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CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 226-233页

作者： Rui Dong xu-kai ma Guo-Wei Li Li Yang CAS Key Laboratory of Computational Biology CAS-MPG Partner Institute for Computational Biology Shanghai Institute of Nutrition and Health Shanghai Institutes for Biological Sciences University of Chinese Academy of Sciences Chinese Academy of Sciences School of Life Science and Technology ShanghaiTech University

Circular RNAs （circRNAs） from back-splicing of exon（s） have been recently identified to be broadly expressed in eukaryotes, in tissue-and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic. Here, we report CIRCpedia v2, an updated database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse, and download circRNAs with expression features in various cell types/tissues, including disease samples. In addition, the updated database incorporates conservation analysis of circRNAs between humans and mice. Finally, the web interface also contains computational tools to compare circRNA expression among samples. CIRCpedia v2 is accessible at http：//***/rnomics/circpedia.

关键词： Circular RNACircRNA Back-splicing Database CIR Cpedia

Hydrologic Response to Future Climate Change in the Dulong-Irra-waddy River Basin Based on Coupled Model Intercomparison Project 6

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Chinese Geographical Science 2024年第2期34卷 294-310页

作者： xu Ziyue ma kai YUAN xu HE Daming Institute of International Rivers and Eco-security Yunnan UniversityKunming 650500China Yunnan Key Laboratory of International Rivers and Transboundary Eco-security Kunming 650500China

Within the context of the Belt and Road Initiative(BRI)and the China-Myanmar Economic Corridor(CMEC),the Dulong-Ir-rawaddy(Ayeyarwady)River,an international river among China,India and Myanmar,plays a significant role as both a valuable hydro-power resource and an essential ecological ***,the water resources and security exhibit a high degree of vulnerabil-ity to climate change *** research evaluates climate impacts on the hydrology of the Dulong-Irrawaddy River Basin(DIRB)by using a physical-based hydrologic *** crafted future climate scenarios using the three latest global climate models(GCMs)from Coupled Model Intercomparison Project 6(CMIP6)under two shared socioeconomic pathways(SSP2-4.5 and SSP5-8.5)for the near(2025-2049),mid(2050-2074),and far future(2075-2099).The regional model using MIKE SHE based on historical hydrologic processes was developed to further project future streamflow,demonstrating reliable performance in streamflow simulations with a val-idation Nash-Sutcliffe Efficiency(NSE)of *** showed that climate change projections showed increases in the annual precip-itation and potential evapotranspiration(PET),with precipitation increasing by 11.3%and 26.1%,and PET increasing by 3.2%and 4.9%,respectively,by the end of the century under SSP2-4.5 and *** changes are projected to result in increased annual streamflow at all stations,notably at the basin’s outlet(Pyay station)compared to the baseline period(with an increase of 16.1%and 37.0%at the end of the 21st century under SSP2-4.5 and SSP5-8.5,respectively).Seasonal analysis for Pyay station forecasts an in-crease in dry-season streamflow by 31.3%-48.9%and 22.5%-76.3%under SSP2-4.5 and SSP5-8.5,respectively,and an increase in wet-season streamflow by 5.8%-12.6%and 2.8%-33.3%,***,the magnitude and frequency of flood events are pre-dicted to escalate,potentially impacting hydropower production and food security *** res

关键词： climate change hydrologic response Coupled Model Intercomparison Project 6(CMIP6) MIKE SHE(Système Hydrologique Europeén) Dulong-Irrawaddy River Basin

Contrasts of bimodal tropical instability waves(TIWs)-induced wind stress perturbations in the Pacific Ocean among observations,ocean models,and coupled climate models

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Journal of Oceanology and Limnology 2024年第1期42卷 1-23页

作者： kai ma Chuanyu LIU Junli xu Fan WANG School of mathematics and Physics Research Institute for Mathematics and Interdisciplinary SciencesQingdao University of Science and TechnologyQingdao 266100China Key Laboratory of Ocean Circulation and Waves Institute of OceanologyChinese Academy of SciencesQingdao 266071China Pilot National Laboratory for marine Science and Technology(Qingdao) Qingdao 266237China

The coupling between wind stress perturbations and sea surface temperature(SST)perturbations induced by tropical instability waves(TIWs)in the Pacific Ocean has been revealed previously and proven crucial to both the atmosphere and ***,an overlooked fact by previous studies is that the loosely defined“TIWs”actually consist of two modes,including the Yanai wave-based TIW on the equator(hereafter eTIW)and the Rossby wave-based TIW off the equator(hereafter vTIW).Hence,the individual feedbacks of the wind stress to the bimodal TIWs remain *** this study,individual coupling relationships are established for both eTIW and v TIW,including the relationship between the TIW-induced SST perturbations and two components of wind stress perturbations,and the relationship between the TIW-induced wind stress perturbation divergence(curl)and the downwind(crosswind)TIW-induced SST *** show that,due to different distributions of eTIW and vTIW,the coupling strength induced by the eTIW is stronger on the equator,and that by the vTIW is stronger off the *** results of any of eTIW and vTIW are higher than those of the loosely defined *** further investigated how well the coupling relationships remained in several widely recognized oceanic general circulation models and fully coupled climate ***,the coupling relationships cannot be well represented in most numerical ***,we confirmed that higher resolution usually corresponds to more accurate ***,the coupling models established in this study are complementary to previous research and can be used to refine the oceanic and coupled climate models.

关键词： bimodal tropical instability waves mesoscale air-sea interaction coupled models Yanai wave

CIRCexplorer3:A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression

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Genomics, Proteomics & Bioinformatics 2019年第5期17卷 511-521页

作者： xu-kai ma Meng-Ran Wang Chu-Xiao Liu Rui Dong Gordon G.Carmichael Ling-Ling Chen Li Yang CAS Key Laboratory of Computational Biology CAS-MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China State Key Laboratory of Molecular Biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Department of Genetics and Genome Sciences University of Connecticut Health CenterFarmingtonCT 06030USA School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China

Sequences of circular RNAs(circ RNAs)produced from back-splicing of exon(s)completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction(BSJ)***,examination of global circ RNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites,which is different from the quantification of linear RNA expression by normalized RNA-seq fragments mapped to whole gene ***,direct comparison of circular and linear RNA expression from the same gene loci in a genome-wide manner has remained ***,we update the previously-reported CIRCexplorer pipeline to version 3 for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq(CIRCexplorer3-CLEAR).A new quantitation parameter,fragments per billion mapped bases(FPB),is applied to evaluate circular and linear RNA expression individually by fragments mapped to circ RNA-specific BSJ sites or to linear RNA-specific splicing junction(SJ)*** of circular and linear RNA expression levels is directly achieved by dividing FPBcircby FPBlinearto generate a CIRCscore,which indicates the relative circ RNA expression level using linear RNA expression level as the *** circ RNAs with low cognate linear RNA expression background can be readily identified by CIRCexplorer3-CLEAR for further ***3-CLEAR is publically available at https://***/Yang Lab/CLEAR.

关键词： Circular RNA Back-splicing Linear RNA Pre-mRNA splicing Ribo-RNA-seq

Carbon nanocages bridged with graphene enable fast kinetics for dual-carbon lithium-ion capacitors

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Green Energy & Environment 2024年第3期9卷 573-583页

作者： Shani Li Yanan xu Wenhao Liu xudong Zhang Yibo ma Qifan Peng Xiong Zhang Xianzhong Sun kai Wang Yanwei ma Institute of Electrical Engineering Chinese Academy of SciencesBeijing100190China University of Chinese Academy of Sciences Beijing100049China Innovation Academy for Green manufacture Beijing100190China Beijing Institute of Technology Beijing100081China School of materials Science and Engineering Zhengzhou UniversityZhengzhou450001China

Lithium-ion capacitors(LICs) combining the advantages of lithium-ion batteries and supercapacitors are considered a promising nextgeneration energy storage device. However, the sluggish kinetics of battery-type anode cannot match the capacitor-type cathode, restricting the development of LICs. Herein, hierarchical carbon framework(HCF) anode material composed of 0D carbon nanocage bridged with 2D graphene network are developed via a template-confined synthesis process. The HCF with nanocage structure reduces the Li^(+) transport path and benefits the rapid Li^(+) migration, while 2D graphene network can promote the electron interconnecting of carbon nanocages. In addition, the doped N atoms in HCF facilitate to the adsorption of ions and enhance the pseudo contribution, thus accelerate the kinetics of the anode. The HCF anode delivers high specific capacity, remarkable rate capability. The LIC pouch-cell based on HCF anode and active HCF(a-HCF) cathode can provide a high energy density of 162 Wh kg^(-1) and a superior power density of 15.8 kW kg^(-1), as well as a long cycling life exceeding 15,000cycles. This study demonstrates that the well-defined design of hierarchical carbon framework by incorporating 0D carbon nanocages and 2D graphene network is an effective strategy to promote LIC anode kinetics and hence boost the LIC electrochemical performance.

关键词： Hierarchical carbon framework Nanocage ZIF Graphene Lithium-ion capacitors

Membrane tension evolution and mechanical regulation of melittin-induced membrane poration

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Chinese Physics B 2024年第10期33卷 465-475页

作者： Wanting Zhang Rong xu Wendong ma Zhao Lin kai Yang Bing Yuan Center for Soft Condensed matter Physics and Interdisciplinary Research&School of Physical Science and Technology Soochow UniversitySuzhou 215006China Songshan Lake materials Laboratory Dongguan 523808China Biomedicine Discovery Institute Infection&Immunity ProgramMonash UniversityMelbourneAustralia Beijing National Laboratory for Condensed matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China

Membrane tension plays a crucial role in various fundamental cellular processes,with one notable example being the T cell-mediated elimination of tumor cells through perforin-induced membrane perforation by amplifying cellular ***,the mechanisms governing the regulation of biomolecular activities at the cell interface by membrane tension remain *** this study,we investigated the correlation between membrane tension and poration activity of melittin,a prototypical pore-forming peptide,using dynamic giant unilamellar vesicle leakage assays combined with flickering tension analysis,molecular dynamics simulations,and live cell *** results demonstrate that an increase in membrane tension enhances the activity of melittin,particularly near its critical pore-forming ***,peptide actions such as binding,insertion,and aggregation in the membrane further influence the evolution of membrane *** cell experiments reveal that artificially enhancing membrane tension effectively enhances melittin’s ability to induce pore formation and disrupt membranes,resulting in up to a ten-fold increase in A549 cell mortality when exposed to a concentration of 2.0-μg·mL^(-1)*** findings elucidate the relationship between membrane tension and the mechanism of action as well as pore-forming efficiency of melittin,while providing a practical mechanical approach for regulating functional activity of molecules at the cell-membrane interface.

关键词： membrane tension mechanical regulation membrane poration giant unilamellar vesicle leakage assay

Feasibility study of the photonuclear reaction cross section of medical radioisotopes using a laser Compton scattering gamma source

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Nuclear Science and Techniques 2024年第9期35卷 168-177页

作者： Yu-Ning Gu Wei-Juan Zhao Xi-Guang Cao Yu-xuan Yang Ting-kai ma Zheng-Li Liao Fei-Long xu Yu-Gang ma School of Physics and Microeletronics Zhengzhou UniversityZhengzhou 450001China Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai 201210China Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800China University of Chinese Academy of Sciences Beijing 100049China School of Nuclear Science and Technology University of South ChinaHengyang 421001China Key Laboratory of Nuclear Physics and Ion-beam Application(MOE) Institute of Modern PhysicsFudan UniversityShanghai 200433China Shanghai Research Center for Theoretical Nuclear Physics NSFC and Fudan UniversityShanghai 200438China

In recent years,the gap between the supply and demand of medical radioisotopes has increased,necessitating new methods for producing medical *** reactions based on gamma sources have unique advantages in terms of producing high specific activity and innovative medical ***,the lack of experimental data on reaction cross sections for photonuclear reactions of medical radioisotopes of interest has severely limited the development and production of photonuclear transmutation medical *** this study,the entire process of the generation,decay,and measurement of medical radioisotopes was simulated using online gamma activation and offline gamma measurements combined with a shielding gamma-ray *** on a quasi-monochromatic gamma beam from the Shanghai Laser Electron Gamma Source(SLEGS),the feasibility of this measurement of production cross section for surveyed medi-cal radioisotopes was simulated,and specific solutions for measuring medical radioisotopes with ultra-low production cross sections were *** feasibility of this method for high-precision measurements of the reaction cross section of medical radioisotopes was demonstrated.

关键词： Medical radioisotope Photonuclear reaction GEANT4 Shanghai Laser Electron Gamma Source(SLEGS) Low-background gamma-ray spectrometer

Geochemical characteristics and exploration significance of ultra-deep Sinian oil and gas from Well Tashen 5,Tarim Basin,NW China

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Energy Geoscience 2024年第1期5卷 24-36页

作者： Zicheng Cao Anlai ma Qinqi xu Quanyong Pan kai Shang Fan Feng Yongli Liu Northwest Petroleum Oilfield Company SINOPECUrumqi830011China Petroleum Exploration and Production Research Institute SINOPEC102260BeijingChina

The Well Tashen 5(TS5),drilled and completed at a vertical depth of 9017 m in the Tabei Uplift of the Tarim Basin,NW China,is the deepest well in *** has been producing both oil and gas from the Sinian at a depth of 8780e8840 m,also the deepest in Asia in terms of oil *** this paper,the geochemical characteristics of Sinian oil and gas from the well were investigated and compared with those of Cambrian oil and gas discovered in the same *** oil samples,with Pr/Ph ratio of 0.78 and a whole oil carbon isotopic value of31.6‰,have geochemical characteristics similar to those of Ordovician oils from the No.1 fault in the North Shuntuoguole area(also named Shunbei area)and the Middle Cambrian oil from wells Zhongshen 1(ZS1)and Zhongshen 5(ZS5)of Tazhong *** maturity of light hydrocarbons,diamondoids and aromatic fractions all suggest an approximate maturity of 1.5%e1.7%Ro for the ***(4-+3-)methyldiamantane concentration of the samples is 113.5 mg/g,indicating intense cracking with a cracking degree of about 80%,which is consistent with the high bottom hole temperature(179℃).The Sinian gas samples are dry with a dryness coefficient of *** gas is a mixture of kerogen-cracking gas and oil-cracking gas and has Ro values ranging between 1.5%and 1.7%,and methane carbon isotopic values of41.6‰.Based on the equivalent vitrinite reflectance(R_(eqv)=1.51%e1.61%)and the thermal evolution of source rocks from the Cambrian Yu'ertusi Formation of the same well,it is proposed that the Sinian oil and gas be mainly sourced from the Cambrian Yu'ertusi Formation during the Himalayan period but probably also be joined by hydrocarbon of higher maturity that migrated from other source rocks in deeper *** discovery of Sinian oil and gas from Well TS5 suggests that the ancient ultra-deep strata in the northern Tarim Basin have the potential for finding volatile oil or condensate reservoirs.

关键词： Ultra-deep Sinian oil and gas Oil-cracking Well Tashen 5 Tarim Basin

One-Step Scalable Fabrication of Nitrogen and Chlorine Co-doped Graphene by Electrochemical Exfoliation for High-Performance Supercapacitors

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Transactions of Tianjin University 2024年第5期30卷 448-458页

作者： Qian Li Hu Zheng Binbin Liu Tianzhen Jian Wenqing ma Caixia xu kai Wang Institute for Advanced Interdisciplinary Research(iAIR) School of Chemistry and Chemical EngineeringUniversity of JinanJinan 250022China Institute of Electrical Engineering Chinese Academy of SciencesBeijing 100190China

The stacking and aggregation of graphene nanosheets have been obstacles to their application as electrode materials for microelectronic *** study deploys a one-step,scalable,facile electrochemical exfoliation technique to fabricate nitrogen(N)and chlorine(Cl)co-doped graphene nanosheets(i.e.,N-Cl-G)via the application of constant voltage on graphite in a mixture of 0.1 mol/L H_(2)SO_(4)and 0.1 mol/L NH_(4)Cl without using dangerous and exhaustive *** introduction of Cl(with its large radius)and N,both with high electrical negativity,facilitates the modulation of the electronic structure of graphene and creation of rich structural defects in ***,in the as-constructed supercapacitors,N-Cl-G exhibits a high specific capacitance of 77 F/g at 0.2 A/g and remarkable cycling stability with 91.7%retention of initial capacitance after 20,000 cycles at 10 A/***,a symmetrical supercapacitor assembled with N-Cl-G as the positive and negative electrodes(denoted as N-Cl-G//N-Cl-G)exhibits an energy density of 3.38 Wh/kg at a power density of 600 W/kg and superior cycling stability with almost no capacitance loss after 5000 cycles at 5 A/*** study provides a scalable protocol for the facile fabrication of high-performance co-doped graphene as an electrode material candidate for supercapacitors.

关键词： Graphene Electrochemical exfoliation Supercapacitor Nitrogen Chlorine