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De novo sequencing and comparative analysis of three red algal species of Family Solieriaceae to discover putative genes associated with carrageenan biosysthesis

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Acta Oceanologica Sinica 2014年第2期33卷 45-53页

作者： song lipu WU Shuangxiu SUN Jing WANG Liang LIU Tao CHI Shan LIU Cui LI Xingang YIN Jinlong WANG Xumin YU Jun CAS Key Laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of Sciences Beijing Key Laboratory of Functional Genomics for Dao-di Herbs Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences College of Marine Life Science Ocean University of China

Betaphycus gelatinus, Kappaphycus alvarezii and Eucheuma denticulatum of Family Solieriaceae, Order Gi-gartinales, Class Rhodophyceae are three important carrageenan-producing red algal species, which pro-duce different types of carrageenans, beta （β）-carrageenan, kappa （κ）-carrageenan and iota （ι）-carrageenan. So far the carrageenan biosynthesis pathway is not fully understood and few information is about the So-lieriaceae genome and transcriptome sequence. Here, we performed the de novo transcriptome sequencing, assembly, functional annotation and comparative analysis of these three commercial-valuable species using an Illumina short-sequencing platform Hiseq 2000 and bioinformatic software. Furthermore, we compared the different expression of some unigenes involved in some pathways relevant to carrageenan biosynthe-sis. We finally found 861 different expressed KEGG orthologs which contained a glycolysis/gluconeogenesis pathway （21 orthologs）, carbon fixation in photosynthetic organisms （16 orthologs）, galactose metabolism （5 orthologs）, and fructose and mannose metabolism （9 orthologs） which are parts of the carbohydrate me-tabolism. We also found 8 different expressed KEGG orthologs for sulfur metabolism which might be impor-tantly related to biosynthesis of different types of carrageenans. The results presented in this study provided valuable resources for functional genomics annotation and investigation of mechanisms underlying the biosynthesis of carrageenan in Family Solieriaceae.

关键词： Betaphycus gelatinus Kappaphycus alvarezii Eucheuma denticulatum Solieriaceae de novo transcriptome sequencing carrageenan

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涉及科技伦理问题的撤稿论文研究

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科学通报 2023年第13期68卷 1621-1625页

作者：宋利璞杨卫平中国科学院监督与审计局北京100864 中国科学院大学北京101408

科技论文的伦理治理是科技伦理治理体系的重要组成部分.论文所涉及的科研活动应遵守科技伦理规范.本文利用Retraction Watch Database信息,收集国际科技期刊中因伦理问题而撤稿的论文案例.从发表时间、撤稿时间、学科领域、所属国家等... 详细信息

科技论文的伦理治理是科技伦理治理体系的重要组成部分.论文所涉及的科研活动应遵守科技伦理规范.本文利用Retraction Watch Database信息,收集国际科技期刊中因伦理问题而撤稿的论文案例.从发表时间、撤稿时间、学科领域、所属国家等不同维度进行比较,挖掘其中的规律和特点.从时间角度, 2000年以来因伦理问题而撤稿的论文开始出现并逐步增多,表明科学共同体伦理意识增强,更加关注论文所涉及科研活动的伦理合规性.所有国家中,我国因伦理问题撤稿论文数量共92篇,居世界第三位.从学科领域角度看,超过90%的论文涉及生命健康研究.我们进一步将撤稿原因细化为违反伦理审查、知情同意、伦理共识规范等三大类17个方面,其中研究活动未获得伦理委员会前置性批准是最主要的原因.基于此,建议当前科技伦理治理的工作切入点是强化规范的科技活动伦理审查.此外,建议我国要积极参与国际伦理治理,加强伦理研究、提升伦理意识、普及伦理教育、加强对悖于科技伦理规范行为的调查处理等.

关键词：科技伦理撤稿论文伦理审查知情同意伦理共识

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陕西紫阳地区(过渡带)志留纪地层及古生物

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西北地质科学 1986年第14期 1-8页

作者：傅力浦宋礼生

紫阳地区志留系的系统生物地层工作是以古生物增大定律为主线,根据下志留统四个笔石谱系的演化关系,结合剖面中微量元素最优分割与火山活动等地质事件的关系,以及奥陶纪末期冰川使海平面下降、笔石生物分异度的降低,对下志留统顶、底及... 详细信息

紫阳地区志留系的系统生物地层工作是以古生物增大定律为主线,根据下志留统四个笔石谱系的演化关系,结合剖面中微量元素最优分割与火山活动等地质事件的关系,以及奥陶纪末期冰川使海平面下降、笔石生物分异度的降低,对下志留统顶、底及四个阶段作出论证。建议中国下志留统划分为龙马溪阶（包括S11麻柳树湾亚阶和S12斑鸠关亚阶）、S13陡山沟阶、S14吴家河阶,后两阶可以紫阳芭蕉口剖面为层型。

关键词：下志留统笔石古生物紫阳

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Tectonic modes of mantle convection and their implications for Earth's tectonic evolution based on three-dimensional numerical simulations

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Science China Earth Sciences 2025年第1期68卷 270-296页

作者： song XIANG Jinshui HUANG Bingcheng WU School of Earth and Space Sciences University of Science and Technology of China CAS Center of Excellence in Comparative Planetary Studies

Five tectonic modes of mantle convection are obtained and analyzed with three-dimensional numerical models in a spherical shell domain. The five tectonic convective modes are non-plate mobile-lid, plate-like mobile-lid, episodic plate-like mobile-lid, episodic stagnant-lid, and stagnant-lid convective modes, respectively. The typical characteristics of these five tectonic modes and their numerical classification criteria based on plateness, mobility, and their standard deviations are presented and discussed. The results show that the yield stress of the lithosphere has profound effects on the tectonic convective *** the gradual increase of yield stress, the tectonic mode of mantle convection changes from one to another sequentially through the aforementioned five modes. Additionally, as the Rayleigh number increases, the range of yield stress for the platelike mobile-lid convective mode decreases, and the dimensionless transition stress between different tectonic modes ***, the dimensional transition stress between the non-plate mobile-lid convective mode and plate-like mobile-lid convective mode increases with the increase of Rayleigh number, but decreases between other tectonic modes. Furthermore, we find that the transition stress between different tectonic modes is inversely proportional to the internal heating rate, with the transition stress decreasing as the internal heating rate increases. The fitting analysis of the transition stress between tectonic modes shows that Earth's current plate tectonics correspond to a lithospheric yield stress of 150–250 MPa, which aligns with the strength of serpentinized mantle rock determined by experimental petrography. If the Archean mantle was 300°C warmer than it is today, then the Earth was in an episodic stagnant-lid convective mode. The tectonic evolution of the Earth's surface is closely related to the lithospheric strength and the process of thermal evolution. If the lithospheric strength w

关键词： Tectonic mode of mantle convection Plate-like mobile-lid convection Episodic plate-like mobile-lid convection Episodic stagnant-lid convection Plate tectonics and tectonic evolution of the Earth

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江西某酸性火山岩风化壳中粘土矿物及其形成条件的讨论

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矿物学报 1982年第3期 207-212页

作者：宋云华沈丽璞中国科学院地球化学研究所

江西某酸性火山岩风化壳中离子吸附型稀土元素矿床具有规模大、品位高、易开采和有用元素提取简便等特点,是一种重要的稀土元素矿床工业类型。本文拟就与该矿床直接有关的粘土矿物的组成、变化规律、成因以及对稀土的吸附性能等问题作... 详细信息

江西某酸性火山岩风化壳中离子吸附型稀土元素矿床具有规模大、品位高、易开采和有用元素提取简便等特点,是一种重要的稀土元素矿床工业类型。本文拟就与该矿床直接有关的粘土矿物的组成、变化规律、成因以及对稀土的吸附性能等问题作一初步探讨。一、样品及其产状本区广泛出露侏罗-白垩纪火山岩。火山岩可分为（1）火山通道相:凝灰角砾岩、熔结角砾岩和爆发角砾岩等;（2）爆发相:火山角砾岩、集块岩和熔结凝灰岩等;（3）喷溢

关键词：火山岩风化壳结晶程度高岭石铝矿物风化层粘土矿物粘粒矿物硅酸盐矿物酸性江西

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Molecular dynamics simulations of helium transport through inorganic mineral nanopores

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Science China Earth Sciences 2025年第1期68卷 237-252页

作者： Dandan song Ping GUAN Chi ZHANG Jiahao REN School of Earth and Space Sciences Peking University

Helium transport through nanoscale inorganic mineral pores and pore throats is essential for its overall migration. To elucidate helium's transport dynamics within nanopores, we employed equilibrium and non-equilibrium molecular dynamics simulations to investigate helium's static self-diffusion and pressure-driven flow in quartz slit-shaped nanopores. We also introduced water and various gases, including hydrogen, methane, ethane, nitrogen, and carbon dioxide, into the nanopores to assess their influence on helium transport. Our findings indicate minimal helium adsorption on quartz pore surfaces. Under conditions where the pore size is less than 5 nm and the pressure under 10 MPa, environmental factors markedly influence helium diffusion. Large pore sizes, high temperatures, and low gas pressures enhance helium desorption and facilitate faster diffusion. We observed a positive correlation between helium flow velocity and factors such as pore size, pressure gradient, and surface smoothness of the pores. Notably, the presence of pore water and carrier gases in quartz nanopores, which diffuse more slowly than helium, tends to reduce helium surface adsorption and slow its diffusion. Among the carrier gases studied, nitrogen showed similar adsorption capacity, diffusivity, and stability to helium, while carbon dioxide displayed the highest adsorption capacity and the slowest diffusion rate, markedly differing from helium. Based on the simulation results, we concluded that water and carrier gases primarily function as transport mediums in helium migration, moving together with helium. Nitrogen, which shares similar properties with helium, effectively assists in this co-migration process. Conversely, carbon dioxide, due to its high adsorption capacity and slow diffusion, tends to be lost during co-migration. As a result, gas reservoirs with high nitrogen levels and low carbon dioxide levels are more likely to have higher helium concentrations. Additionally, the smaller por

关键词： Helium transport Slit nanopores Molecular dynamics simulations Diffusion Flow carriers

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CAF-derived exosome-miR-3124-5p promotes malignant biological processes in NSCLC via the TOLLIP/TLR4-MyD88-NF-κB pathway

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Oncology Research 2025年第1期33卷 133-148页

作者： TAO SUN QINGHUA song HUA LIU Department of Respiratory and Critical Care Medicine Affiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong226001China Department of Emergency The People’s Hospital of RugaoNantong226500China Department of Haematology The People’s Hospital of RugaoNantong226500China

Background:Lung cancer is a life-threatening disease that occurs worldwide,but is especially common in *** crucial role of the tumour microenvironment(TME)in non-small cell lung cancer(NSCLC)has attracted recent ***-associated fibroblasts(CAFs)are the main factors that contribute to the TME function,and CAF exosomes are closely linked to ***:The expression levels of miR-3124-5p and Toll-interacting protein(TOLLIP)were analysed by bioinformatics prediction combined with RT-qPCR/Western Blot *** were isolated and identified from clinical NSCLC *** electron microscopy and Western Blot were used to identify exosomes from these *** in proliferation(CCK-8 and clone formation),migration(wound healing),and invasion(transwell)of NSCLC cells were *** Luciferase reporter test was applied to clarify the binding of miR-3124-5p to *** TOLLIP/TLR4/MyD88/NF-κB pathway proteins were determined using Western blot ***:MiR-3124-5p is overexpressed in clinical tissues and cells of ***-3124-5p was dramatically enriched in CAF-derived *** experiments revealed that CAFs delivered miR-3124-5p into NSCLC cells via exosomes,stimulating cancer cell ***-3124-5p acted as a sponge to negatively regulate TOLLIP expression,which activated the TLR4/MyD88/NF-κB axis to promote the occurrence and development of *** salvage tests were performed to determine whether CAF-exosome-derived miR-3124-5p plays a pro-cancer role in NSCLC by affecting the TOLLIP signalling ***:These results provide an interesting direction for the diagnosis and therapy of NSCLC.

关键词： Non-small cell lung cancer(NSCLC) Cancer-associated fibroblasts(CAFs) Exosomes miR-3124-5p Toll-interacting protein(TOLLIP)

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Constraints on holographic QCD phase transitions from PTA observations

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 71-78页

作者： song He Li Li Sai Wang Shao-Jiang Wang Center for Theoretical Physics and College of Physics Jilin University School of Physical Science and Technology Ningbo University Max Planck Institute for Gravitational Physics (Albert Einstein Institute) CAS Key Laboratory of Theoretical Physics Institute of Theoretical Physics Chinese Academy of Sciences School of Fundamental Physics and Mathematical Sciences Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of Sciences (UCAS) School of Physical Sciences University of Chinese Academy of Sciences (UCAS) Theoretical Physics Division Institute of High Energy Physics Chinese Academy of Sciences

The underlying physics of QCD phase transition in the early Universe remains largely unknown due to its strong-coupling nature during the quark-gluon plasma/hadron gas transition, yet a holographic model has been proposed to quantitatively fit the lattice QCD data while with its duration of the first-order phase transition(FoPT) left undetermined. At specific baryon chemical potential, the first-order QCD phase transition agrees with the observational constraint of baryon asymmetry. It, therefore, provides a scenario for phase transition gravitational waves(GWs) within the standard model of particle physics. If these background GWs could contribute dominantly to the recently claimed common-spectrum red noise from pulsar timing array(PTA) observations, the duration of this FoPT can be well constrained, and the associated primordial black holes are still allowed by current observations.

关键词： pulsar timing array QCD phase transition gravitational waves primordial black holes

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Neuronal regulated cell death in aging-related neurodegenerative diseases:key pathways and therapeutic potentials

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Neural Regeneration Research 2025年第8期20卷 2245-2263页

作者： Run song Shiyi Yin Jiannan Wu Junqiang Yan Department of Neurology The First Affiliated HospitalCollege of Clinical Medicine of Henan University of Science and TechnologyLuoyangHenan ProvinceChina Neuromolecular Biology Laboratory The First Affiliated HospitalCollege of Clinical Medicine of Henan University of Science and TechnologyLuoyangHenan ProvinceChina

Regulated cell death(such as apoptosis,necroptosis,pyroptosis,autophagy,cuproptosis,ferroptosis,disulfidptosis)involves complex signaling pathways and molecular effectors,and has been proven to be an important regulatory mechanism for regulating neuronal aging and ***,excessive activation of regulated cell death may lead to the progression of aging-related *** review summarizes recent advances in the understanding of seven forms of regulated cell death in age-related ***,the newly identified ferroptosis and cuproptosis have been implicated in the risk of cognitive impairment and neurodegenerative *** forms of cell death exacerbate disease progression by promoting inflammation,oxidative stress,and pathological protein *** review also provides an overview of key signaling pathways and crosstalk mechanisms among these regulated cell death forms,with a focus on ferroptosis,cuproptosis,and *** instance,FDX1 directly induces cuproptosis by regulating copper ion valency and dihydrolipoamide S-acetyltransferase aggregation,while copper mediates glutathione peroxidase 4 degradation,enhancing ferroptosis ***,inhibiting the Xc-transport system to prevent ferroptosis can increase disulfide formation and shift the NADP^(+)/NADPH ratio,transitioning ferroptosis to *** insights help to uncover the potential connections among these novel regulated cell death forms and differentiate them from traditional regulated cell death *** conclusion,identifying key targets and their crosstalk points among various regulated cell death pathways may aid in developing specific biomarkers to reverse the aging clock and treat age-related neurodegenerative conditions.

关键词： apoptosis autophagy cuproptosis disulfidptosis ferroptosis necroptosis neurodegenerative disease neurological aging diseases PANoptosis pyroptosis

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Passive activity enhances residual control ability in patients with complete spinal cord injury

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Neural Regeneration Research 2025年第8期20卷 2337-2347页

作者： Yanqing Xiao Mingming Gao Zejia He Jia Zheng Hongming Bai Jia-Sheng Rao Guiyun song Wei song Xiaoguang Li Beijing Key Laboratory for Biomaterials and Neural Regeneration Beijing Advanced Innovation Center for Biomedical EngineeringSchool of Biological Science and Medical EngineeringBeihang UniversityBeijingChina Department of Rehabilitation Evaluation China Rehabilitation Research CenterBeijingChina Cardiac Center Beijing Children’s HospitalCapital Medical UniversityBeijingChina The State Key Laboratory of Virtual Reality Technology and Systems Beihang UniversityBeijingChina Department of Rehabilitation Engineering China Rehabilitation Science InstituteBeijingChina

Patients with complete spinal cord injury retain the potential for volitional muscle activity in muscles located below the spinal injury ***,because of prolonged inactivity,initial attempts to activate these muscles may not effectively engage any of the remaining neurons in the descending pathway.A previous study unexpectedly found that a brief clinical round of passive activity significantly increased volitional muscle activation,as measured by surface *** this study,we further explored the effect of passive activity on surface electromyographic signals during volitional control tasks among individuals with complete spinal cord *** patients with chronic complete thoracic spinal cord injury were *** electromyography data from eight major leg muscles were acquired and compared before and after the passive activity *** results indicated that the passive activity led to an increased number of activated volitional muscles and an increased frequency of *** the cumulative root mean square of surface electromyography amplitude for volitional control of movement showed a slight increase after passive activity,the difference was not statistically *** findings suggest that brief passive activity may enhance the ability to initiate volitional muscle activity during surface electromyography tasks and underscore the potential of passive activity for improving residual motor control among patients with motor complete spinal cord injury.

关键词： complete spinal cord injury cycle training epidural electrical stimulation motor training passive activity physiological state spinal cord circuit surface electromyography volitional control task

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