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Metabolic Module Mining Based on Independent Component Analysis in Arabidopsis thaliana
Xiao Han,김재연,Cong Chen,현태경,Ritesh Kumar 한국분자세포생물학회 2012 Molecules and cells Vol.34 No.3
Independent Component Analysis (ICA) has been intro-duced as one of the useful tools for gene-functional dis-covery in animals. However, this approach has been poorly utilized in the plant sciences. In the present study, we have exploited ICA combined with pathway enrichment analysis to address the statistical challenges associated with genome-wide analysis in plant system. To generate an Arabidopsis metabolic platform, we collected 4,373 Affy- metrix ATH1 microarray datasets. Out of the 3,232 metabolic genes and transcription factors, 99.47% of these genes were identified in at least one component, indicating the coverage of most of the metabolic pathways by the components. During the metabolic pathway enrichment analysis, we found components that indicate an independent regulation between the isoprenoid biosynthesis pathways. We also utilized this analysis tool to investigate some transcription factors involved in secondary cell wall bio-genesis. This approach has identified remarkably more transcription factors compared to previously reported analysis tools. A website providing user-friendly searching and downloading of the entire dataset analyzed by ICA is available at http://kimjy.gnu.ac.kr/ICA.files/slide0002.htm. ICA combined with pathway enrichment analysis might provide a powerful approach for the extraction of the components responsible for a biological process of interest in plant systems.
Xiaohan Wang(Xiaohan Wang),Yu-Mi Choi(Yu-Mi Choi),Sukyeung Lee(Sukyeung Lee),Myoung-Jae Shin(Myoung-Jae Shin),Jung Yoon Yi(Jung Yoon Yi),Kebede Taye Desta(Kebede Taye Desta ),Hyemyeong Yoon(Hyemyeong 한국자원식물학회 2022 한국자원식물학회지 Vol.35 No.6
Traditional germplasms are unsuitable for mechanized production, limiting adzuki bean production. The creation of cultivars that can be harvested by mechanized means is an urgent task for breeders. The bottom pod height (BPH), lodging resistance, and synchronous maturing of adzuki beans are critical factors for the reduction of losses due to mechanized harvesting. In this study, 14 traits of 806 adzuki bean accessions were analyzed. All growth stages and the yield, lodging score, and synchronous maturing correlated negatively with the BPH. These negative correlations reflect the increased difficulty of breeding to simultaneously satisfy the needs for no lodging, high synchronous maturing rates, BPHs > 10 ㎝, and high yield. We screened three germplasms with no lodging, high synchronous maturing rates, and BPHs > 10 ㎝ that were used as mechanization-adapted breeding material for crossing with high-yield cultivars. Agronomic trait diversity in adzuki beans was also examined in this study. Principal component and cluster analyses were conducted for 806 germplasms resulting in three clusters with the yield and three growth stage traits serving as the main discriminating factors. Cluster 1 included high-yield germplasms with the number of pods per plant and the number of seeds per pod being the major discriminant factors. Cluster 2 included germplasms with long growth periods and large 100-seed weights while cluster 3 contained germplasms with high BPHs. In general, the characteristics that make mechanical harvesting feasible and those assessed in this study could be utilized to choose and enhance adzuki beans production.
miRNA Pattern Discovery from Sequence Alignment
Xiaohan Sun,Junying Zhang 한국정보처리학회 2017 Journal of information processing systems Vol.13 No.6
MiRNA is a biological short sequence, which plays a crucial role in almost all important biological process. MiRNA patterns are common sequence segments of multiple mature miRNA sequences, and they are ofsignificance in identifying miRNAs due to the functional implication in miRNA patterns. In the proposedapproach, the primary miRNA patterns are produced from sequence alignment, and they are then cut intoshort segment miRNA patterns. From the segment miRNA patterns, the candidate miRNA patterns areselected based on estimated probability, and from which, the potential miRNA patterns are further selectedaccording to the classification performance between authentic and artificial miRNA sequences. Threeparameters are suggested that bi-nucleotides are employed to compute the estimated probability of segmentmiRNA patterns, and top 1% segment miRNA patterns of length four in the order of estimated probabilitiesare selected as potential miRNA patterns.
Xiaohan Chen,Yingmin Jia 제어·로봇·시스템학회 2014 International Journal of Control, Automation, and Vol.12 No.6
This paper uses the ceiling vision and the odometry to achieve localization for mobile robots in indoor environment. Given that the fluorescent lights with rectangular lampshades are distributed regularly on the ceiling in most indoor environments, the corners of lampshades are selected as features to navigate the mobile robot. An efficient extraction algorithm is proposed to identify the corner features. In addition, the extrinsic parameters of the visual system are calibrated by our developed method. The approach to estimate the initial pose of the mobile robot is proposed, which is also used to provide the ground truth for the robot pose. Experimental results are included to verify the effectiveness and robustness of the proposed localization method.
Multifactorial Regulation of G Protein-Coupled Receptor Endocytosis
( Xiaohan Zhang ),( Kyeong-man Kim ) 한국응용약물학회 2017 Biomolecules & Therapeutics(구 응용약물학회지) Vol.25 No.1
Endocytosis is a process by which cells absorb extracellular materials via the inward budding of vesicles formed from the plasma membrane. Receptor-mediated endocytosis is a highly selective process where receptors with specific binding sites for extracel-lular molecules internalize via vesicles. G protein-coupled receptors (GPCRs) are the largest single family of plasma-membrane receptors with more than 1000 family members. But the molecular mechanisms involved in the regulation of GPCRs are believed to be highly conserved. For example, receptor phosphorylation in collaboration with β-arrestins plays major roles in desensitization and endocytosis of most GPCRs. Nevertheless, a number of subsequent studies showed that GPCR regulation, such as that by endocytosis, occurs through various pathways with a multitude of cellular components and processes. This review focused on i) functional interactions between homologous and heterologous pathways, ii) methodologies applied for determining receptor en-docytosis, iii) experimental tools to determine specific endocytic routes, iv) roles of small guanosine triphosphate-binding proteins in GPCR endocytosis, and v) role of post-translational modification of the receptors in endocytosis.
Xiaohan Liu,Xiao Liang,Kaiyue Gong,Siqi An,Xu Peng,Jun Cai,Xinyu Zhu,Chao Zhou 전력전자학회 2022 JOURNAL OF POWER ELECTRONICS Vol.22 No.8
The three-phase cascaded H-bridge rectifier (CHBR) is widely used in high power and high voltage applications. This paper focuses on the load removed from the DC port of a three-phase CHBR, which can cause single-phase DC-port voltage unbalance issues and three-phases DC-port voltage unbalance issues. This paper proposes a voltage balance control strategy based on negative sequence current injection for three-phase CHBR to deal with the unbalance problem. An individual DC-port voltage control strategy is designed to balance the DC-port voltage in the faulty phase. In addition, a negative sequence current injection control strategy is responsible for balancing the DC-port voltages in the three phase CHBR. The effectiveness and feasibility of the proposed voltage control strategy based on negative sequence current injection is verified by the experimental results.
Elasto-plastic time history analysis of a 117-story high structure
Xiaohan Wu,Yimiao Li,Yunlei Zhang 사단법인 한국계산역학회 2017 Computers and Concrete, An International Journal Vol.19 No.1
In Chinese Design Codes, for super high-rise buildings with complex structural distribution, which are regarded as code-exceeding buildings, elasto-plastic time history analysis is needed to validate the requirement of “no collapse under rare earthquake”. In this paper, a 117-story super high-rise building is discussed. It has a height of 597 m and a height-width ratio of 9.5, which have both exceeded the limitations stipulated by the Chinese Design Codes. Mega columns adopted in this structure have cross section area of about 45 m2 at the bottom, which is infrequent in practical projects. NosaCAD and Perform-3D, both widely used in nonlinear analyses, were chosen in this study, with which two model were established and analyzed, respectively. Elasto-plastic time history analysis was conducted to look into its seismic behavior, emphasizing on the stress state and deformation abilities under intensive seismic excitation.From the comparisons on the results under rare earthquake obtained from NosaCAD and Perform-3D, the overall responses such as roof displacement, inter story drift, base shear and damage pattern of the whole structure from each software show agreement to an extent. Besides, the deformation of the structure is below the limitation of the Chinese Codes, the time sequence and distribution of damages on core tubes are reasonable, and can dissipate certain inputted energy, which indicates that the structure can meet the requirement of “no collapse under rare earthquake”.