SM-RCNV: a statistical method to detect recurrent copy number variations in sequenced samples

Yaoyao Li,Xiguo Yuan,Junying Zhang,Liying Yang,Jun Bai,Shan Jiang 한국유전학회 2019 Genes & Genomics Vol.41 No.5

Background Copy number variation (CNV) is an important form of genomic structural variation and is linked to dozens of human diseases. Using next-generation sequencing (NGS) data and developing computational methods to characterize such structural variants is significant for understanding the mechanisms of diseases. Objective The objective of this study is to develop a new statistical method of detection recurrent CNVs across multiple samples from genomic sequences. Methods A statistical method is carried out to detect recurrent CNVs, referred to as SM-RCNV. This method uses a statistic associated with each location by combining the frequency of variation at one location across whole samples and the correlation among consecutive locations. The weights of the frequency and correlation are trained using real datasets with known CNVs. P-value is assessed for each location on the genome by permutation testing. Results Compared with six peer methods, SM-RCNV outperforms the peer methods under receiver operating characteristic curves. SM-RCNV successfully identifies many consistent recurrent CNVs, most of which are known to be of biological significance and associated with diseased genes. The validation rate of SM-RCNV in the CEU call set and YRI call set with Database of Genomic Variants are 258/328 (79%) and (157/309) 51%, respectively. Conclusion SM-RCNV is a well-grounded statistical framework for detecting recurrent CNVs from multiple genomic sequences, providing valuable information to study genomes in human diseases. The source code is freely available at https ://sourc eforg e.net/proje cts/sm-rcnv/.

Parameter optimization of five-axis polishing using abrasive belt flap wheel for blisk blade

Junfeng Zhang,Yaoyao Shi,Xiaojun Lin,Zhishan Li 대한기계학회 2017 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.31 No.10

Considering the weak rigidity of blisk blades and the limited accessibility of blisk tunnels, polishing blisk blades is difficult when using tools with poor flexibility and large dimension. Hence, to reduce the surface roughness (SR) of a blisk blade, five-axis polishing method with abrasive belt flap wheel (ABFW) is employed to polish the blisk blade based on the analysis of the blisk structure and advantages of ABFW polishing. Polishing experiments based on central composite design are performed using ABFW. Response surface method (RSM) is employed to establish a predictive model between SR and various parameters, including ABFW size, contact force, spindle speed, and feed rate. Analysis of variance is then performed to evaluate the proposed model. The degree of influence of each factor on SR after polishing using ABFW is determined by plotting main effects. The interactions of polishing factors on SR are analyzed by RSM. Optimal parameters are obtained by response surface optimization. Finally, an experiment on blisk blade polishing using ABFW on a five-axis polishing machine is carried out for confirmation. Results indicate that the surface quality of the blisk blade after polishing is significantly improved, with SR being less than 0.4 μm.

Association of the Serotonin Receptor 3E Gene as a Functional Variant in the MicroRNA-510 Target Site with Diarrhea Predominant Irritable Bowel Syndrome in Chinese Women

( Yu Zhang ),( Yaoyao Li ),( Zhenfeng Hao ),( Xiangming Li ),( Ping Bo ),( Weijuan Gong ) 대한소화기기능성질환·운동학회 2016 Journal of Neurogastroenterology and Motility (JNM Vol.22 No.2

Background/Aims The functional variant (rs56109847) in the 3′-untranslated regions (3′-UTR) of the serotonin receptor 3E (HTR3E) gene is associated with female diarrhea predominant irritable bowel syndrome (IBS-D) in British populations. However, the relationship of the polymorphism both to HTR3E expression in the intestine and to the occurrence of Chinese functional gastrointestinal disorders has yet to be examined. Methods Polymerase chain reaction amplification and restriction fragment length polymorphism analyses were employed to detect polymorphisms among Chinese Han women, particularly 107 patients with IBS-D, 99 patients with functional dyspepsia (FD), 115 patients with mixed IBS and 69 patients with IBS-D + FD. We also assessed microRNA-510 (miR-510) and HTR3E expression in human colonic mucosal tissues with immunohistochemistry and other methods. Dual-luciferase reporter assays were conducted to examine the binding ability of miR-510 and HTR3E 3′-UTR. Results Genotyping data showed the variant rs56109847 was significantly associated with IBS-D, but not with FD, mixed-IBS, or FD + IBS-D. HTR3E was abundantly expressed around the colonic mucosal glands but less expressed in the stroma. miR-510 expression decreased, whereas HTR3E expression increased in the colonic mucosal tissue of patients with IBS-D compared with those in controls. HTR3E expression was significantly higher in patients with the GA genotype than that in patients with the GG genotype. The single nucleotide polymorphisms disrupted the binding site of miR-510 and significantly upregulated luciferase expression in HEK293 and HT-29 cells. Conclusions The single-nucleotide polymorphisms rs56109847 led to reduced microRNA binding and overexpression of the target gene in intestinal cells, thereby increasing IBS-D risk in the Chinese Han population. The decreased expression of miR-510 might contribute to IBS-D. (J Neurogastroenterol Motil 2016;22:272-281)

A Bacillus coagulans and its Application in Pine Pollen Fermentation

Shanyan Yang,Yaoyao Wu,Chubo Luo,Zhihong Di,Yunpeng Wu,Jie Zhang,Yaomei Xu 한국식품과학회 2015 Food Science and Biotechnology Vol.24 No.6

In the study, a potential L-lactic acid-producing bacillus-strain LT1 was isolated. It was identified as Bacillus coagulans based on its morphological, physiological, biochemical properties, and phylogenetic similarity of 16S rDNA. The fermentation conditions of pine pollen by strain LT1 were optimized using Box-Behnken design and response surface methodology. Optimum values of the tested variables for production of viable counts were an inoculum size of 9.22%, temperature= 49.21℃, and an initial pH of 6.82. Under optimized conditions, the viable count was 5.49×109 CFU/mL. Finally, the single factor experiment as preliminary research for fermentation product treatment was performed.

Complexity of Driving Scenarios Based on Traffic Accident Data

Dong Xinchi,Zhang Daowen,Mu Yaoyao,Zhang Tianshu,Tang Kaiwen 한국자동차공학회 2024 International journal of automotive technology Vol.25 No.1

To solve the problems of diffi cult quantifi cation of complex driving scenes and unclear classifi cation, a method of complex measurement and scene classifi cation was proposed. Based on the Bayesian network, the posterior probability distribution was obtained, the variable weights were determined by information entropy theory and BP neural network, and the gravitational model was improved so that the complex metric model of the driving scene was established, the static and dynamic complexity of the scene was quantifi ed respectively, and a weighted fusion of the two was conducted. The K-means clustering method was used to divide the driving scenario into three categories, i.e., simple scenario, medium complex scenario, and complex scenario, and the rationality of the method was verifi ed by experiments. This scenario complex metric method can provide a reference for studying the complex metrics and scene classifi cation of smart vehicle test scenarios.

P14.5 functions to inhibit cell migration and can be used as a prognostic marker in hepatocellular carcinoma

Song Sa,Pan Jian,Zhang Yaoyao,Xu Yuehuan,Zhang Qingmei,Xie Xiaoxun,Zhou Qingniao,Mo Farong,Luo Guorong,Chao Naixia 한국유전학회 2023 Genes & Genomics Vol.45 No.1

Background Hepatocellular carcinoma (HCC) is the most common primary liver malignancy with a high mortality rate. P14.5 is a member of the highly conserved YER057c/YIL051c/YjgF subfamily and is highly expressed in the liver. However, its low expression is associated with carcinogenesis in HCC. Objective This study aimed to investigate the role and prognostic significance of P14.5 in HCC. Methods The clinical significance of P14.5 in HCC was examined using ONCOMINE, UALCAN, Human Protein Atlas, and Kaplan–Meier plotter. The DNA methylation profile of the P14.5 promoter was examined in 103 HCC and paired precancerous tissues; the HCC cell lines HepG2, MHCC-97L, SMMC-7721, SK-Hep-1, and Huh7; and the normal hepatic cell line HL-7702 via MALDI-TOF mass spectrometry. In addition, in vitro experiments were performed to examine the effects of P14.5 overexpression on the proliferation and migration of SMMC-7721 cells. Results Low expression of P14.5 was correlated with shorter overall survival (OS) and disease-free survival (DFS) in HCC. Based on the results of MALDI-TOF mass spectrometry, no difference was observed in the methylation level between HCC cells and normal human hepatic cells and between HCC and paired precancerous tissues. Additionally, P14.5 overexpression promoted the proliferation and inhibited the migration of SMMC7721 cells in vitro. Conclusions P14.5 may serve as a prognostic biomarker in HCC and plays a role in the migration and proliferation of HCC cells. Low expression of P14.5 during hepatocarcinogenesis is not attributed to DNA methylation.

LGR5 Modulates Differentiated Phenotypes of Chondrocytes Through PI3K/AKT Signaling Pathway

Wu Xu,Fu Yaoyao,Ma Jing,Li Chenlong,He Aijuan,Zhang Tianyu 한국조직공학과 재생의학회 2024 조직공학과 재생의학 Vol.21 No.5

Background: Tissue engineering is increasingly viewed as a promising avenue for functional cartilage reconstruction. However, chondrocyte dedifferentiation during in vitro culture remains an obstacle for clinical translation of tissue engineered cartilage. Re-differentiated induction have been employed to induce dedifferentiated chondrocytes back to their original phenotype. Regrettably, these strategies have been proven to be only moderately effective. Methods: To explore underlying mechanism, RNA transcriptome sequencing was conducted on primary chondrocytes (P0), dedifferentiated chondrocytes (P5), and redifferentiated chondrocytes (redifferentiation-induction of P5, P5.R). Based on multiple bioinformatics analysis, LGR5 was identified as a target gene. Subsequently, stable cell lines with LGR5 knocking-down and overexpression were established using P0 chondrocytes. The phenotypic changes in P1 and P5 chondrocytes with either LGR5 knockdown or overexpression were assessed to ascertain the potential influence of LGR5 dysregulation on chondrocyte phenotypes. Regulatory mechanism was then investigated using bioinformatic analysis, protein–protein docking, immunofluorescence co-localization and immunoprecipitation. Results: The current study found that dysregulation of LGR5 can significantly impact the dedifferentiated phenotypes of chondrocytes (P5). Upregulation of LGR5 appears to activate the PI3K/AKT signal via increasing the phosphorylation levels of AKT (p-AKT1). Moreover, the increase of p-AKT1 may stabilize β-catenin and enhance the intensity of Wnt/β-catenin signal, and help to restore the dedifferentated phenotype of chondrocytes. Conclusion: LGR5 can modulate the phenotypes of chondrocytes in P5 passage through PI3K/AKT signaling pathway.

Immobilization of ammonium and phosphate in aqueous solution by zeolites synthesized from fly ashes with different compositions

Xiaodong Ji,Mulan Zhang,Yujie Wang,Yichu Song,Yaoyao Ke,Yunqi Wang 한국공업화학회 2015 Journal of Industrial and Engineering Chemistry Vol.22 No.-

Immobilization of ammonium and phosphate by zeolites synthesized from low-calcium (LC-Z) and highcalcium (HC-Z) fly ashes is studied. LC-Z has higher ammonium immobilization capacity while HC-Z has better performance in phosphate uptake. As part of Ca2+ released from HC-Z compete with ammonium the exchangeable sites in LC-Z, LC-Z can affect phosphate immobilization of HC-Z, and HC-Z also lowers ammonium uptake of LC-Z. Separate dosing of LC-Z and HC-Z, i.e., first LC-Z and then HC-Z, is proved better than mixed dosing at simultaneous immobilization of ammonium and phosphate. The effect parameters for phosphate and ammonium immobilization of LTH-Z are investigated.

Active control of amplitude and phase of high-power RF systems in EAST ICRF heating experiments

Zhu Guanghui,Liu Lunan,Mao Yuzhou,Zhang Xinjun,Guo Yaoyao,Ai Lin,Jiang Runhao,Qin Chengming,Zhang Wei,Yang Hua,Yuan Shuai,Wang Lei,Ju Songqing,Wang Yongsheng,Sun Xuan,Yang Zhida,Wang Jinxin,Cheng Yan 한국원자력학회 2023 Nuclear Engineering and Technology Vol.55 No.2

The EAST ICRF system operating space has been extended in power and phase control with a low-level RF system for the new double-strap antenna. Then the multi-step power and periodic phase scanning experiment were conducted in L-mode plasma, respectively. In the power scanning experiment, the stored energy, radiation power, plasma impedance and the antenna's temperature all have positive responses during the short ramp-ups of PL;ICRF. The core ion temperature increased from 1 keV to 1.5 keV and the core heating area expanded from jZj 5 cmto jZj 10 cm during the injection of ICRF waves. In the phasing scanning experiment, in addition to the same conclusions as the previous relatively phasing scanning experiment, the superposition effect of the fluctuation of stored energy, radiation power and neutron yield caused by phasing change with dual antenna, resulting in the amplitude and phase shift, was also observed. The active control of RF output facilitates the precise control of plasma profiles and greatly benefits future experimental exploration.

Study on Mechanical Properties and Fracture Behavior of Granite after Thermal Treatment under Brazilian Splitting Test

Hanxiang Liu,Hongwen Jing,Qian Yin,Zhenlong Zhao,Yaoyao Meng,Liang Zhang 대한토목학회 2023 KSCE JOURNAL OF CIVIL ENGINEERING Vol.27 No.2

In this paper, the effects of thermal treatment on the mechanical properties, fracturecharacteristics, and roughness of the fracture surface of granite under the Brazilian splitting testare studied using an electro-hydraulic servo testing machine with an acoustic emission (AE)and digital image correlation (DIC) system. The test results show that: 1) Thermal treatmentdegrades the physical and mechanical properties. Density, P-wave velocity, and peak load ofgranite decrease with the increase in thermal treatment temperature (T). 2) With the increasing T,the fracture pattern changes from “I” type tensile fractures to “Y” type tensile-shear mixedfailure. The DIC results show that the fracture process changes from transient to progressive. 3) AE counts show that granite gradually changes from brittleness to ductility with the increaseof T. Furthermore, the variations in the RA and AF values of the AE events indicate that theincreasing T leads to an increase in shear cracks in granite. After the test, 4) the roughness ofthe fracture surface of the specimen was analyzed using a spatial digitizer. The results showthat thermal treatment significantly improved the fracture surface's asperity height androughness. 5) Scanning electron microscopy (SEM) results revealed that thermal treatmentleads to the generation of micro-cracks in granite and the desquamation of mineral grains,which influences the macro properties of granite.