Retrieval of Interacting Genes database,then the CytoNCA and CytoHubba components of Cytoscape software were used to visualize the genes.Hub genes with high scores and co-expression were identified,and the Database for Annotation,Visualization and Integrated Discovery was used to perform enrichment analysis of these genes.The diagnostic and prognostic values of the hub genes were calculated using receiver operating characteristic curves and Kaplan-Meier survival analysis,and gene-set enrichment analysis was conducted.The University of Alabama at Birmingham Cancer data analysis portal was used to analyze relationships between the hub genes and normal specimens,as well as their expression during tumor progression.Lastly,validation of protein expression was conducted on the identified hub genes via the Human Protein Atlas database.RESULTS Three hub genes with high connectivity were identified;cellular retinoic acid binding protein 2(CRABP2),matrix metallopeptidase 12(MMP12),and DNA topoisomerase II alpha(TOP2A).High expression of these genes was associated with a poor LUAD prognosis,and the genes exhibited high diagnostic value.CONCLUSION Expression levels of CRABP2,MMP12,and TOP2A in LUAD were higher than those in normal lung tissue.This observation has diagnostic value,and is linked to poor LUAD prognosis.These genes may be biomarkers and therapeutic targets in LUAD,but further research is warranted to investigate their usefulness in these respects.
基金This work was supported by the CAMS Innovation Fund for Medical Sciences[2017-I2M-1-010].
文摘Programmed cell death protein 1(PD-1)/programmed cell death ligand 1(PD-L1)blockade is an important therapeutic strategy for melanoma,despite its low clinical response.It is important to identify genes and pathways that may reflect the clinical outcomes of this therapy in patients.We analyzed clinical dataset GSE96619,which contains clinical information from five melanoma patients before and after anti-PD-1 therapy(five pairs of data).We identified 704 DEGs using these five pairs of data,and then the number of DEGs was narrowed down to 286 in patients who responded to treatment.Next,we performed KEGG pathway enrichment and constructed a DEG-associated protein-protein interaction network.Smooth muscle actin 2(ACTA2)and tyrosine kinase growth factor receptor(KDR)were identified as the hub genes,which were significantly downregulated in the tumor tissue of the two patients who re-sponded to treatment.To confirm our analysis,we demonstrated similar expression tendency to the clinical data for the two hub genes in a B16F10 subcutaneous xeno-graft model.This study demonstrates that ACTA2 and KDR are valuable responsive markers for PD-1/PD-L1 blockade therapy.
文摘A physical method,based on the simplification of surface radiation terms in remote sensing equations, has been suggested to retrieve the surface temperature,vertical temperature profile and surface emissivity from the first eight channel observations of TIROS-N/HIRS2.Analyses of several examples indicate that this method can obtain much more accurate temperatures in the lower atmosphere than a statistical technique, and that the surface temperature and emissivity retrieved are also reasonable.