Expression and Clinical Significance of MIS18BP1 in Bladder Cancer Tissues / 肿瘤防治研究

Objective To explore the expression, correlation with clinicopathologic parameters, and clinical significance of MIS18 binding protein 1 (MIS18BP1) in bladder cancer. Methods TCGA and GEO databases were used to analyze the mRNA expression of MIS18BP1 in tumors and controls, and the results were verified via qRT-PCR. UALCAN online database was utilized in the analysis of the expression of MIS18BP1 and its correlation with clinicopathological parameters and the degree of immune cell infiltration. Immunohistochemistry was employed to analyze the expression of MIS18BP1 in bladder cancer and its relationship with clinicopathological features. The ROC curve was applied to evaluate the diagnostic value of MIS18BP1 mRNA in bladder cancer. Results Bioinformatics analysis and qRT-PCR results revealed the increased expression of MIS18BP1 mRNA in bladder cancer compared with that in the control group (P<0.05). Immunohistochemistry unveiled the significantly high positive rate of MIS18BP1 protein in bladder cancer (P<0.05) and its correlation with the clinical stage of tumors, depth of invasion, and lymph node metastasis (P<0.05). The immune infiltration analysis showed the association of MIS18BP1 with immune cell infiltration in bladder cancer. Conclusion The increased expression level of MIS18BP1 gene and protein in bladder cancer may regulate the development of bladder cancer by influencing immune cell infiltration.

IDENTIFYING THE ECOTOURISM SUITABILITY SCORE FOR MARINA BEACH AND ELLIOT'S BEACH OF CHENNAI COAST, TAMIL NADU, INDIA.

At the Chennai Coast in Tamil Nadu, India, research is done. Finding out whether Marina Beach and Elliott's Beach are suitable for ecotourism is the study's main goal. For the research using the ecotourism suitability index methodology, land use, land cover, erosion, accretion, beach type, beach width, proximity to bus stop, proximity to train station, and suspended sediment load have all been taken into account. The suitability index of eco tourism is assigned into 4 (four) classes, which are: Class S1 (Highly suitable), Class S2 (Quite Suitable), Class S3 (Suitable with condition) and Class N (Not Suitable). Result of analysis indicates that coast area of Marina Beach and Elliots beach area comes in the class of Highly suitable (S1) by score total of 129 or 95.5 % and 116 or 85.9 % respectively. According to the research, Marina Beach has a sand feature as a land use land cover, 213 metres of beach width, good clarity (500 mg/L), is located 361 metres from a bus stop and 681 metres from a train station, has moderate erosion, and has not experienced any accretion. The beach type is white sand. Likewise, Elliots Beach has a sand feature as a land use land cover, with 222 metres of beach width, good clarity (600 mg/L), 642 metres from the bus stop, and 2351 metres from the railway station, which is high. There is moderate erosion and no accretion, and the sand is of the beach type, which is white. Marina beach has high tourism suitability index as compared to Elliot's beach. By considering marina beach, all the eight parameters are considered to be ne whereas Elliot's beach has far away accessibility this is the main reason for lowering the tourism suitability.

Analysis of expression of m 6A regulators in colorectal tumor samples based on TCGA and GEO databases / 中国基层医药

Objective:To detect the expression of N6-methyladenosine (m 6A) regulators in colorectal tumor samples and its clinical significance. Methods:From September to December 2021, the data regarding the expression of m 6A regulators in colorectal tumor samples were collected using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) and the expression of m 6A regulators was compared between different clinical pathological characteristics and between different molecular subtypes. Survival analysis was conducted in patients with colorectal cancer with different m 6A expression levels. Results:In TCGA, insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1), insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3), and YTH N6-methyladenosine RNA binding protein 1 (YTHDF1) were higher in colorectal tumor samples than normal tissue samples (TCGA-COAD: IGF2BP3: 12.80 vs. 204.46, logFC = 4.00, P = 0.003; YTHDF1: 2 347.56 vs. 3712.77, logFC = 0.66, P < 0.001; TCGA-READ: IGF2BP1: 6.20 vs. 359.32, logFC = 5.82, P = 0.007; YTHDF1: 2 470.10 vs. 4 369.09, logFC = 0.82, P = 0.020). The intersection of TCGA and GEO databases showed that methyltransferase like 14 (METTL14), YTH domain m 6A RNA binding protein 3 (YTHDF3), and α-ketoglutarate dependent dioxygenase AlkB homolog 5 (ALKBH5) were downregulated in colorectal tumor samples compared with normal tissue samples (TCGA-COAD: METTL14: 1 051.56 vs. 711.40, logFC = -0.56, P < 0.001; YTHDF3:4 613.85 vs. 3 155.05, logFC = -0.55, P < 0.001, ALKBH5: 4 250.10 vs. 2 555.55, logFC = -0.73, P < 0.001; TCGA-READ vs. METTL14: 1 113.3 vs. 674.36, logFC = -0.72, P < 0.001; YTHDF3: 5 034.30 vs. 3 331.95, logFC = -0.60, P = 0.004; ALKBH5: 4 902.20 vs. 2 529.71, logFC = -0.95, P < 0.001; GEO-CRC vs. METTL14: 6.58 vs. 6.33, logFC = -0.06, P < 0.001; YTHDF3: 6.28 vs. 6.20, logFC = -0.02, P = 0.002; ALKBH5: 5.07 vs. 4.98, logFC = -0.02, P < 0.001). In colorectal tumor samples of different molecular subtypes, IGF2BP2, HNRNPC, TP53 and YTHDF2 expression was low in KRAS (IGF2BP2: 48.53 vs. 44.04, t = 2.64, P = 0.008; HNRNPC: 121.30 vs. 112.60, t = 2.32, P = 0.020; TP53: 65.30 vs. 60.26, t = 2.11, P = 0.034; YTHDF2: 54.07 vs. 51.19; t = 1.97, P = 0.048). Different clinical pathological characteristics showed that IGF2BP1 was higher in colorectal cancer with positive lymph nodes (8.97 vs. 6.11, W = 20 008, P = 0.002), distant metastasis (8.94 vs. 6.41, W = 19 104, P = 0.009), or stage Ⅲ-Ⅳ (7.46 vs. 7.13, W = 8 779, P = 0.025) than normal tissue. ALKBH5 overexpression, advanced age, presence of vascular invasion, and late pathological staging were significantly related to a short survival period (high ALKBH5 expression vs. low ALKBH5 expression: 5.85 years vs. not available, HR: 1.63, 95% CI: 1.071-2.491, P = 0.021; > 68 years vs. < 68 years: 6.78 years vs. not available, HR: 1.59, 95% CI: 1.049-2.422, P = 0.047; stage Ⅲ-Ⅳ vs. stage Ⅰ-Ⅱ: 4.55 years vs. 8.33 years, HR: 2.89, 95% CI: 1.895-4.425, P < 0.001; presence of vein invasion vs. absence of vein invasion: 5.48 years vs. not available, HR: 2.82, 95% CI: 1.672-4.783, P < 0.001). Conclusion:Some of the m 6A regulators are associated with the biological characteristics and prognosis of colorectal cancer.

Analysis on mechanism of Kaixin San in the treatment of Alzheimer disease based on integrated pharmacology and GEO chip technology / 国际中医中药杂志

Objective:To analyze the mechanism of Kaixin San in treating Alzheimer disease (AD) based on the TCM integrated pharmacology platform combined with GEO chip differential gene analysis method.Methods:By searching TCMIP and Drugbank database, the active components and related molecular targets of Kaixin San were obtained. GSE4757 chip data was obtained through GEO database, and its differential genes were obtained using R language to draw heat map and volcano map. Molecular target map of differentially expressed genes between Kaixin San and AD was constructed through Cytoscape 3.7.2. Bisogenet and CytoNCA were used to draw the target topological network, and GO enrichment analysis and KEGG enrichment analysis of Kaixin San and AD gene were carried out.Results:86 active components of Kaixin San were obtained to treat AD, and 29 differential genes shared with GEO were obtained. PPI topological network was constructed. 6 core candidate genes were screened, and were merged with KEGG pathway enriched genes to obtain important genes for disease treatment, such as CHRM1, CHRM2, ACHE, CHRM3, CASP8, PTGS2, DRD1, CACN1S, ADRB1. 375 GO entries were obtained, mainly involving biological processes such as vasoconstriction, postsynaptic membrane plasticity, neurotransmitter transmission, etc. KEGG enrichment analysis mainly involved cholinergic synaptic signal pathway, cAMP signal pathway, calcium signal pathway, nerve ligand receptor interaction signal pathway, etc.Conclusions:Kaixin San shows the features of multi-component, multi-target and multi-channel in treating AD. It can play a role in the treatment of AD by inhibiting inflammatory reaction, reducing the activity of acetylcholinesterase and regulating the concentration of calciumion.

Analysis of Significant Genes and Pathways in Esophageal Cancer Based on Gene Expression Omnibus Database / 中国医学科学杂志(英文版)

Objective To screen antigen targets for immunotherapy by analyzing over-expressed genes, and to identify significant pathways and molecular mechanisms in esophageal cancer by using bioinformatic methods such as enrichment analysis, protein-protein interaction (PPI) network, and survival analysis based on the Gene Expression Omnibus (GEO) database.Methods By screening with highly expressed genes, we mainly analyzed proteins MUC13 and EPCAM with transmembrane domain and antigen epitope from TMHMM and IEDB websites. Significant genes and pathways associated with the pathogenesis of esophageal cancer were identified using enrichment analysis, PPI network, and survival analysis. Several software and platforms including Prism 8, R language, Cytoscape, DAVID, STRING, and GEPIA platform were used in the search and/or figure creation.Results Genes MUC13 and EPCAM were over-expressed with several antigen epitopes in esophageal squamous cell carcinoma (ESCC) tissue. Enrichment analysis revealed that the process of keratinization was focused and a series of genes were related with the development of esophageal cancer. Four genes including ALDH3A1, C2, SLC6A1,and ZBTB7C were screened with significant P value of survival curve.Conclusions Genes MUC13 and EPCAM may be promising antigen targets or biomarkers for esophageal cancer. Keratinization may greatly impact the pathogenesis of esophageal cancer. Genes ALDH3A1, C2, SLC6A1,and ZBTB7C may play important roles in the development of esophageal cancer.

Screening crucial lncRNAs and genes in osteoarthritis by integrated analysis

Abstract Background Osteoarthritis (OA) is one of the most frequent chronic diseases with high morbidity worldwide, marked by degradation of the cartilage and bone, joint instability, stiffness, joint space stenosis and subchondral sclerosis. Due to the elusive mechanism of osteoarthritis (OA), we aimed to identify potential markers for OA and explore the molecular mechanisms underlying OA. Methods Expression profiles data of OA were collected from the Gene Expression Omnibus database to identify differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) in OA. Functional annotation and protein-protein interaction (PPI) networks were performed. Then, nearby DEmRNAs of DElncRNAs was obtained. Moreover, GO and KEGG pathway enrichment analysis of nearby DEmRNAs of DElncRNAs was performed. Finally, expression validation of selected mRNAs and lncRNAs was performed by quantitative reverse transcriptase-polymerase chain reaction. Results In total, 2080 DEmRNAs and 664 DElncRNAs were determined in OA. PI3K-Akt signaling pathway, Endocytosis and Rap1 signaling pathway were significantly enriched KEGG pathways in OA. YWHAB, HSPA8, NEDD4L and SH3KBP1 were four hub proteins in PPI network. The AC093484.4/TRPV2 interact pair may be involved in the occurrence and development of OA. Conclusion Our study identified several DEmRNAs and DElncRNAs associated with OA. The molecular characters could provide more information for further study on OA.

Identification of potential hub genes involved in alcohol use disorder via bioinformatics analysis / 四川精神卫生

BackgroundAlcohol use disorder （AUD） is a type of chronic relapsing brain disorder. Genetic factors play an important role in the pathogenesis of AUD. And screening for molecular markers of AUD is of great significance for further elucidating the pathogenesis of the disease， discovering novel therapeutic targets and preventing relapse. ObjectiveTo explore relevant hub genes and potential signal pathways associated with the development of AUD through bioinformatics analysis， and to provide a new direction for the prevention and treatment of AUD. MethodsThe GSE161986 dataset was acquired from the Gene Expression Omnibus （GEO） database. The limma package in R was utilized to identify differentially expressed genes （DEGs）. Gene set enrichment analysis （GSEA） was carried out using the Database for Annotation， Visualization and Integrated Discovery （DAVID）. A protein–protein interaction （PPI） network of DEGs was assessed using the STRING database and visualized by Cytoscape software. Finally， hub genes were validated in GSE44456 dataset. ResultsA total of 114 DEGs were identified. GSEA revealed that these genes were mainly involved in the regulation of signal transduction， protein binding， membrane trafficking and MAPK signaling pathway. PPI network and validation study indicated that GAD1， TIMP1 and CD44 were potential hub genes involved in AUD. ConclusionAberrant expression of GAD1 and TIMP1 as well as MAPK signaling pathway may play a key role in the pathogenesis of AUD， and may serve as potential molecular targets for the diagnosis and treatment of AUD. ［Funded by "Flying Project" of Shanghai Mental Health Center （number， 2022-FX-01）］

ALDH5A1 Downregulation Promotes Tumor Metastasis and Contributes to Poor Prognosis in Ovarian Cancer / 肿瘤防治研究

Objective To investigate the expression level and clinical significance of ALDH5A1 in ovarian cancer (OC) tissues, as well as to explore the possible mechanism associated with the invasion and migration of OC cells. Methods We initially compared ALDH5A1 expression in metastatic tissues and the primary site of OC based on the GEO database. Then, wound-healing and Transwell assays were utilized to determine the biological role of OC cells transfected with ALDH5A1 siRNA. To unravel the potential mechanism of ALDH5A1 meditating the metastasis of OC, the coexpression profile of ALDH5A1 in OC cell lines and OC patients were generated using cBioPortal. Moreover, the TCGA and GEO databases were used to analyze the relationship between ALDH5A1 expression and the prognosis of OC patients. The HPA database was further used to confirm the relative expression of ALDH5A1 and MMPs in OC patients. Results ALDH5A1 expression was downregulated in metastatic tissues compared with the primary site of OC, and ALDH5A1 knockdown promoted the malignant behavior of OC cells. Additionally, the coexpression profile of ALDH5A1 was significantly enriched in the extracellular matrix (ECM) organization pathway. Western blot assay further confirmed that the expression of MMP, which played an important role in the ECM pathway, was negatively correlated with ALDH5A1 expression in OC. These results indicated that ALDH5A1 may participate in the metastasis and invasion of OC via the ECM organization pathway. Finally, KM survival plots revealed that the survival rates of OC patients with lower ALDH5A1 expression were obviously lower. Conclusion ALDH5A1 downregulation may promote the tumor metastasis and contribute to poor prognosis in OC.

Nematódeos de interesse médico veterinário em represa urbana no município de Catalão, no sudeste do estado de Goiás, Brasil / Nematodes of veterinary medical interest in an urban reservoir in the municipality of Catalão, southeastern Goiás State, Brazil

Objetivo: realizar análises parasitológicas em amostras de solo provenientes da represa da Bica situada no município de Catalão-GO. Métodos: a área do entorno da represa foi dividida em cinco parcelas, sendo realizadas coletas em dois pontos de cada parcela, superior e inferior. Foram realizadas quatro coletas em dias alternados, totalizando 40 amostras de, aproximadamente, 50g da camada superficial do solo, com profundidade máxima de cinco centímetros. As amostras foram processadas no Setor de Diagnóstico Parasitológico do Laboratório de Biologia Molecular da Universidade Federal de Catalão (UFCAT). Para as análises parasitológicas, foram utilizados cinco métodos encontrados na literatura, Rugai, Willis, Sedimentação espontânea, Ritchie e Ritchie modificado. Resultados: pelo método de Rugai, foi possível detectar larvas rabditoides do gênero Ancylostoma e Strongyloides. Utilizando o método de Ritchie modificado, foram encontrados ovos de Ascaris lumbricoidese Ancylostoma sp. Conclusão: a presença de formas evolutivas no solo da represa indica contaminação por dejetos animais e humanos, favorecendo o estabelecimento de ciclos biológicos das espécies encontradas e de outras diferentes zoonoses. Os dados obtidos demonstram a importância de sensibilizar a população de medidas de promoção da saúde, além de ações preventivas e programas de educação em saúde.

Objective: to conduct parasitological analyses in soil samples from the Bica reservoir located in the municipality of Catalão-GO. Methods: the area around the dam was divided into five plots, and samples were collected from two points in each plot, upper and lower. Four samples were collected on alternate days, totaling 40 samples of approximately 50g of topsoil, with a maximum depth of five centimeters. The samples were processed in the Parasitological Diagnostic Sector of the Molecular Biology Laboratory of the Federal University of Catalão (UFCAT). For the parasitological analyses, we used five methods found in the literature, Rugai, Willis, spontaneous sedimentation, Ritchie, and modified Ritchie. Results: by the Rugai method, it was possible to detect rhabditoid larvae of the genus Ancylostoma and Strongyloides. Using the modified Ritchie method, eggs of Ascaris lumbricoidesand Ancylostoma sp were found. Conclusion: the presence of evolutive forms in the soil of the reservoir indicates contamination by animal and human waste, favoring the establishment of biological cycles of the species found and of other different zoonoses. The data obtained demonstrated the importance of raising the population's awareness of health promotion measures besides preventive actions and health education programs.

Covid-19 Hazard Index: A Spatiotemporal Risk Forecast Tool

Background: In each geographic region, risk of new cases of COVID19 are driven by internal factors such as agent, host, and environment characteristics, as well as external factors, such as population mo-bility and cross border transmission of disease. COVID19 control measures are best implemented when local governments and health teams are well aware of these internal and external risks. These risks are dynamic in nature and hence need to be reviewed at regular intervals. The study conducted to develop a composite spatiotemporal Hazard Index comprising of three factors – presence of susceptible popula-tion, population density and presence of active cases with corresponding growth rates, to rank areas within an administrative boundary by their fortnightly risk of active COVID19 cases. Methods: Using Principal Component Analysis, the weights of each of these factors were determined and applied to transformed values of factors in the districts of Gujarat state for months of January to July 2021. Hazard Index thus obtained was used to rank the districts. Results: Spearman correlation between the Hazard Index and number of active cases 15 days later was moderate and significant (p<0.01) throughout the study period. Conclusion: Hazard Index can predict Districts at highest risk of active cases in the given time period. These districts with high Hazard Index would require different control measures, depending on the fac-tor that resulted in higher index value.

Identification of hub genes in airway epithelial cells of asthma patients by WGCNA and PPI network

Bronchial asthma is a common chronic disease of airway inflammation, high mucus secretion and airway hyper responsiveness. The pathogenetic mechanisms of asthma remain unclear. In this study, we aimed at identifying genes playing an import role in disease-related pathways in airway epithelial cells of asthma patients. Microarray data GSE41861 of asthma airway epithelial cells was used to screen differentially expressed genes (DEGs) through GEO2R analysis. The weighted gene co-expression network analysis (WGCNA) was performed to identify gene co-expression network modules in bronchial asthma. The DAVID database was then used to perform functional and pathway enrichment analysis of these DEGs. In addition, we have conducted protein-protein interaction (PPI) network of DEGs by STRING, and eventually found key genes and significant modules. A total of 315 DEGs (111 up-regulated and 204 down-regulated) were identified between severe asthma and healthy individual, which were mainly involved in pathways of cilium assembly, cilium morphogenesis, axon guidance, positive regulation of fat cell differentiation, and positive regulation of cell substrate adhesion. A total of 60 genes in the black module and green module were considered to be correlated with the severity of asthma. Combining PPI network, several key genes were identified, such as BP2RY14, PTGS1, SLC18A2, SIGLEC6, RGS13, CPA3, and HPGDS. Our findings revealed several genes that may be involved in the process of development of bronchial asthma and potentially be candidate targets for diagnosis or therapy of bronchial asthma.

Screening of Hub genes contributing to acute T lymphoblastic leukemia induced by ultra-high dose rate radiotherapy based on GEO database / 中华放射医学与防护杂志

Objective:To analyze the data of ultra-high dose rate (FLASH) radiotherapy in GEO (Gene Expression Omnibus) database by bioinformatics method, in order to find the hub genes involved in flash radiotherapy induced acute T-lymphoblastic leukemia.Methods:The gene expression profiles of malignant tumors receiving FLASH radiotherapy were downloaded from GEO database. The R software was used to screen the differential expressed genes (DEGs) and analyze their biological functions and signal pathways. The protein-protein interaction (PPI) network of DEGs was analyzed by online tool of STRING, and Hub genes were screened by Cytoscape plug-in. The expressions of screened Hub genes in acute T lymphoblastic leukemia were identified with TCGA (The Cancer Genome Atlas) and GTEx (Genotype-Tissue Expression) database.Results:Based on the analysis of GSE100718 microarray dataset of GEO database, a total of 12 800 genes were found to be associated with radiosensitivity of acute T lymphoblastic leukemia, of which 61 significantly altered DEGs were selected for further analysis. It was found that these genes were involved in the biological processes of metabolism, stress response, and immune response through the pathways of oxidative phosphorylation, unfolded protein response, fatty acid metabolism, and so on. PPI analysis indicated that HSPA5 and SCD belonged to the Hub genes involved in the regulation of FLASH radiosensitivity, and they were significantly highly expressed in acute T lymphoblastic leukemia combined with TRD/LMO2-fusion gene.Conclusions:Through bioinformatics analysis, the Hub genes involved in regulating the sensitivity of FLASH radiotherapy and conventional radiotherapy can be effectively screened, and thus the gene expression profiles can be used to guide the stratification of cancer patients to achieve a precise radiotherapy.

Exploring the miRNA-mRNA regulatory network in schizophrenia based on GEO database / 四川精神卫生

ObjectiveTo provide a new idea for exploring the molecular genetic approach to the pathogenesis of schizophrenia via construction of microRNA-messenger RNA （miRNA-mRNA） regulatory network in schizophrenia. MethodsThe microarray datasets of GSE54578 miRNA expression profiles in peripheral blood and GSE145554 mRNA expression in the anterior cingulate in postmortem brain of schizophrenic subjects were downloaded from Gene Expression Omnibus （GEO） database since July 2021. The GEO2R was used to identify the differentially expressed miRNAs and mRNAs， screen the miRNA with target differentially expressed mRNA， and predict their potential upstream transcription factors. The overlapping genes from the mRNA targeted by the differentially expressed miRNA and the mRNA differentially expressed in GSE145554 dataset were collected. Then the biological features of hub genes were analyzed via Gene Ontology （GO） analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analysis， and the protein-protein interaction （PPI） network and miRNA-mRNA regulatory network of hub genes were constructed. ResultsA total of 8 up-regulated differentially expressed miRNAs with targeted mRNA were screened out in GSE54578 datasets regarding schizophrenia， which involved in the regulation of 10 transcription factors， 247 down-regulated differentially expressed mRNAs were screened out in GSE145554 datasets， and 17 overlapping mRNAs were obtained. GO analysis showed that the target mRNAs were mainly involved in astrocyte differentiation and development. KEGG pathway enrichment analysis showed that the target mRNAs were mainly involved in Rap1 and Ras signaling pathways. PPI network analysis showed that the mRNAs （KRAS and CD28） might be key genes in schizophrenia. ConclusionThe integrated bioinformatics analysis based on GEO database can identify potential susceptibility genes in schizophrenia， and it also contributes to the construction of miRNA-mRNA regulatory network in schizophrenia.

Screening of key immune genes and pathways related to the ineffectiveness of interferon alpha treatment in patients with chronic hepatitis B based on GEO database / 西安交通大学学报(医学版)

【Objective】 To screen the differentially expressed immune genes between responders （Rs） and non-responders （NRs） in chronic hepatitis B patients receiving interferon alpha （IFN-α） treatment and to explore the molecular basis of IFN-α treatment failure. 【Methods】 The gene expression profile GSE27555 which contained 6 Rs and 7 NRs was obtained from the Gene Expression Omnibus （GEO） database； then differentially expressed genes between liver tissues of Rs and NRs were selected by the R software. The iconic immune gene set consisting of 1793 genes was downloaded from the immunology database and analysis portal （ImmPort）. The immune genes were extracted from the differentially expressed genes to obtain the differentially expressed immune genes. Subsequently， Gene Ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses of the differentially expressed immune genes were performed by the R software. Protein-protein interaction （PPI） network of the differentially expressed immune genes was constructed using the STRING online tool. The plugin CytoHubba of the Cytoscape software was applied to identify the top 10 genes by using Degree， MCC， MNC， and Closeness algorithms； then the intersection was taken to obtain the hub genes. 【Results】 A total of 88 differentially expressed immune genes， consisting of 13 upregulated and 75 downregulated genes， were identified between Rs and NRs. GO analysis showed that the differentially expressed immune genes were significantly enriched in T cell activation， cell chemotaxis， regulation of cell-cell adhesion， antigen processing and presentation. KEGG pathway analysis suggested that the differentially expressed immune genes were significantly enriched in cytokine-cytokine receptor interactions， Th cell differentiation， antigen processing and presentation， interactions between viral proteins and cytokines and cytokine receptors， chemokine signaling pathways， T cell receptor signaling pathway， IL-17 signaling pathway， natural killer cell-mediated cytotoxicity， Toll-like receptor signaling pathway， and other immune response signaling pathways. The top 7 hub genes， identified by the plugin cytoHubba of the Cytoscape software by using Degree， MCC， MNC and Closeness algorithms， were CD8A， IFNG， CCL2， CCL5， CXCL10， CCL4， and FCGR3A. 【Conclusion】 This study made a comprehensive analysis of the differentially expressed immune genes and signal pathways between Rs and NRs by bioinformatics， and identified 7 Hub genes related to the ineffectiveness of IFN-α treatment in CHB patients. These hub genes may serve as potential biomarkers for predicting the response of IFN-α treatment in CHB patients.

Evaluation of vegetables grown in dry mountainous regions for soil transmitted helminths contamination / Avaliação de vegetais para contaminação por helmintos transmitida pelo solo em quatro distritos da divisão de Malakand: noroeste do Paquistão

Infection caused by geo-helminth parasites are called geohelminthiasis are one of the global health problems. Vegetables eaten raw is the principal source of transmission of geo-helminth parasites. Pakistani people believe that eating raw vegetables are a significant source to get important vitamins and minerals. Based on the high incidence of pathogenic parasites and cultivating different vegetable types in the study areas, we conducted this study to evaluate the geo-helminth contamination of raw vegetables in northwest Khyber Pakhtunkhwa, Pakistan. This is a descriptive study comprised, 1942 samples of 25 various types of vegetables. The samples were examined in physiological saline solution using sedimentation and centrifugation methods. The findings were analyzed by Graph-Pad version 5. P value less than 0.05 (95% CI) was considered significant. Results showed that 16.5% (n=322) of all vegetables were contaminated with one or more type of geo-helminth parasites. Garlic was the highest (35%) and cauliflower the lowest (4%) contaminated samples respectively. Ascaris lumbricoides was the most common geo helminth found followed by hook worm species while Trichuris trichura was the least in all the vegetable samples. Leafy vegetables were highly contaminated 25.3% than vegetables with root parts 21.2% and fruity 9.09%. More than half of the contaminated vegetables were contaminated with single species of geo-helminth (P0.05) species of geo-helminth parasites. Education level of vendors and means of display were not significantly associated while types of vegetable used were significantly associated with the prevalence of parasites. The findings of this study provide evidence that consumption of raw [...].

As infecções causadas por parasitas geo-helmínticos são chamados de geohelmintíases e são um dos problemas de saúde globais. Os vegetais comidos crus são a principal fonte de transmissão dos parasitas geo-helmínticos. O povo paquistanês acredita que comer vegetais crus é uma fonte significativa para obter vitaminas e minerais importantes. Com base na alta incidência de parasitas patogênicos e no cultivo de diferentes tipos de vegetais nas áreas de estudo, conduzimos este estudo para avaliar a contaminação por geo-helmintos de vegetais crus no noroeste de Khyber Pakhtunkhwa, Paquistão. Trata-se de um estudo descritivo composto por 1942 amostras de 25 tipos diversos de vegetais. As amostras foram examinadas em solução salina fisiológica utilizando métodos de sedimentação e centrifugação. Os achados foram analisados pelo Graph-Pad versão 5. O valor de P menor que 0,05 (IC 95%) foi considerado significativo. Os resultados mostraram que 16,5% (n = 322) de todas as hortaliças estavam contaminadas com um ou mais tipos de parasitas geo-helmínticos. O alho foi a amostra mais contaminada (35%) e a couve-flor a menos (4%), respectivamente. Ascaris lumbricoides foi o geo-helmíntico mais comum encontrado, seguido por espécies de verme-anzol, enquanto Trichuris trichura foi o menos encontrado em todas as amostras de vegetais. Os vegetais folhosos foram altamente contaminados 25,3% do que os vegetais com partes de raiz 21,2% e frutados 9,09%. Mais da metade dos vegetais contaminados estavam contaminados com uma única espécie de geo-helmintos (P 0,05) espécies de parasitas geo-helmínticos. O nível de escolaridade dos vendedores e os meios de exibição não [...].

Evaluation of vegetables grown in dry mountainous regions for soil transmitted helminths contamination

Abstract Infection caused by geo-helminth parasites are called geohelminthiasis are one of the global health problems. Vegetables eaten raw is the principal source of transmission of geo-helminth parasites. Pakistani people believe that eating raw vegetables are a significant source to get important vitamins and minerals. Based on the high incidence of pathogenic parasites and cultivating different vegetable types in the study areas, we conducted this study to evaluate the geo-helminth contamination of raw vegetables in northwest Khyber Pakhtunkhwa, Pakistan. This is a descriptive study comprised, 1942 samples of 25 various types of vegetables. The samples were examined in physiological saline solution using sedimentation and centrifugation methods. The findings were analyzed by Graph-Pad version 5. P value less than 0.05 (95% CI) was considered significant. Results showed that 16.5% (n=322) of all vegetables were contaminated with one or more type of geo-helminth parasites. Garlic was the highest (35%) and cauliflower the lowest (4%) contaminated samples respectively. Ascaris lumbricoides was the most common geo-helminth found followed by hook worm species while Trichuris trichura was the least in all the vegetable samples. Leafy vegetables were highly contaminated 25.3% than vegetables with root parts 21.2% and fruity 9.09%. More than half of the contaminated vegetables were contaminated with single species of geo-helminth (P 0.05) while less than half with multiple types of geo-helminth contamination. Ninety two vegetables samples were contaminated with 2 species of parasites (P 0.05) and 45 with 3 (P>0.05) species of geo-helminth parasites. Education level of vendors and means of display were not significantly associated while types of vegetable used were significantly associated with the prevalence of parasites. The findings of this study provide evidence that consumption of raw vegetable has a high risk of acquiring geo-helminth infections. The authors believe that preventing the human to enter to the vegetable farmland for defecation, avoiding the irrigation of agricultural fields via night soil, and educating the people on proper washing and cooking of vegetables may be useful in reducing parasitic infections.

Resumo As infecções causadas por parasitas geo-helmínticos são chamados de geohelmintíases e são um dos problemas de saúde globais. Os vegetais comidos crus são a principal fonte de transmissão dos parasitas geo-helmínticos. O povo paquistanês acredita que comer vegetais crus é uma fonte significativa para obter vitaminas e minerais importantes. Com base na alta incidência de parasitas patogênicos e no cultivo de diferentes tipos de vegetais nas áreas de estudo, conduzimos este estudo para avaliar a contaminação por geo-helmintos de vegetais crus no noroeste de Khyber Pakhtunkhwa, Paquistão. Trata-se de um estudo descritivo composto por 1942 amostras de 25 tipos diversos de vegetais. As amostras foram examinadas em solução salina fisiológica utilizando métodos de sedimentação e centrifugação. Os achados foram analisados pelo Graph-Pad versão 5. O valor de P menor que 0,05 (IC 95%) foi considerado significativo. Os resultados mostraram que 16,5% (n = 322) de todas as hortaliças estavam contaminadas com um ou mais tipos de parasitas geo-helmínticos. O alho foi a amostra mais contaminada (35%) e a couve-flor a menos (4%), respectivamente. Ascaris lumbricoides foi o geo-helmíntico mais comum encontrado, seguido por espécies de verme-anzol, enquanto Trichuris trichura foi o menos encontrado em todas as amostras de vegetais. Os vegetais folhosos foram altamente contaminados 25,3% do que os vegetais com partes de raiz 21,2% e frutados 9,09%. Mais da metade dos vegetais contaminados estavam contaminados com uma única espécie de geo-helmintos (P 0,05), enquanto menos da metade com vários tipos de contaminação com geo-helmintos. Noventa e duas amostras de vegetais estavam contaminadas com 2 espécies de parasitas (P 0,05) e 45 com 3 (P> 0,05) espécies de parasitas geo-helmínticos. O nível de escolaridade dos vendedores e os meios de exibição não foram significativamente associados, enquanto os tipos de vegetais usados foram significativamente associados à prevalência de parasitas. Os resultados deste estudo fornecem evidências de que o consumo de vegetais crus tem um alto risco de adquirir infecções por geo-helmintos. Os autores acreditam que impedir que o ser humano entre na terra de hortaliças para defecação, evitar a irrigação de campos agrícolas via solo noturno e educar as pessoas sobre a lavagem e cozimento adequados de vegetais pode ser útil na redução de infecções parasitárias.

Mechanisms of Compound Kushen Injection for the treatment of bladder cancer based on bioinformatics and network pharmacology with experimental validation / 中国天然药物

Bladder cancer is the most common malignancy of the urinary system. Compound Kushen Injection (CKI) is a Chinese medicinal preparation that has been widely used in the treatment of various types of cancers in the past two decades. However, the pharmacological effect of CKI on bladder cancer is not still completely understood. In the current study, network pharmacology combined with bioinformatics was used to elucidate the therapeutic mechanism and potential targets of CKI in bladder cancer. The mechanism by which CKI was effective against bladder cancer was further verified in vitro using human bladder cancer cell line T24. Network pharmacology analysis identified 35 active compounds and 268 target genes of CKI. Bioinformatics data indicated 5500 differentially expressed genes associated with bladder cancer. Common genes of CKI and bladder cancer suggested that CKI exerted anti-bladder cancer effects by regulating genes such as MMP-9, JUN, EGFR, and ERK1. Functional enrichment analysis indicated that CKI exerted therapeutic effects on bladder cancer by regulating certain biological processes, including cell proliferation, cell migration, and cell apoptosis. In addition, Kyoto Encyclopedia of Genes and Genomes enrichment analysis implicated pathways related to cancer, bladder cancer, and the PI3K-Akt signaling pathway. Consistently, cell experiments indicated that CKI inhibited the proliferation and migration of T24 cells, and induced their apoptosis. Moreover, RT-qPCR and Western blot results demonstrated that CKI was likely to treat bladder cancer by down-regulating the gene and protein expression of MMP-9, JUN, EGFR, and ERK1. CKI inhibited the proliferation and migration, and induced the apoptosis of T24 bladder cancer cells through multiple biological pathways and targets. CKI also exhibited significant effects on the regulation of key genes and proteins associated with bladder cancer. Overall, our findings provide solid evidence and deepen current understanding of the therapeutic effects of CKI for bladder cancer, and further support its clinical use.

Clinical relevance of miR-423-5p levels in chronic obstructive pulmonary disease patients

Abstract Objective: This study aimed to examine changes in miRNAs expression profile of COPD patients. Methods: Thirty-six COPD patients as well as thirty-three healthy volunteers were recruited. Total RNAs were collected from the plasma of each participant. The differentially expressed miRNAs in COPD were screened from the GEO database. RT-qPCR was carried out to detect miRNA expression. Results: In total, 9 out of 55 miRNAs were expressed differentially in COPD patients. Confirmed by RT-qPCR validation, 6 miRNAs increased while 3 miRNAs decreased. Further analysis of miR-423-5p, which has not been reported in COPD, showed that AUC for the diagnosis of COPD was 0.9651, and miR-423-5p levels was inversely correlated with the duration of smoking. Conclusion: The present study demonstrates that miR-423-5p is a potential marker for identifying COPD patients.

Evaluation of vegetables grown in dry mountainous regions for soil transmitted helminths contamination / Avaliação de vegetais para contaminação por helmintos transmitida pelo solo em quatro distritos da divisão de Malakand: noroeste do Paquistão

Infection caused by geo-helminth parasites are called geohelminthiasis are one of the global health problems. Vegetables eaten raw is the principal source of transmission of geo-helminth parasites. Pakistani people believe that eating raw vegetables are a significant source to get important vitamins and minerals. Based on the high incidence of pathogenic parasites and cultivating different vegetable types in the study areas, we conducted this study to evaluate the geo-helminth contamination of raw vegetables in northwest Khyber Pakhtunkhwa, Pakistan. This is a descriptive study comprised, 1942 samples of 25 various types of vegetables. The samples were examined in physiological saline solution using sedimentation and centrifugation methods. The findings were analyzed by Graph-Pad version 5. P value less than 0.05 (95% CI) was considered significant. Results showed that 16.5% (n=322) of all vegetables were contaminated with one or more type of geo-helminth parasites. Garlic was the highest (35%) and cauliflower the lowest (4%) contaminated samples respectively. Ascaris lumbricoides was the most common geohelminth found followed by hook worm species while Trichuris trichura was the least in all the vegetable samples. Leafy vegetables were highly contaminated 25.3% than vegetables with root parts 21.2% and fruity 9.09%. More than half of the contaminated vegetables were contaminated with single species of geo-helminth (P<0.05) while less than half with multiple types of geo-helminth contamination. Ninety two vegetables samples were contaminated with 2 species of parasites (P<0.05) and 45 with 3 (P>0.05) species of geo-helminth parasites. Education level of vendors and means of display were not significantly associated while types of vegetable used were significantly associated with the prevalence of parasites. The findings of this study provide evidence that consumption of raw vegetable has a high risk of acquiring geo-helminth infections. The authors believe that preventing the human to enter to the vegetable farmland for defecation, avoiding the irrigation of agricultural fields via night soil, and educating the people on proper washing and cooking of vegetables may be useful in reducing parasitic infections.

As infecções causadas por parasitas geo-helmínticos são chamados de geohelmintíases e são um dos problemas de saúde globais. Os vegetais comidos crus são a principal fonte de transmissão dos parasitas geo-helmínticos. O povo paquistanês acredita que comer vegetais crus é uma fonte significativa para obter vitaminas e minerais importantes. Com base na alta incidência de parasitas patogênicos e no cultivo de diferentes tipos de vegetais nas áreas de estudo, conduzimos este estudo para avaliar a contaminação por geo-helmintos de vegetais crus no noroeste de Khyber Pakhtunkhwa, Paquistão. Trata-se de um estudo descritivo composto por 1942 amostras de 25 tipos diversos de vegetais. As amostras foram examinadas em solução salina fisiológica utilizando métodos de sedimentação e centrifugação. Os achados foram analisados pelo Graph-Pad versão 5. O valor de P menor que 0,05 (IC 95%) foi considerado significativo. Os resultados mostraram que 16,5% (n = 322) de todas as hortaliças estavam contaminadas com um ou mais tipos de parasitas geo-helmínticos. O alho foi a amostra mais contaminada (35%) e a couve-flor a menos (4%), respectivamente. Ascaris lumbricoides foi o geo-helmíntico mais comum encontrado, seguido por espécies de verme-anzol, enquanto Trichuris trichura foi o menos encontrado em todas as amostras de vegetais. Os vegetais folhosos foram altamente contaminados 25,3% do que os vegetais com partes de raiz 21,2% e frutados 9,09%. Mais da metade dos vegetais contaminados estavam contaminados com uma única espécie de geo-helmintos (P <0,05), enquanto menos da metade com vários tipos de contaminação com geo-helmintos. Noventa e duas amostras de vegetais estavam contaminadas com 2 espécies de parasitas (P <0,05) e 45 com 3 (P> 0,05) espécies de parasitas geo-helmínticos. O nível de escolaridade dos vendedores e os meios de exibição não foram significativamente associados, enquanto os tipos de vegetais usados foram significativamente associados à prevalência de parasitas. Os resultados deste estudo fornecem evidências de que o consumo de vegetais crus tem um alto risco de adquirir infecções por geo-helmintos. Os autores acreditam que impedir que o ser humano entre na terra de hortaliças para defecação, evitar a irrigação de campos agrícolas via solo noturno e educar as pessoas sobre a lavagem e cozimento adequados de vegetais pode ser útil na redução de infecções parasitárias.

Identification of key genes and pathways associated with esophageal adenocarcinoma development based on GEO database and bioinformatics / 西安交通大学学报(医学版)

【Objective】 To investigate the potential genes and pathways associated with esophageal adenocarcinoma through microarray expression profiling data analysis and bioinformatics approaches. 【Methods】 The mRNA expression microarray data related to esophageal adenocarcinoma development were screened out with GEO database, and the biological processes, signaling pathways and network of these genes were statistically analyzed using "R" software. 【Results】 The GSE26886 was obtained from GEO database. A total of 1383 differentially expressed genes were associated with carcinogenesis of esophageal adenocarcinoma, including 607 up-regulated and 776 down-regulated genes. These genes were involved in metabolism, stimulate responses, cell adhesion, cell regeneration and immune biological processes. Eight significantly enriched pathways were identified by pathway analysis. 【Conclusion】 The bioinformatic method can analyze the gene chip data effectively. Multiple genes and signaling pathways are involved in the carcinogenesis of esophageal adenocarcinoma, which provides a new idea or approach for exploring biomarkers of early screening and therapeutic targets.