Community Discovery in Weighted Networks Based on the Similarity of Common Neighbors

Miaomiao Liu,Jingfeng Guo,Jing Chen 한국정보처리학회 2019 Journal of information processing systems Vol.15 No.5

In view of the deficiencies of existing weighted similarity indexes, a hierarchical clustering method initializeexpand-merge (IEM) is proposed based on the similarity of common neighbors for community discovery inweighted networks. Firstly, the similarity of the node pair is defined based on the attributes of their commonneighbors. Secondly, the most closely related nodes are fast clustered according to their similarity to form initialcommunities and expand the communities. Finally, communities are merged through maximizing themodularity so as to optimize division results. Experiments are carried out on many weighted networks, whichhave verified the effectiveness of the proposed algorithm. And results show that IEM is superior to weightedcommon neighbor (CN), weighted Adamic-Adar (AA) and weighted resources allocation (RA) when usingthe weighted modularity as evaluation index. Moreover, the proposed algorithm can achieve more reasonablecommunity division for weighted networks compared with cluster-recluster-merge-algorithm (CRMA)algorithm.

Genome-wide identification of the valine-glutamine motif containing gene family and the role of VQ25-1 in pollen germination in Brassica oleracea

Yang Miaomiao,Liu Ziwei,Yu Yuanhui,Yang Min,Guo Li,Han Xuejie,Ma Xiangjie,Huang Ziya,Gao Qiguo 한국유전학회 2023 Genes & Genomics Vol.45 No.7

Background The plant-specific valine-glutamine (VQ) motif containing proteins tightly regulate plant growth, development, and stress responses. However, the genome-wide identification and functional analysis of Brassica oleracea (B. oleracea) VQ genes have not been reported. Objective To identify the VQ gene family in B. oleracea and analyze the function of Bo25-1 in pollen germination. Methods The Hidden Markov Model (HMM) of VQ family was used to query the BoVQ genes in the B. oleracea genome. The BoVQ genes preferentially expressed in anthers were screened by qRT-PCR. Subcellular localization of VQ25-1 was observed in Nicotiana benthamiana (N. benthamiana) leaves. To analysis the role of BoVQ25-1 in pollen germination, the expression of BoVQ25-1 was suppressed using antisense-oligonucleotides (AS-ODN). Results A total of 64 BoVQ genes were identified in the B. oleracea genome. BoVQ25-1 was found to be preferentially expressed in the B. oleracea anthers. BoVQ25-1 was cloned from the anthers of the B. oleracea cultivar ‘Fast Cycle’. BoVQ25-1 is localized to the nucleus. The pollen germination rate significantly decreased after AS-ODN treatment. Conclusion Sixty-four BoVQ genes were identified in the B. oleracea genome, of which BoVQ25-1 plays an important role in pollen germination.

Community Discovery in Weighted Networks Based on the Similarity of Common Neighbors

Liu, Miaomiao,Guo, Jingfeng,Chen, Jing Korea Information Processing Society 2019 Journal of information processing systems Vol.15 No.5

In view of the deficiencies of existing weighted similarity indexes, a hierarchical clustering method initialize-expand-merge (IEM) is proposed based on the similarity of common neighbors for community discovery in weighted networks. Firstly, the similarity of the node pair is defined based on the attributes of their common neighbors. Secondly, the most closely related nodes are fast clustered according to their similarity to form initial communities and expand the communities. Finally, communities are merged through maximizing the modularity so as to optimize division results. Experiments are carried out on many weighted networks, which have verified the effectiveness of the proposed algorithm. And results show that IEM is superior to weighted common neighbor (CN), weighted Adamic-Adar (AA) and weighted resources allocation (RA) when using the weighted modularity as evaluation index. Moreover, the proposed algorithm can achieve more reasonable community division for weighted networks compared with cluster-recluster-merge-algorithm (CRMA) algorithm.

Model diagnostics of parametric Tobit model based on cumulative residuals

Sun Zhihua,Guo Yuanyuan,Xie Tianfa,Wang Miaomiao 한국통계학회 2021 Journal of the Korean Statistical Society Vol.50 No.1

In this paper, we investigate the adequate check of the parametric Tobit model. A Cramér–Von Mises type test statistic is constructed, and its asymptotic properties under the null and alternative hypotheses are rigorously studied. The method is efective for the adequacy check of parametric regression models with a scalar or multivariate covariate. Furthermore, it avoids the nonparametric smoothing of the regression function and the choice of the smoothing parameter. Simulation studies are conducted to compare the performance of the proposed test procedure and the existing methods in the literature. A real data set of income is analyzed by applying the proposed method.

Effects of Friction and Anvil Design on Plastic Deformation during the Compression Stage of High-Pressure Torsion

( Yuepeng Song ),( Miaomiao Chen ),( Baoyan Xu ),( Dongsheng Gao ),( Jing Guo ),( Lingfeng Xu ),( Zheng Wang ),( Hyoung Seop Kim ) 대한금속재료학회(구 대한금속학회) 2016 대한금속·재료학회지 Vol.54 No.11

Herein, we report the results of our investigation on the effect of friction and anvil design on the heterogeneous plastic-deformation characteristics of copper during the compressive stage of high-pressure torsion (HPT), using the finite element method. The results indicate that the friction and anvil geometry play important roles in the homogeneity of the deformation. These variables affect the heterogeneous level of strain in the HPT compressed disks, as well as the flash in the disk edge region. The heterogeneous plastic deformation of the disks becomes more severe with the increasing depth of the cavity, as anvil angle and friction coefficient increase. However, the homogeneity increases with increases in the wall angle. The length of flash and the area of the dead metal zone increase with the depth of the cavity, while they decrease at a wall angle of 180°. (Received March 17, 2016; Accepted May 25, 2016)

A Core-Shell Spherical Silica Molecularly Imprinted Polymer for Efficient Selective Recognition and Adsorption of Dichlorophen

Xiao Wei,Miaomiao Yu,Jifeng Guo 한국섬유공학회 2019 Fibers and polymers Vol.20 No.3

A core-shell surface-imprinted polymer was successfully synthesized on the surface of silica spheres by precipitation polymerization. The polymers were used to selectively identify dichlorophen in complex environmental system. The physical-chemical properties of the silica sphere molecularly imprinted polymers were analyzed by scanning electron microscopy and transmission electron microscopy scans characterization. The adsorption properties of core-shell polymers were examined by adsorption isotherms, kinetics and selectivity experiments. The Langmuir adsorption isotherm well fitted the adsorption experimental data, and an increase of temperature enhanced the adsorption capacity. The maximum binding capacity of imprinted polymers reached 72.46 mg g-1 at 318 K. Meanwhile, the adsorption data of binding experiments were well-fitting by the pseudo-second-order equation. Compared with nonimprinted polymer, the imprinted polymer not only has specific selectivity towards dichlorophen but also has higher adsorption performance. Moreover, via the regeneration experiments, it has been demonstrated that the MIPs have certain stability to the adsorption for the target, which provides a good reference for the adsorption of dichlorophen by the imprinted polymer in water.

Analysis of Peripheral B Cell Subsets in Patients With Allergic Rhinitis

Jing Luo,Huanhuan Guo,Zhuofu Liu,Tao Peng,Xianting Hu,Miaomiao Han,Xiangping Yang,Xuhong Zhou,Huabin Li 대한천식알레르기학회 2018 Allergy, Asthma & Immunology Research Vol.10 No.3

Purpose: Recent evidence suggests that B cells can both promote and inhibit the development and progression of allergic disease. However, the characteristics of B cell subsets in patients with allergic rhinitis (AR) have not been well documented. This study aimed to analyze the characteristics of B cell subsets in the peripheral blood of AR patients. Methods: Forty-seven AR patients and 54 healthy controls were enrolled in this study, and the B cell subsets in peripheral blood of all subjects were analyzed by flow cytometry. Moreover, the serum total immunoglobulin E (IgE) and IgE concentrations secreted into the cultured peripheral blood mononuclear cells (PBMCs) were measured by using enzyme-linked immunosorbent assay. Results: We found the peripheral blood of AR patients contained higher percentages of memory B cells, plasma cells, and CD19+CD24hiCD27+ regulatory B cells (Bregs) than those of age-matched healthy controls (P<0.05), while the percentages of naïve B cells and CD19+CD24hiCD38hi Bregs were significantly lower in AR patients than in healthy individuals (P<0.05). In addition, the serum total IgE and IgE concentrations secreted into the cultured PBMCs were elevated in AR patients than in the healthy controls (P<0.05). Conclusions: Our findings indicate that AR patients were characterized by increase in terminally differentiated memory B cells or plasma cells and decreases in CD19+CD24hiCD38hi Breg cells in the peripheral blood.

Rational design of porous NiCo2S4 nanotubes for hybrid supercapacitor

Wang Haiyang,Liang Miaomiao,He Zemin,Guo Zhun,Zhao Yang,Li Kexuan,Song Wenqi,Zhang Yongming,Zhang Xin,Zhao Yuzhen,Miao Zongcheng 한국물리학회 2022 Current Applied Physics Vol.35 No.-

The nanotube-consisted flower-like NiCo2S4 is successfully fabricated by a novel two-step hydrothermal technique. X-ray diffraction (XRD) identifies the spinel structure, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) imply the flower-like morphology of the synthesized NiCo2S4. The electrochemical behaviors are studied by cyclic voltammetry and galvanostatic charge-discharge measurements. The NiCo2S4 nanotubes demonstrate enhanced pseudocapacitive performance of 429.5 C g− 1 at current density of 0.5 A g− 1 . The NiCo2S4//AC device delivers high energy density of 37.69 Wh kg− 1 , maximum power density of 4000.6 W kg− 1 and satisfied cycle property of 96% capacitance retention after over 7000 cycles. The results show that the NiCo2S4 nanotubes are promising electrode material for high performance supercapacitor applications.

Bacillus subtilis Spore Surface Display Technology: A Review of Its Development and Applications

( Guoyan Zhang ),( Yingfeng An ),( Hossain M. Zabed ),( Qi Guo ),( Miaomiao Yang ),( Jiao Yuan ),( Wen Li ),( Wenjin Sun ),( Xianghui Qi ) 한국미생물 · 생명공학회 2019 Journal of microbiology and biotechnology Vol.29 No.2

Bacillus subtilis spore surface display (BSSD) technology is considered to be one of the most promising approaches for expressing heterologous proteins with high activity and stability. Currently, this technology is used for various purposes, such as the production of enzymes, oral vaccines, drugs and multimeric proteins, and the control of environmental pollution. This paper presents an overview of the latest developments in BSSD technology and its application in protein engineering. Finally, the major limitations of this technology and future directions for its research are discussed.

VDR promotes testosterone synthesis in mouse Leydig cells via regulation of cholesterol side chain cleavage cytochrome P450 (Cyp11a1) expression

Hu Yuanyuan,Wang Ling,Yang Ge,Wang Shanshan,Guo Miaomiao,Lu Hongzhao,Zhang Tao 한국유전학회 2023 Genes & Genomics Vol.45 No.11

Background The vitamin D receptor (VDR) mediates the pleiotropic biological actions that include osteoporosis, immune responses and androgen synthesis.VDR is widely expressed in testis cells such as Leydig cells, Sertoli cells, and sperm. The levels of steroids are critical for sexual development. In the early stage of steroidogenesis, cholesterol is converted to pregnenolone (precursor of most steroid hormones) by cholesterol side-chain lyase (CYP11A1), which eventually synthesizes the male hormone testosterone. Objective This study aims to reveal how VDR regulates CYP11A1 expression and affects testosterone synthesis in murine Leydig cells. Methods The levels of VDR, CYP11A1 were determined by quantitative real-time polymerase chain reaction (RT-qPCR) or western blot. Targeted relationship between VDR and Cyp11a1 was evaluated by dual-luciferase reporter assay. The levels of testosterone concentrations in cell culture media serum by enzyme-linked immunosorbent assay (ELISA). Results Phylogenetic and motif analysis showed that the Cyp11a1 family had sequence loss, which may have special biological functions during evolution. The results of promoter prediction showed that vitamin D response element (VDRE) existed in the upstream promoter region of murine Cyp11a1. Dual-luciferase assay confirmed that VDR could bind candidate VDREs in upstream region of Cyp11a1, and enhance gene expression. Tissue distribution and localizatio analysis showed that Cyp11a1 was mainly expressed in testis, and dominantly existed in murine Leydig cells. Furthermore, over-expression VDR and CYP11A1 significantly increased testosterone synthesis in mice Leydig cells. Conclusions Active vitamin D3 (VD3) and Vdr interference treatment showed that VD3/VDR had a positive regulatory effect on Cyp11a1 expression and testosterone secretion. VDR promotes testosterone synthesis in male mice by up-regulating Cyp11a1 expression, which played an important role for male reproduction.