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CpG Island Definition and Methylation Mapping of the T2T-YAO Genome

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 69-79页

作者： ming Xiao Rui Wei jun Yu Chujie gao Fengyi Yang Le Zhang College of Computer Science Sichuan UniversityChengdu 610065China Key Laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Precisely defining and mapping all cytosine(C)positions and their clusters,known as CpG islands(CGIs),as well as their methylation status,are pivotal for genome-wide epigenetic studies,especially when population-centric reference genomes are ready for timely ***,we first align the two high-quality reference genomes,T2T-YAO and T2T-CHM13,from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined ***,by mapping some representative genome-wide methylation data from selected organs onto the two genomes,we find that there are about 4.7%–5.8%sequence divergency of variable categories depending on quality *** among the divergent sequences are mostly associated with neurological ***,CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG(O/E)ratio between the two ***,we find that the T2T-YAO genome not only has a greater CpG coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing(WGBS)data from the European and American populations are mapped to each reference,but also shows more hyper-methylated CpG sites as compared to the T2T-CHM13 *** study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.

关键词： T2T-YAO Position-defined CpG island Density-defined CpG island DNA methylation Genome analysis

Bio-inspired Backstepping Adaptive Sliding Mode Control for Parallel Mechanism with Actuation Redundancy

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International Journal of Automation and computing 2014年第5期11卷 555-564页

作者： Xue-Mei Niu Guo-Qin gao Xin-jun Liu Zhi-ming Fang School of Electrical and Information Engineering Jiangsu University Department of Mechanical Engineering Tsinghua University

This paper presents a bio-inspired backstepping adaptive sliding mode control strategy for a novel 3 degree of freedom(3-DOF) parallel mechanism with actuation redundancy. Based on the kinematic model and the dynamic model, a sliding mode controller is designed to assure the tracking performance, and an adaptive law is introduced to approximate the system uncertainty including parameters variation, external disturbances and un-modeled part. Furthermore, a bio-inspired model is introduced to solve the inherent chattering problem of sliding mode control and provide a chattering free control. The simulation and experimental results testify that the proposed bio-inspired backstepping adaptive sliding mode control can achieve better performance(the tracking accuracy,robustness, response speed, etc.) than the conventional slide mode control.

关键词： Parallel mechanism redundant actuation kinematics analysis dynamics analysis adaptive sliding mode control bioinspired model

Correlation between mitochondrial TRAP-1 expression and lymph node metastasis in colorectal cancer

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World Journal of Gastroenterology 2012年第41期18卷 5965-5971页

作者： Jing-Yan gao Bao-Rong Song jun-Jie Peng Yuan-ming Lu Department of Colorectal Cancer Fudan University ShanghaiCancer Center Shanghai Medical College Fudan UniversityShanghai 200032 China Department of Human Anatomy and Histo-Em-bryology Shanghai Medical College Fudan University Shanghai200032 China Department of Oncology Shanghai MedicalCollege Fudan University Shanghai 200032 China

AIM： To evaluate the effect of mitochondrial tumor ne- crosis factor receptor-associated protein-1 （TRAP-l） on the lymph node metastasis （LNM） in Chinese colorectal cancer （CRC） patients, and develop potential LNM- associated biomarkers for CRC using quantitative real- time polymerase chain reaction （RT-PCR） analysis. METHODS： Differences in mitochondrial TRAP-1 gene expression between primary CRC with LNM （LNM CRC） and without LNM （non-LNM CRC） were assessed in 96 Chinese colorectal carcinoma samples using quantita- tive RT-PCR analysis, Western blotting, and confirmed with immunohistochemical assay. The relationship between clinicopathological parameters and potential diaclnostic biomarkers was also ***： TRAP-1 was significantly upregulated in LNM CRC compared with non-LNM CRC, which was confirmed by RT-PCR, Western blotting and immuno- histochemical assay. The expression of TRAP-1 in two different metastatic potential human colorectal cancer cell lines, LoVo and HT29, was analyzed with Western blotting. The expression level of TRAP-1 was dramati- cally higher in LoVo than in HT29. Overexpression of TRAP-1 was significantly associated with LNM （90.2% in LNM group vs 22% in non-LNM group, P 〈 0.001）, the advanced tumor node metastasis stage （89.1% in LNM group vs 26.9% in non-LNM group, P 〈 0.001）, the increased 5-year recurrence rate （82.7% in LNM group vs 22.6% in non-LNM group, P 〈 0.001） and the decreased 5-year overall survival rate （48.4% in LNM vs 83.2% in non-LNM group, P 〈 0.001）. Univariate and multivariate analyses indicated that TRAP-1 expression was an independent prognostic factor for recurrence and survival of CRC patients （Hazard ratio of 2.445 in recurrence, P = 0.017; 2.867 in survival, P = 0.028）. CONCLUSION： Mitochondria TRAP-1 affects the lymph node metastasis in CRC, and may be a potential bio- marker for LNM and a prognostic factor in CRC. Over- expression of TRAP-1 is a predictive factor for the poor outcome of colorectal cancer

关键词： Colorectal cancer Lymph node metastasis Prognosis Quantitative real-time polymerase chain reaction analysis Hsp90 family Mitochondria tumor necrosis factor receptor-associated protein-1

Evidence of anisotropic Landau level splitting in topological semimetal ZrSiS under high magnetic fields

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Frontiers of physics 2019年第6期14卷 83-87,F0004页

作者： jun-Ran Zhang Bo Liu ming gao Yong-Bing Xu Rong Zhang Jiangsu Provincial Key Laboratory of Advanced Photonic and Electronic Materials Collaborative Innovation Center of Advanced MicrostructuresSchool of Electronic Science and EngineeringNanjing UniversityNanjing 210023China

Magneto-transport study has been performed in topological semimetal ZrSiS single crystals under high pulsed magnetic *** dependence of Landau level splitting on temperature and angular was *** strong three-dimensional anisotropic nature of Landau level splitting under high pulsed magnetic fields was revealed by the angular dependent measurements,in which the orbital contribution is more dominant than Zeeman *** studies provide more insights into the physical properties of topological semimetals ZrSiS and shed light on future spintronic applications of ZrSiS.

关键词： topological semimetal Landau level splitting high magnetic field

Non-Gaussian Random Bi-matrix Models for Bi-free Central Limit Distributions with Positive Definite Covariance Matrices

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Acta Mathematica Sinica,English Series 2019年第12期35卷 1891-1905页

作者： ming Chu gao School of Mathematics and Information Science Baoji University of Arts and Sciences Department of Mathematics Louisiana College

In this paper,we construct random two-faced families of matrices with non-Gaussian entries to approximate a bi-free central limit distribution with a positive definite covariance *** prove that,under modest conditions weaker than independence,a family of random two-faced families of matrices with non-Gaussian entries is asymptotically bi-free from a two-faced family of constant diagonal matrices.

关键词： Bi-free central limit distributions non-Gaussian random matrices asymptotic bi-freeness

An Explicit Exact Solution of a Nonlinear Schrödinger Equation for Short Ultraintense Laser Pulse in an Underdense Plasma

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Chinese Physics Letters 1996年第8期13卷 561-564页

作者： gao Hong-jun Laboratory of Computational Physics Institute of Applied Physics and Computational MathematicsBeijing 100088

A nonlinear Schrödinger equation for short ultraintense laser pulses in an underdense plasma has been discussed,and three types explicit exact solutions of this equation are obtained by using analytical method.

关键词： method intense equation

Identification of terrigenous and autochthonous organic carbon in sediment cores from cascade reservoirs in the upper stream of Pearl River and Wujiang River,southwest China:lignin phenol as a tracer

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Acta Geochimica 2022年第5期41卷 753-764页

作者： Li gao Xin Lin jun Fan ming Yang Xueping Chen FushunWang Jing Ma School of Environmental and Chemical Engineering Shanghai UniversityShanghai 200444China Shimadzu(Shanghai) Global Laboratory Consumables Co.LtdShanghai 200233China

Organic carbon(OC)source attribution for cascade reservoir sediments has been identified as a critical gap in understanding the effective carbon sink of inland *** this study,nine sediment cores were collected from cascade reservoirs in the Wujiang and Pearl *** analyzed lignin phenol(Λ8),total organic carbon(TOC)content,and stable carbon isotopic composition(δC)of the sediments,focusing on the changes of terrigenous OC,and the variation of OC source in cascade reservoir sediments after *** results showed that theΣ8 and TOC contents decreased from upstream to downstream reservoirs,indicating the significant interception of terrigenous OC by cascade ***,theΛ8 content in the Pearl River reservoir sediments was much higher than that in the Wujiang *** the three-end-member mixing model,we estimated that OC in reservoir sediments mainly comes from soil and *** damming,the proportion of plankton OC in TOC slightly increased in seasonal and annual regulation reservoirs due to the limnetic evolution of the *** findings suggest that the cascade damming increases the interception capacity of the river to terrigenous OC and nutrients,and that slowing of water velocity caused by damming affected primary productivity and fluvial carbon cycling.

关键词： Cascade reservoirs Terrigenous OC Lignin Autochthonous OC Three-end-member mixing model

Low temperature laser absorption spectra of methane in the near-infrared at 1.65 μm for lower state energy determination

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Chinese Physics B 2012年第1期21卷 260-267页

作者： gao Wei Chen Wei-Dong Zhang Wei-jun Yuan Yi-Qian gao Xiao-ming Key Laboratory of Atmospheric Composition and Optical Radiation Chinese Academy of SciencesHefei 230031China Anhui Institute of Optics and Fine Mechanics Chinese Academy of SciencesHefei 230031China Laboratoire de Physicochimie de l'Atmosphère Universitédu Littoral Côte d'Opale189AAv.Maurice Schumann59140 DunkerqueFrance

Direct absorption spectra of the 2v3 band of methane （CH4） from 6038 to 6050 cm 1 were studied at different low temperatures using a newly developed cryogenic cell in combination with a distributed feedback （DFB） diode laser. The cryogenic cell can operate at any stabilized temperature ranging from room temperature down to 100 K with temperature fluctuation less than =t=1 K within 1 hour. In the present work, the CH4 spectra in the range of 6038-6050 cm-1 were recorded at 296, 266, 248, 223, 198, and 176 K. The lower state energy Ett and the rotational assignment of the angular momentum J were determined by a ＂2-low-temperature spectra method＂ using the spectra recorded at 198 and 176 K. The results were compared with the data from the GOSAT and the recently reported results from Campargue and co-workers using two spectra measured at room temperature and 81 K. We demonstrated that the use of a 2-low-temperature spectra method permits one to complete the Ett and J values missed in the previous studies.

关键词： methane laser absorption spectroscopy cryogenic cell low temperature absorption spec-trum

High resolution scanning optical imaging of a frozen planar polymer light-emitting electrochemical cell： an experimental and modelling study

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Science China Chemistry 2017年第4期60卷 497-503页

作者： Faleh AITal jun gao Department of Physics Engineering Physics and Astronomy Queen's University Kingston Ontario K7L 3N6 Canada

Light-emitting electrochemical cells(LECs) are organic photonic devices based on a mixed electronic and ionic *** active layer of a polymer-based LEC consists of a luminescent polymer,an ion-solvating/transport polymer,and a compatible *** LEC p-n or p-i-n junction is ultimately responsible for the LEC *** LEC junction,however,is still poorly understood due to the difficulties of characterizing a dynamic-junction *** this paper,we present an experimental and modeling study of the LEC junction using scanning optical imaging *** LECs with an interelectrode spacing of 560μm have been fabricated,activated,frozen and scanned using a focused laser *** optical-beam-induced-current(OBIC)and photoluminescence(PL) data have been recorded as a function of beam *** OBIC profile has been simulated in COMSOL that allowed for the determination of the doping concentration and the depletion width of the LEC junction.

关键词： light-emitting electrochemical cell optical beam induced current frozen junction planar LECs polymer p-n junction