Dynamic Metro Stations Importance Evaluation Based on Network Topology and Real-Time Passenger Flows

Peipei Peng,Zhao Liu,Jianhua Guo,Chao Wang 대한토목학회 2023 KSCE Journal of Civil Engineering Vol.27 No.10

Identifying the importance of metro stations is crucial for enhancing the efficiency and safety of the urban rail transit system. This study proposes an integrated approach to evaluate the importance of metro stations based on jointly the static metro network topology and the dynamic real-time passenger flows. The static characteristics of metro stations are reflected through node degree and clustering coefficient of metro network topology based on the complex network theory. The dynamic characteristics of metro stations are assessed using the passenger flow time series, which were modeled using the autoregressive integrated moving average plus autoregressive conditional heteroscedasticity model (i.e., ARIMA+GARCH model). By combining the static and dynamic characteristics of metro stations, a comprehensive index is proposed to quantify the importance of metro stations. The integrated approach is tested using metro network and passenger flow data collected from Suzhou, China. The resultsindicate that compared with the topology analysis, the passenger flows could strengthen the importance of transfer stations and their neighboring stations. Especially for the loop lines that formed by the intersection of two or more lines within the network, the importance index of metro stations within these loop lines is inversely proportional to the number of stations in the loop. It indicates that as a metro network continues to expand with the addition of new lines and stations, this is a high likelihood of increased concentration of importance with the network. The concentration of importance in the metro network can be attributed to the emergence of highly connected loop lines that facilitate efficient movement of passengers.

Epigenetic inactivation of ACAT1 promotes epithelial-mesenchymal transition of clear cell renal cell carcinoma

Han Peipei,Wu Shu,Li Limei,Li Danping,Zhao Jun,Zhang Haishan,Wang Yifang,Zhong Xuemin,Zhang Zhe,Li Ping,Matskova Liudmila,Zhou Xiaoying 한국유전학회 2022 Genes & Genomics Vol.44 No.4

Background: Acetyl-CoA acyltransferase 1 (ACAT1) is a key enzyme catalyzing the production of mitochondrial ketone bodies. We have shown that ACAT1 is down-regulated in kidney renal clear cell carcinoma (KIRC) previously. Objective: To investigate the reasons for downregulation of ACAT1 in KIRC and explore the underlying mechanisms involved in metastatic inhibition regulated by ACAT1. Methods: The Gene Expression Omnibus (GEO) database was queried for meta-analysis of ACAT1 mRNA expression in KIRC. The UALCAN website was used to compare the methylation levels of the ACAT1 promoter region in KIRC and normal tissues. RT-qPCR was used to quantitate ACAT1 transcription levels. The GCBI and Tarbase V.8 databases were used to predict miRNAs that may target the mRNA of ACAT1. The correlation between mRNA expression of ACAT1, MMP7 (matrix metallopeptidase 7), CDH1 (E-cadherin), EpCAM (epithelial cell adhesion molecule), and VIM (vimentin) was analyzed. Extracellular MMP7 protein was quantitated using an ELISA assay. Results: The methylation level of the ACAT1 promoter region in KIRC was significantly higher than that in the normal kidney tissues. The ACAT1 mRNA expression in the KIRC cell lines was restored after treatment with 5-aza-dC (p < 0.05). MiR-21-5p is a conserved microRNA targeting ACAT1. It is expressed at a significantly higher level in KIRC than in normal tissues (p < 0.001). MiR-21-5p miRNA expression negatively correlates with ACAT1 mRNA expression. The expression of miR-21-5p is higher at the T3-T4 stages and in the histologic grades G3-G4. Patients with high miR-21-5p expression tended to have lower overall survival, suggesting that miR-21-5p could serve as a potentially valuable diagnostic biomarker for KIRC (AUC = 0.957; p < 0.001). A mimetic of miR-21-5p inhibited the expression of ACAT1 mRNA and protein. In addition, ACAT1 mRNA expression positively correlates with CDH1 and EpCAM but is negatively correlated with VIM. Overexpression of ACAT1 suppresses the secretion of MMP7 in KIRC cells. Conclusion: Expression of ACAT1 in KIRC is controlled at two levels, firstly by the hypermethylation of the ACAT1 promoter region and secondly by overexpression of miR-21-5p. Downregulation of ACAT1 expression correlates with epithelial-mesenchymal transition (EMT).

Isolation, identification and characterization of a novel elastase from Chryseobacterium indologenes

Yunlong Lei,Peipei Zhao,Chenglei Li,Haixia Zhao,Zhi Shan,Qi Wu 한국응용생명화학회 2018 Applied Biological Chemistry (Appl Biol Chem) Vol.61 No.3

Elastase is a type of protease that specifically degrades elastin. It has broad application prospects in medicine, food industry, and daily-use chemical industry. In this study, we isolated a bacterial strain WZE87 with high elastin-hydrolysis activity, which was identified as Chryseobacterium indologenes based on morphology, physiological and biochemical characteristics, and 16S rDNA sequence analysis. The elastase produced by this strain was purified by three steps: ammonium sulfate precipitation, Q-Sepharose fast-flow anion-exchange chromatography, and Sephadex G-75 gel-filtration chromatography. The purified elastase was 2376.5 U/mg in activity (a 8.3-fold increase in specific activity), and the recovery was 5.8%. Its molecular mass was estimated to be 26 kDa by sodium dodecyl sulfate–polyacrylamide gel electrophoresis. This enzyme was stable in the pH range of 5.0–10.5 at 37 C. The optimal temperature and pH were 37 C and 7.5, respectively. The activity of this elastase was found to decrease when the temperature was higher than 50 C. The activity was also inhibited by Zn2?, Fe2?, Fe3?, and Mn2? ions. The specific hydrolytic ability of this enzyme was similar to that of papain on substrates like gelatin, casein, soybean-isolated protein and bovine hemoglobin. However, this elastase preferentially hydrolyzed elastin in a protein mixture because of its specific adsorption. Considering its promising properties, this protease may be considered a potential candidate for applications in related industries.

Isolation, identification and characterization of a novel elastase from Chryseobacterium indologenes

Lei, Yunlong,Zhao, Peipei,Li, Chenglei,Zhao, Haixia,Shan, Zhi,Wu, Qi The Korean Society for Applied Biological Chemistr 2018 Applied Biological Chemistry (Appl Biol Chem) Vol.61 No.3

Elastase is a type of protease that specifically degrades elastin. It has broad application prospects in medicine, food industry, and daily-use chemical industry. In this study, we isolated a bacterial strain WZE87 with high elastin-hydrolysis activity, which was identified as Chryseobacterium indologenes based on morphology, physiological and biochemical characteristics, and 16S rDNA sequence analysis. The elastase produced by this strain was purified by three steps: ammonium sulfate precipitation, Q-Sepharose fast-flow anion-exchange chromatography, and Sephadex G-75 gel-filtration chromatography. The purified elastase was 2376.5 U/mg in activity (a 8.3-fold increase in specific activity), and the recovery was 5.8%. Its molecular mass was estimated to be 26 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This enzyme was stable in the pH range of 5.0-10.5 at $37^{\circ}C$. The optimal temperature and pH were $37^{\circ}C$ and 7.5, respectively. The activity of this elastase was found to decrease when the temperature was higher than $50^{\circ}C$. The activity was also inhibited by $Zn^{2+}$, $Fe^{2+}$, $Fe^{3+}$, and $Mn^{2+}$ ions. The specific hydrolytic ability of this enzyme was similar to that of papain on substrates like gelatin, casein, soybean-isolated protein and bovine hemoglobin. However, this elastase preferentially hydrolyzed elastin in a protein mixture because of its specific adsorption. Considering its promising properties, this protease may be considered a potential candidate for applications in related industries.

Inactivation of epithelial sodium ion channel molecules serves as effective diagnostic biomarkers in clear cell renal cell carcinoma

Zheng Qian,Wang Yifang,Zhao Ran,Han Peipei,Zhao Jun,Li Limei,Zhou Xiaohui,Li Ping,Mo Yingxi,Pan Xinli,Luo Wenqi,Zhou Xiaoying 한국유전학회 2023 Genes & Genomics Vol.45 No.7

Background Non-voltage-gated sodium channel, also known as the epithelial sodium channel (ENaC), formed by heteromeric complexes consisting of SCNN1A, SCNN1B, and SCNN1G, is responsible for maintaining sodium ion and body fluid homeostasis in epithelial cells. However, no systematic study of SCNN1 family members has been conducted in renal clear cell carcinoma (ccRCC) to date. Objective To investigate the abnormal expression of SCNN1 family in ccRCC and its potential correlation with clinical parameters. Methods The transcription and protein expression levels of SCNN1 family members in ccRCC were analyzed based on the TCGA database, and were confirmed by quantitative RT-PCR and immunohistochemical staining assays, respectively. The area under curve (AUC) was used to evaluate the diagnostic value of SCNN1 family members for ccRCC patients. Results The mRNA and protein expression of SCNN1 family members was significantly downregulated in ccRCC compared with normal kidney tissues, which might be due to DNA hypermethylation in the promoter region. It is worth noting that the AUC of SCNN1A, SCNN1B, and SCNN1G were 0.965, 0.979, and 0.988 based on the TCGA database (p < 0.0001), respectively. The diagnostic value was even higher when combing these three members together (AUC = 0.997, p < 0.0001). Intriguingly, the mRNA level of SCNN1A was significantly lower in females compared with males, while SCNN1B and SCNN1G were increased with the progression of ccRCC and remarkably associated with a worse outcome for patients. Conclusion The aberrantly decrease of SCNN1 family members might serve as valuable biomarkers for the diagnosis of ccRCC.

Phase II trial of VEGFR2 inhibitor apatinib for metastatic sarcoma: focus on efficacy and safety

Zhichao Liao,Feng Li,Chao Zhang,Lei Zhu,Yehui Shi,Gang Zhao,Xu Bai,Shafat Hassan,Xinyue Liu,Ting Li,Peipei Xing,Jun Zhao,Jin Zhang,Ruwei Xing,Sheng Teng,Yun Yang,Kexin Chen,Jilong Yang 생화학분자생물학회 2019 Experimental and molecular medicine Vol.51 No.-

Apatinib (YN968D1) is a novel tyrosine kinase inhibitor targeting vascular endothelial growth factor receptor 2 (VEGFR- 2). We conducted a single-arm, nonrandomized phase II study (NCT03121846) to assess the efficacy and safety of apatinib in patients with stage IV sarcoma. We recruited 64 patients with stage IV sarcoma who had failed chemotherapy. The primary endpoint was progression-free survival (PFS), and the secondary endpoints were progression-free survival rate (PFR), objective response rate (ORR), and disease control rate (DCR) at week 12. Treatment-related adverse effects (AEs) were evaluated. Fifty-nine patients were assessed for efficacy and 64 patients for AEs. The median PFS was 7.93 months. At 12 weeks, the PFR was 74%, the ORR was 16.95% (10/59), and the DCR was 86.44% (51/59). The final ORR was 15.25% (9/59) and the DCR was 57.63% (34/59). Notably, 22 patients (34.38%) who developed hypertension, hand-foot-skin reaction, or proteinuria had significantly longer OS than those without these AEs (18.20 vs. 10.73 months; P = 0.002). We conclude that apatinib is effective and well tolerated in patients with advanced sarcoma. The development of hypertension, hand-foot-skin reaction, or proteinuria may indicate a favorable prognosis, representing a novel finding in sarcoma patients.

Over-expression of FaGalLDH Increases Ascorbic Acid Concentrations and Enhances Salt Stress Tolerance in Arabidopsis thaliana

Dun Wanwan,Wei Xuan,Wang Lu,Liu Jingjing,Zhao Jing,Sun Peipei,Fang Congbing,Xie Xingbin 한국식물학회 2023 Journal of Plant Biology Vol.66 No.1

The strawberry (Fragaria×ananassa) is an economically important perennial crop plant, and its fruits are rich in vitamin C (l-ascorbic acid [AsA]) and other nutrients. l-galactono-1,4-lactone dehydrogenase (GalLDH) is a key enzyme in the terminal step of AsA biosynthesis pathway in plants. Here, the GalLDH gene (FaGalLDH) was cloned from ‘Benihoppe’ strawberries. AsA content increased during fruit development and peaked at the red-ripening stage, and AsA concentrations in diferent tissues were correlated with enzyme activity and transcription level of FaGalLDH. Transient over-expression of FaGalLDH in strawberry fruit increased its overall expression and AsA production signifcantly, whereas transient RNAi of FaGalLDH decreased its expression and AsA content. Furthermore, the optimum pH and temperature for FaGalLDH activity were 8.0 and 25 °C, respectively. Ectopic expression of the FaGalLDH gene in Arabidopsis resulted in higher AsA content and enzyme activity in transgenic lines than in wild-type plants. FaGalLDH over-expression resulted in enhanced tolerance to salt stress due to reduced accumulation of malondialdehyde, H2O2, and O2 .−, as well as higher survival rates, root length, proline content, and superoxide dismutase, peroxidase, and catalase activities. These results provide useful information regarding AsA biosynthesis and salt tolerance, which may help to improve strawberry fruit quality and productivity.

Establishment and Application of Target Gene Disruption System in Saccharomyces boulardii

Longjiang Wang,Hui Sun,Jie Zhang,Qing Liu,Tiantian Wang,Peipei Chen,Hongmei Li,Yihong Xiao,Fangkun Wang,Xiaomin Zhao 한국생물공학회 2015 Biotechnology and Bioprocess Engineering Vol.20 No.1

Saccharomyces boulardii is the best knownprobiotic yeast, widely used as a therapeutic agent for thetreatment or prevention of diarrhea and intestine disorders. In the present work, we established a target gene disruptionsystem for S. boulardii based on the Cre-loxP system usedfor S. cerevisiae and other fungi by screening out selectionmarkers, working out the transformation method, andconstructing essential plasmids for S. boulardii. Theestablished system was successfully applied to the URA3gene disruption and created an ura3 null mutant strain ofS. boulardii. The system can be used for PCR mediatedgene disruption, cloning mediated gene disruption, andreintroduction of the deleted gene back to the mutant. Allthe introduced exogenous DNAs in the gene disruptionprocedures were removed from the final mutant strainexcept the two 34 bp loxP pieces left in deleted gene loci.