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International Joint Conference on Neural Networks (IJCNN)

作者： cao, buwen Luo, Jiawei Liang, Cheng Wang, Shulin Hunan Univ Coll Comp Sci & Elect Engn Changsha 410082 Hunan Peoples R China Shandong Normal Univ Sch Informat Sci & Engn Jinan 250014 Peoples R China

ISBN: (纸本)9781509006199

Detecting overlapping protein complexes in proteinprotein interaction (PPI) networks can provide insight into cellular functional organization and thus elucidate underlying cellular mechanisms. Recently, various algorithms for protein complex detection have been developed for PPI networks. However, the majority of algorithms primarily depend on network topological features and/ or gene expression profile, failing to consider the inherent biological meanings between protein pairs. In this paper, we propose a method of pseudoclique extension based on fuzzy relation (PCE-FR) that detects protein complexes from PPI networks weighted with the biological significance hidden in protein pairs. The proposed algorithm operates in three stages: it first forms the nonoverlapping protein sub-structure based on fuzzy relation and then expands each sub-structure by adding neighbor proteins to maximize the cohesive score. Finally, highly overlapped candidate protein complexes are merged to form the final protein complex set. We apply PCE-FR to two yeast PPI networks and a human PPI network and validate our results by using CYC2008 and CHPC2012, respectively. Experimental results show that our method outperforms classical algorithms such as CFinder, ClusterONE, CMC, RRW, HC-PIN and ProRank+, and that it achieves ideal overall performance in terms of Precision, Accuracy, and Separation.

关键词： Proteins

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Inferring human miRNA functional similarity based on gene ontology annotations 12

Inferring human miRNA functional similarity based on gene on...

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12th International Conference on Natural Computation, Fuzzy Systems and Knowledge Discovery (ICNC-FSKD)

作者： Luo, Jiawei Dai, Di cao, buwen Yi, Ying Hunan Univ Coll Comp Sci & Elect Engn Changsha 410082 Hunan Peoples R China Hunan Univ Collaborat & Innovat Ctr Digital Chinese Med 2011 Changsha 410082 Hunan Peoples R China

ISBN: (纸本)9781509040933

Even though miRNAs participate in many critical biological processes, the most miRNA functions are ambiguous. To understand the functions of miRNAs, biologists focus on comparing targets of miRNAs, and aim to determine the interactions between targets. However, existing methods may not satisfy the demand accurately because of various limitations. Uncovering the functional associations of miRNAs is also a challenge. Here, we developed MFS_GO to infer miRNA functional similarity using their target genes. We apply MFS_GO to the miRNA families and miRNA clusters and validate our results using miRNA expression, miRNA-disease associations and computational complexity. Compared with the miFRunSim, MFS_GO shows its strong performance. We also conducted our method on breast neoplasms, colorectal neoplasms, and ovarian neoplasms. Experimental results showed that MFS_GO can find novel candidate cancer-related miRNAs with no need for presetting the number of known cancer-related miRNAs.

关键词： miRNA functional similarity gene ontology annotations breast neoplasms colorectal neoplasms ovarian neoplasms

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Theoretical Analysis of InGaAs/InAlAs Single-Photon Avalanche Photodiodes

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NANOSCALE RESEARCH LETTERS 2019年第1期14卷 1-8页

作者： cao, Siyu Zhao, Yue Feng, Shuai Zuo, Yuhua Zhang, Lichun Cheng, buwen Li, Chuanbo Minzu Univ China Sch Sci Beijing 100081 Peoples R China Chinese Acad Sci Inst Semicond State Key Lab Integrated Optoelect Beijing 100083 Peoples R China Univ Chinese Acad Sci Ctr Mat Sci & Optoelect Engn Beijing 100049 Peoples R China Ludong Univ Sch Phys & Optoelect Engn Yantai 264025 Peoples R China

Theoretical analysis and two-dimensional simulation of InGaAs/InAlAs avalanche photodiodes (APDs) and single-photon APDs (SPADs) are reported. The electric-field distribution and tunneling effect of InGaAs/InAlAs APDs and SPADs are studied. When the InGaAs/InAlAs SPADs are operated under the Geiger mode, the electric field increases linearly in the absorption layer and deviate down from its linear relations in the multiplication layer. Considering the tunneling threshold electric field in multiplication layer, the thickness of the multiplication layer should be larger than 300nm. Moreover, SPADs can work under a large bias voltage to avoid tunneling in absorption layer with high doping concentrations in the charge layer.

关键词： Single-photon avalanche photodiodes Theoretical analysis Simulation Tunneling effect

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Inferring human miRNA functional similarity based on gene ontology annotations

Inferring human miRNA functional similarity based on gene on...

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International Conference on Fuzzy Systems and Knowledge Discovery (FSKD)

作者： Jiawei Luo Di Dai buwen cao Ying Yin College of Computer Science and Electronics Engineering&& Hunan University Changsha China

ISBN: (纸本)9781509040940

关键词： Conferences Fuzzy systems Knowledge discovery

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Detecting Overlapping Protein Complexes in Weighted Protein-Protein Interaction Networks Using Pseudo-Clique Extension Based on Fuzzy Relation

Detecting Overlapping Protein Complexes in Weighted Protein-...

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International Joint Conference on Neural Networks

作者： buwen cao Jiawei Luo Cheng Liang Shulin Wang College of Computer Science and Electronic Engineering Hunan University Changsha 410082 China School of Information Science and Engineering Shandong Normal University Jinan 250014 China

ISBN: (纸本)9781509006212

Detecting overlapping protein complexes in protein-protein interaction (PPI) networks can provide insight into cellular functional organization and thus elucidate underlying cellular mechanisms. Recently, various algorithms for protein complex detection have been developed for PPI networks. However, the majority of algorithms primarily depend on network topological features and/or gene expression profile, failing to consider the inherent biological meanings between protein pairs. In this paper, we propose a method of pseudo-clique extension based on fuzzy relation (PCE-FR) that detects protein complexes from PPI networks weighted with the biological significance hidden in protein pairs. The proposed algorithm operates in three stages: it first forms the non-overlapping protein sub-structure based on fuzzy relation and then expands each sub-structure by adding neighbor proteins to maximize the cohesive score. Finally, highly overlapped candidate protein complexes are merged to form the final protein complex set. We apply PCE-FR to two yeast PPI networks and a human PPI network and validate our results by using CYC2008 and CHPC2012, respectively. Experimental results show that our method outperforms classical algorithms such as CFinder, ClusterONE, CMC, RRW, HC-PIN and ProRank+, and that it achieves ideal overall performance in terms of Precision, Accuracy, and Separation.

关键词： Proteins Transforms Clustering algorithms Symmetric matrices Gene expression Prediction algorithms

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MOEPGA: A novel method to detect protein complexes in yeast protein-protein interaction networks based on Multi Objective Evolutionary Programming Genetic Algorithm

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COMPUTATIONAL BIOLOGY AND CHEMISTRY 2015年 58卷 173-181页

作者： cao, buwen Luo, Jiawei Liang, Cheng Wang, Shulin Song, Dan Hunan Univ Coll Comp Sci & Elect Engn Changsha 410082 Hunan Peoples R China

The identification of protein complexes in protein-protein interaction (PPI) networks has greatly advanced our understanding of biological organisms. Existing computational methods to detect protein complexes are usually based on specific network topological properties of PPI networks. However, due to the inherent complexity of the network structures, the identification of protein complexes may not be fully addressed by using single network topological property. In this study, we propose a novel Multi-Objective Evolutionary Programming Genetic Algorithm (MOEPGA) which integrates multiple network topological features to detect biologically meaningful protein complexes. Our approach first systematically analyzes the multiobjective problem in terms of identifying protein complexes from PPI networks, and then constructs the objective function of the iterative algorithm based on three common topological properties of protein complexes from the benchmark dataset, finally we describe our algorithm, which mainly consists of three steps, population initialization, subgraph mutation and subgraph selection operation. To show the utility of our method, we compared MOEPGA with several state-of-the-art algorithms on two yeast PPI datasets. The experiment results demonstrate that the proposed method can not only find more protein complexes but also achieve higher accuracy in terms of fscore. Moreover, our approach can cover a certain number of proteins in the input PPI network in terms of the normalized clustering score. Taken together, our method can serve as a powerful framework to detect protein complexes in yeast PPI networks, thereby facilitating the identification of the underlying biological functions. (C) 2015 Elsevier Ltd. All rights reserved.

关键词： Protein protein interaction (PPI) network Protein complex Multiobjective evolutionary Normalized clustering score

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Theoretical Studies on InGaAs/InAlAs SAGCM Avalanche Photodiodes

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NANOSCALE RESEARCH LETTERS 2018年第1期13卷 1-15页

作者： cao, Siyu Zhao, Yue Rehman, Sajid Ur Feng, Shuai Zuo, Yuhua Li, Chuanbo Zhang, Lichun Cheng, buwen Wang, Qiming Chinese Acad Sci Inst Semicond State Key Lab Integrated Optoelect Beijing 100083 Peoples R China Minzu Univ China Sch Sci Beijing 100081 Peoples R China Univ Chinese Acad Sci Coll Mat Sci & Optoelect Technol Beijing 100049 Peoples R China Ludong Univ Sch Phys & Optoelect Engn Yantai 264025 Peoples R China

In this paper, we provide a detailed insight on InGaAs/InAlAs separate absorption, grading, charge, and multiplication avalanche photodiodes (SAGCM APDs) and a theoretical model of APDs is built Through theoretical analysis and two-dimensional (2D) simulation, the influence of charge layer and tunneling effect on the APDs is fully understood. The design of charge layer (including doping level and thickness) can be calculated by our predictive model for different multiplication thickness. We find that as the thickness of charge layer increases, the suitable doping level range in charge layer decreases. Compared to thinner charge layer, performance of APD varies significantly via several percent deviations of doping concentrations in thicker charge layer. Moreover, the generation rate (G(btt) ) of band-to-band tunnel is calculated, and the influence of tunneling effect on avalanche field was analyzed. We confirm that avalanche field and multiplication factor (M-n) in multiplication will decrease by the tunneling effect. The theoretical model and analysis are based on InGaAs/InAlAs APD;however, they are applicable to other APD material systems as well.

关键词： Avalanche photodiodes Theoretical analysis Simulation Charge layer Tunneling effect

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BUDESONIDE SUSPENSION SPRAY

BUDESONIDE SUSPENSION SPRAY

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作者： DING, Dan MOU, Liqiu cao, Li ZHAO, buwen HUANG, Fangfang

The present invention relates to a budesonide suspension spray, and in particular, the active ingredients of the suspension spray contain budesonide with a D(90) of no larger than 7.5 μm.

标准号: WO2017177930(A1)

The present invention relates to a budesonide suspension spray, and in particular, the active ingredients of the suspension spray contain budesonide with a D(90) of no larger than 7.5 μm.

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SPRAY, SPRAYING DEVICE AND SPRAY MODULE

SPRAY, SPRAYING DEVICE AND SPRAY MODULE

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作者： MOU, Liqiu DING, Dan cao, Li ZHAO, buwen HUANG, Fangfang

Provided are a spray, a spraying device and a spray module. The active ingredient of the spray is salbutamol or a salt thereof. Droplets with a particle size of 0.5 μm-6.5 μm in the spray take up more than 60％ of t...

标准号: WO2017157265(A1)

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Transport mechanism of novel silicon-riched nitride (SRN)/ silicon-riched oxide (SRO) superlattice quantum dot structure

Transport mechanism of novel silicon-riched nitride (SRN)/ s...

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38th IEEE Photovoltaic Specialists Conference, PVSC 2012

作者： Tao, Yeliao Zuo, Yuhua Zheng, Jun cao, Quan Zhou, Tianwei Xue, Chunlai Cheng, buwen Zeng, Xiangbo Wang, Qiming State Key Laboratory on Integrated Optoelectronics Institute of Semiconductors Chinese Academy of Sciences Beijing 183 China

ISBN: (纸本)9781467300643

Novel structure of silicon-riched nitride (SRN)/silicon-riched oxide (SRO) is demonstrated using RF reactive magnetron sputtering and post-annealed, to increase the density of Si nanocrystals especially in the separated layer made of isolation medium, thus improving the transport ability of Si nanocrystal material. I-V characteristics shows the current of hybrid SRN/SRO system increases up to 2 orders of magnitude at 1V compared to that of SiN x/Si3N4 structure, proving the importance of the existence of sparser Si NCs in the SRO layer to greatly improve the transport ability. Temperature dependent I-V test reveals that direct tunneling dominates at low electrical field (V1V) Poole-Frenkel emission is the dominated one. © 2012 IEEE.

关键词： Nanocrystals

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