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

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

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Variation in the permafrost active layer over the Tibetan Plateau during 1980–2020

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Atmospheric and Oceanic Science Letters 2024年第5期17卷 34-39页

作者： Jinglong Huang Chaofan Li Binghao Jia chujie.gao Ruichao Li College of Oceanography Hohai UniversityNanjingChina Center for Monsoon System Research Institute of Atmospheric PhysicsChinese Academy of SciencesBeijingChina State Key Laboratory of Numerical Modeling for Atmospheric Sciences and Geophysical Fluid Dynamics Institute of Atmospheric PhysicsChinese Academy of SciencesBeijingChina College of Earth and Planetary Sciences University of Chinese Academy of SciencesBeijingChina

The active layer,acting as an intermediary of water and heat exchange between permafrost and atmosphere,greatly influences biogeochemical cycles in permafrost areas and is notably sensitive to climate *** the Chinese Meteorological Forcing Dataset to drive the Community Land Model,version 5.0,this study simulates the spatial and temporal characteristics of active layer thickness(ALT)on the Tibetan Plateau(TP)from 1980 to *** show that the ALT,primarily observed in the central and western parts of the TP where there are insufficient station observations,exhibits significant interdecadal changes after *** average thickness on the TP decreases from 2.54 m during 1980–1999 to 2.28 m during 2000–*** change is mainly observed in the western permafrost region,displaying a sharp regional inconsistency compared to the eastern region.A persistent increasing trend of ALT is found in the eastern permafrost region,rather than an interdecadal *** aforementioned changes in ALT are closely tied to the variations in the surrounding atmospheric environment,particularly air ***,the area of the active layer on the TP displays a profound interdecadal change around 2000,arising from the permafrost thawing and *** consistently decreases before 2000 but barely changes after *** regional variation in the permafrost active layer over the TP revealed in this study indicates a complex response of the contemporary climate under global warming.

关键词： Active layer thickness Permafrost Tibetan plateau Climatological characteristics

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Effects of acid mine drainage on photochemical and biological degradation of dissolved organic matter in karst river water

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Journal of Environmental Sciences 2024年第1期135卷 26-38页

作者： Linwei Li Xingxing Cao chujie Bu Pan Wu Biao Tian Yongheng Dai Yeye Ren College of Resources and Environmental Engineering Guizhou UniversityGuiyang 550025China Key Laboratory of Karst Georesources and Environment Ministry of EducationGuizhou UniversityGuiyang 550025China Guizhou Karst Environmental Ecosystems Observation and Research Station Ministry of EducationGuizhou UniversityGuiyang 550025China

Dissolved organic matter(DOM)can be removed or transformed by photochemical and biological processes,producing the negative effect of transforming organic carbon into inorganic carbon,which plays a vital role in the karst carbon ***,acid mine drainage(AMD)will affect this process,so the degradation of DOM in karst river water(KRW)needs to be studied in this *** this study,to reveal the evolution processes of DOM under photochemical and biological conditions in AMD-impacted KRW,AMD and KRW were mixed in different ratios under conditions of visible light irradiation(VL),biodegradation(BD),ultraviolet irradiation(UV)and ultraviolet irradiation+biodegradation(UV+BD).The average DOC concentrations in samples after mixing AMD and KRW in different proportions decreased significantly(by 23%)in UV+BD,which was 1.2–1.4 times higher than under the other conditions and would lead to a significant release of inorganic *** analysis of the fluorescence parameters via parallel factor analysis(PARAFAC)revealed that the DOM fluorescence components in AMD comprised mainly protein-like substances derived from autochthonous components,while the DOM fluorescence components in KRW were mainly humic-like substances with both autochthonous and allochthonous ***,AMD could promote both the photochemical and biological degradation of DOM in karst receiving streams,resulting in the conversion of DOC to inorganic *** results showed that the synergistic effects of UV+BD and AMD accelerated the degradation of DOM and the release of inorganic carbon in KRW,thus affecting the stability of the karst carbon cycle.

关键词： Acid mine drainage Dissolved organic matter Karst river water Photochemical degradation Biological degradation

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Polyphyllin Ⅰ enhances tumor necrosis factor-related apoptosis-inducing ligand-induced inhibition of human osteosarcoma cell growth via downregulating the Wnt/β-catenin pathway

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Journal of Traditional Chinese Medicine 2024年第2期44卷 251-259页

作者： CHANG Junli ZHAO Fulai SUN Xingyuan MA Xiaoping ZHAO Peng ZHOU chujie SHI Binhao GU Wenchao WANG Yongjun YANG Yanping Spine Disease Institute Longhua Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghai 200032China Department of Diagnostic and Interventional Radiology University of TsukubaIbaraki 315-0114Japan

OBJECTIVE:To investigate the synergistic effects of polyphyllin Ⅰ(PPⅠ)combined with tumor necrosis factorrelated apoptosis-inducing ligand(TRAIL)on the growth of osteosarcoma cells through downregulating the Wnt/β-catenin signaling ***:Cell viability,apoptosis and cell cycle distribution were examined using cell counting kit-8 and flow cytometry *** morphology of cancer cells was observed with inverted phase contrast *** migration and invasion abilities were examined by xCELLigence real time cell analysis DP system and transwell *** expressions of poly(adenosine diphosphate-ribose)polymerase,C-Myc,Cyclin B1,cyclin-dependent kinases 1,N-cadherin,Vimentin,Active-β-catenin,β-catenin,p-glycogen synthase kinase 3β(GSK-3β)and GSK-3βwere determined by Western blotting ***:PPⅠ sensitized TRAIL-induced decrease of viability,migration and invasion,as well as increase of apoptosis and cell cycle arrest of MG-63 and U-2 OS osteosarcoma *** synergistic effect of PPⅠwith TRAIL in inhibiting the growth of osteosarcoma cells was at least partially realized through the inactivation of Wnt/β-catenin signaling ***:The combination of PPⅠ and TRAIL is potentially a novel treatment strategy of osteosarcoma.

关键词： osteosarcoma tumor necrosis factor-related apoptosis-inducing ligand Wnt signaling pathway beta-catenin polyphyllinⅠ

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Record-high efficiency perovskite LEDs achieved by accelerating radiative recombination

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Science China Materials 2024年第9期67卷 3039-3040页

作者： Feng gao Department of Physics Chemistry and BiologyLinköping UniversityLinköping58183Sweden

Light-emitting diodes(LEDs)have revolutionized the lighting and displays due to their superior energy *** increasing demand for more efficient and brighter thin-film LEDs in flat-panel displays and solid-state lighting applications has driven extensive research into perovskite materials,which show great promise for high brightness and efficiency.

关键词： lighting radiative high

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Stress tensor determination by modified hydraulic tests on pre-existing fractures:Method and stress constraints

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第5期16卷 1637-1648页

作者： Guiyun gao Chenghu Wang Ke gao National Institute of Natural Hazards Ministry of Emergency Management of ChinaBeijing100085China Beijing Engineering Research Center of Earthquake Observation Beijing100085China Key Laboratory of Compound and Chained Natural Hazards Dynamics Ministry of Emergency Management of ChinaBeijing100085China Department of Earth and Space Sciences Southern University of Science and TechnologyShenzhen518055China

The hydraulic testing of pre-existing fractures(HTPF)is one of the most promising in situ stress measurement methods,particularly for three-dimensional stress tensor ***,the stress tensor determination based on the HTPF method requires at least six tests or a minimum of 14-15 tests(under different conditions)for reliable *** this study,we modified the HTPF method by considering the shear stress on each pre-existing fracture,which increased the number of equations for the stress tensor determination and decreased the number of tests *** shear stresses were attributed to different fractures by random sampling;therefore,the stress tensors were obtained by searching for the optimal solution using the least squares criterion based on the Monte Carlo ***,we constrained the stress tensor based on the tensile strength criterion,compressive strength criterion,and vertical stress *** inverted stress tensors were presented and analyzed based on the tensorial nature of the stress using the Euclidean mean stress *** stress-measurement campaigns in Weifang(Shandong Province,China)and Mercantour road tunnel(France)were implemented to highlight the validity and efficiency of the modified HTPF(M-HTPF)*** results showed that the M-HTPF method can be applied for stress tensor inversion using only three to four tests on pre-existing fractures,neglecting the stress *** inversion results were confined to relatively small distribution dispersions and were significantly reliable and stable due to the shear stresses on the fractures and the stress constraints *** M-HTPF method is highly feasible and efficient for complete stress tensor determination in a single borehole.

关键词： Stress tensor Hydraulic tests on pre-existing fractures Mean stress Stress constraint Hydraulic fracturing

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Thermal and mechanical behavior of casting copper alloy wheel during wheel and belt continuous casting process

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China Foundry 2024年第1期21卷 82-90页

作者： Kun gao Yan Peng School of Mechanical Engineering Yanshan UniversityQinhuangdao 066004HebeiChina

To investigate the thermal and mechanical behavior of casting wheel,a two-dimensional thermoelastic-plastic finite element model was used to predict the temperature,stress and distortion distribution of the casting wheel during the wheel and belt continuous casting *** effects of grinding thickness and casting speed on the thermal and mechanical behaviors of the center of the hot face of the casting wheel were discussed in *** each rotation,the casting wheel passes through four different spray *** results show that the temperature distribution of the casting wheel in different spray zones is similar,the temperature of the hot face is the highest and the temperature reaches the peak in the spray zoneⅢ.The stress and distortion depend on the temperature distribution,and the maximum stress and distortion of the hot face are 358.2 MPa and 1.82 mm,*** temperature at the center of the hot face decreases with increasing grinding thickness and increases with increasing casting speed.

关键词： casting wheel finite element model grinding thickness casting speed hot face spray zones

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Numerical simulation of fluid flow and free surface fluctuations during wheel and belt casting process

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Journal of Iron and Steel Research International 2024年第5期31卷 1117-1126页

作者： Kun gao Yan Peng National Engineering Research Center for Equipment and Technology of Cold Strip Rolling Yanshan UniversityQinhuangdao066004HebeiChina

The unstable fluid flow and severe free surface fluctuations in the wheel and belt caster can affect the quality of the cast *** lower level height tends to entrap inclusions in the molten *** the other hand,the higher level height makes the production process more dangerous due to the overflow of high temperature fluid from the mold.A computational model of the molten metal pouring process was *** transient fluid flow and free surface fluctuations behavior were calculated using the three-dimensional large eddy simulation model and the volume of fluid *** results show that the flow velocity of the main jet gradually decreases under the influence of the low kinetic energy fluid in the *** is an obvious oscillation in the tail of the jet,while the flow field is asymmetric in *** jet is closer to the inside radius side due to the Coanda effect,and there is a recirculation zone on the inside radius and the outside radius respectively,according to the 10 s time-averaged *** with the industrial observation and simulation results,the shape of the free surface is a wave that varies with *** addition,the free surface height is lowest and the flow velocity is highest in the region near the jet.

关键词： Fluid flow Free surface Wheel and belt caster Large eddy simulation Volume of fluid method

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On the core entropy of Newton maps

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Science China Mathematics 2024年第1期67卷 77-128页

作者： Yan gao Department of Mathematics Shenzhen UniversityShenzhen 518060China

In this paper,we define the core entropy for postcritically-finite Newton maps and study its continuity within this *** show that the entropy function is not continuous in this family,which is different from the polyn... 详细信息

关键词： core entropy extended Newton graph critical marking polynomial Newton map

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Durable poly(binaphthyl-co-p-terphenyl piperidinium)-based anion exchange membranes with dual side chains

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Journal of Energy Chemistry 2024年第2期89卷 324-335,I0008页

作者： Weiting gao Xuelang gao Qiugen Zhang Aimei Zhu Qinglin Liu Department of Chemical&Biochemical Engineering Fujian Provincial Key Laboratory of Theoretical and Computational ChemistryThe College of Chemistry and Chemical EngineeringXiamen UniversityXiamen 361005FujianChina Department of Chemistry Pohang University of Science and Technology(POSTECH)Pohang 790-784South Korea

Building well-developed ion-conductive highways is highly desirable for anion exchange membranes(AEMs).Grafting side chain is a highly effective approach for constructing a well-defined phaseseparated morphological structure and forming unblocked ion pathways in AEMs for fast ion *** of side chains can further enhance phase separation due to the superhydrophobic nature of fluorine ***,their electronic effect on the alkaline stability of side chains and membranes is rarely ***,fluorine-containing and fluorine-free side chains are introduced into the polyaromatic backbone in proper configuration to investigate the impact of the fluorine terminal group on the stability of the side chains and membrane *** poly(binaphthyl-co-p-terphenyl piperidinium)AEM(QBNp TP)has the highest molecular weight and most dimensional stability due to its favorable backbone arrangement among ortho-and meta-terphenyl based ***,by introducing both a fluorinated piperidinium side chain and a hexane chain into the p-terphenyl-based backbone,the prepared AEM(QBNp TP-QFC)presents an enhanced conductivity(150.6 m S cm^(-1))and a constrained swelling at 80℃.The electronic effect of fluorinated side chains is contemplated by experiments and *** results demonstrate that the presence of strong electro-withdrawing fluorine groups weakens the electronic cloud of adjacent C atoms,increasing OH^(-)attack on the C atom and improving the stability of piperidinium *** QBNp TP-QFC possesses a robust alkaline stability at 80℃(95.3%conductivity retention after testing in 2 M Na OH for 2160 h).An excellent peak power density of 1.44 W cm^(-2)and a remarkable durability at 80℃(4.5%voltage loss after 100 h)can be observed.

关键词： Anion exchange membranes Backbone structure Fluorinated side chain Alkaline stability

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