基于优化算法竞赛场景的改进data profile技术

数值比较是评估最优化算法特别是全局优化算法必不可少的手段,通常利用已知全局最优值的测试函数集来对优化算法进行性能评估。Data profile技术是用于比较确定性最优化算法的一种数据分析技术,最近被推广到随机优化算法的数值比较中。但data profile技术存在一个不良性质,得到的profile曲线会随着参与比较的优化算法的不同而改变。这一“传递无效性”缺陷不利于普通用户对该技术的认识和使用。分析表明,导致“传递无效性”的根源在于data profile的“收敛条件”定义,笔者提出的新“收敛条件”可以消除该缺陷,条件是需要用到目标函数的全局最优值,因而适用于最优值已知的众多优化算法竞赛场景。大量数值实验表明,改进的data profile技术消除了“传递无效性”缺陷,有利于不同算法竞赛之间结果的相互验证和推广使用。

Co-expression network analysis of virulence genes exoS and exoU of pseudomonas aeruginosa in lower respiratory tract based on histological data expression profiles

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.

A search for evidence of small-scale inhomogeneities in dense cores from line profile analysis

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.

Semantic Recognition of a Data Structure in Big-Data

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.

Identification of key genes and biological pathways in lung adenocarcinoma by integrated bioinformatics analysis

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.

Identification ACTA2 and KDR as key proteins for prognosis of PD-1/PD-L1 blockade therapy in melanoma

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.

REMOTE SENSING OF AIR TEMPERATURE PROFILE AND SURFACE EMISSIVITY FROM HIRS2 DATA

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.