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Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data

Genomics, Proteomics & Bioinformatics 2024年第2期22卷 27-42页

作者： xi Wang Qiwei Lian Haoyu Dong Shuo Xu Yaru Su xiaohui Wu Pasteurien College Suzhou Medical College of Soochow UniversitySoochow UniversitySuzhou 215000China department of Automation Xiamen UniversityXiamen 361005China College of Mathematics and Computer Science Fuzhou UniversityFuzhou 350116China

Gene set scoring(GSS)has been routinely conducted for gene expression analysis of bulk or single-cell RNA sequencing(RNA-seq)data,which helps to decipher single-cell heterogeneity and cell type-specific variability by incorporating prior knowledge from functional gene ***-cell assay for transposase accessible chromatin using sequencing(scATAC-seq)is a powerful technique for interrogating single-cell chromatin-based gene regulation,and genes or gene sets with dynamic regulatory potentials can be regarded as cell type-specific markers as if in single-cell RNA-seq(scRNA-seq).However,there are few GSS tools specifically designed for scATAC-seq,and the applicability and performance of RNA-seq GSS tools on scATAC-seq data remain to be ***,we systematically benchmarked ten GSS tools,including four bulk RNA-seq tools,five scRNA-seq tools,and one scATAC-seq ***,using matched scATAC-seq and scRNA-seq datasets,we found that the performance of GSS tools on scATAC-seq data was comparable to that on scRNA-seq,suggesting their applicability to ***,the performance of different GSS tools was extensively evaluated using up to ten scATAC-seq ***,we evaluated the impact of gene activity conversion,dropout imputation,and gene set collections on the results of *** show that dropout imputation can significantly promote the performance of almost all GSS tools,while the impact of gene activity conversion methods or gene set collections on GSS performance is more dependent on GSS tools or ***,we provided practical guidelines for choosing appropriate preprocessing methods and GSS tools in different application scenarios.

关键词： Single-cell ATAC-seq Gene set scoring Pathway analysis Single-cell RNA-seq Benchmark

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A molecular dynamics study on surface properties of supercooled water

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Science china(physics,Mechanics & Astronomy) 2006年第5期49卷 616-625页

作者： Lü Yongjun & WEI Bingbo department of Applied physics, Northwestern Polytechnical University, xi’an 710072, china department of Applied physics Northwestern Polytechnical University Xi’an China

Molecular dynamics simulations were performed to study the surface properties of water in a temperature range from 228 to 293 K by using the extended simple point charge (SPC/E) and four-site TIP4P potentials. The calculated surface tension increases with the decrease of temperature, and moreover the slopes of the surface tension-temperature curves show a weak rise below 273 K, whereas no obvious anomalies appear near 228 K, which accords with the previous experiments. Compared with the measured values, the SPC/E potential shows a good agreement, and the TIP4P potential underestimates the surface tension. The main reason for that may be the reasonable description of the surface structure of supercooled water for the SPC/E. When simulating the orientational distributions of water molecules near the surface, the SPC/E potential produces higher ordering and larger surface potentials than the TIP4P potential.

关键词： surface tension supercooled water molecular dynamics simulation.

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Decoding the Cellular Trafficking of Prion-like Proteins in Neurodegenerative Diseases

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Neuroscience Bulletin 2024年第2期40卷 241-254页

作者： Chenjun Hu Yiqun Yan Yanhong Jin Jun Yang Yongmei xi Zhen Zhong department of Neurology of the Second Afliated Hospital and department of Human Anatomy Histology and EmbryologyZhejiang University School of MedicineHangzhou 310058China department of Physiology and department of Cardiology of the Second Afliated Hospital Zhejiang University School of MedicineHangzhou 310058China Division of Human Reproduction and Developmental Genetics Women’s Hospital and Institute of GeneticsZhejiang University School of MedicineHangzhou 310006China

The accumulation and spread of prion-like proteins is a key feature of neurodegenerative diseases(NDs)such as Alzheimer’s disease,Parkinson's disease,or Amyotrophic Lateral *** a process known as‘seeding’,prion-like proteins such as amyloid beta,microtubule-associated protein tau,α-synuclein,silence superoxide dismutase 1,or transactive response DNA-binding protein 43 kDa,propagate their misfolded conformations by transforming their respective soluble monomers into *** and molecular evidence of prion-like propagation in NDs,the clinical relevance of their‘seeding’capacities,and their levels of contribution towards disease progression have been intensively studied over recent *** review unpacks the cyclic prion-like propagation in cells including factors of aggregate internalization,endo-lysosomal leaking,aggregate degradation,and *** on the importance of the role of prion-like protein aggregates in NDs,whether causal or consequent,are also *** lead to a greater understanding of ND pathogenesis and increased potential for therapeutic strategies.

关键词： Neurodegenerative diseases Prion-like propagation Seeding Endocytosis Endolyosomal leaking Degradation

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Rotating Massive Strangeon Stars and X-Ray Plateau of Short GRBs

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Research in Astronomy and Astrophysics 2024年第3期24卷 47-57页

作者： xi-Yan Yang xiao-Yu Lai Wei-Wei Tan Ren-xin Xu School of physics and Optoelectronic engineering Yangtze UniversityJingzhou 434023China Research Center for Astronomy Hubei University of EducationWuhan 4300205China Key Laboratory of Quark and Lepton physics Central China Normal UniversityMinistry of EducationWuhan 430079China School of physics Peking UniversityBeijing 100871China Kavli Institute for Astronomy and Astrophysics Peking UniversityBeijing 100871China

Strangeon stars,which are proposed to describe the nature of pulsar-like compact stars,have passed various observational *** maximum mass of a non-rotating strangeon star could be high,which implies that the remnants of binary strangeon star mergers could even be long-lived massive strangeon *** study rigidly rotating strangeon stars in the slowly rotating approximation,using the Lennard-Jones model for the equation of *** can significantly increase the maximum mass of strangeon stars with unchanged baryon numbers,enlarging the mass-range of long-lived strangeon *** spin-down after merger,the decrease of radius of the remnant will lead to the release of gravitational *** into account the efficiency of converting the gravitational energy luminosity to the observed X-ray luminosity,we find that the gravitational energy could provide an alternative energy source for the plateau emission of X-ray *** fitting results of X-ray plateau emission of some short gamma-ray bursts suggest that the magnetic dipole field strength of the remnants can be much smaller than that of expected when the plateau emission is powered only by spin-down luminosity of magnetars.

关键词： dense matter-(stars) pulsars general-(stars) gamma-ray burst general

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Multiple pretreatments can effectively improve the functionality of mesenchymal stem cells

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World Journal of Stem Cells 2024年第2期16卷 58-63页

作者： xin-xing Wan xi-Min Hu Kun xiong department of Endocrinology Third Xiangya HospitalCentral South UniversityChangsha 410013Hunan ProvinceChina department of Dermatology Xiangya HospitalCentral South UniversityChangsha 410008Hunan ProvinceChina department of Anatomy and Neurobiology School of Basic Medical ScienceCentral South UniversityChangsha 410013Hunan ProvinceChina

In this editorial,we offer our perspective on the groundbreaking study entitled“Hypoxia and inflammatory factor preconditioning enhances the immunosup-pressive properties of human umbilical cord mesenchymal stem cells”,recently published in World Journal of Stem *** over three decades of research on the clinical application of mesenchymal stem cells(MSCs),only a few therapeutic products have made it to clinical use,due to multiple preclinical and clinical challenges yet to be *** study proved the hypoxia and inflammatory factor preconditioning led to higher immunosuppressive effects of MSCs without damaging their biological characteristics,which revealed the combination of inflammatory factors and hypoxic preconditioning offers a promising approach to enhance the function of *** we delve deeper into the intricacies of pretreat-ment methodologies,we anticipate a transformative shift in the landscape of MSC-based therapies,ultimately contributing to improved patient outcomes and advancing the field as a whole.

关键词： Mesenchymal stem cells Inflammatory factor Hypoxia Pretreatment

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Relationship between disorder,magnetism and band topology in Mn(Sb_(1-x)Bi_(x))_(2)Te_(4) single crystals

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Chinese physics B 2024年第6期33卷 102-107页

作者：席明雷和畅 department of physics and Beijing Key Laboratory of Opto-electronic Functional Materials&Micro-nano Devices Renmin University of ChinaBeijing 100872China Key Laboratory of Quantum State Construction and Manipulation(Ministry of Education) Renmin University of ChinaBeijing 100872China

We investigate the evolution of magnetic properties as well as the content and distribution of Mn for Mn(Sb_(1-x)Bi_(x))_(2)Te_(4) single crystals grown by large-temperature-gradient chemical vapor transport *** is found that the ferromagnetic MnSb_(2)Te_(4) changes to antiferromagnetism with Bi doping when x≥*** analysis implies that the occupations of Mn ions at Sb/Bi site Mn_(Sb/Bi) and Mn site Mn_(Mn) have a strong influence on the magnetic ground states of these *** the decrease of Mn_(Mn) increase of Mn_(Sb/Bi),the system will favor the ferromagnetic ground *** addition,the rapid decrease of T_(C/N) with increasing Bi content when x ≤0.25 and the insensitivity of T_(N) to x when x> 0.25 suggest that the main magnetic interaction may change from the Ruderman-Kittel-Kasuya-Yosida type at low Bi doping region to the van-Vleck type in high Bi doped samples.

关键词： magnetic topological insulator magnetic properties antisite defects chemical vapor transport

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Effective-Medium Theory for Two-Phase Random Composites with and Interfacial Shell

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Journal of Materials Science & Technology 2000年第4期16卷 367-369页

作者： Qingzhong XUE (department of physics, University of Petroleum, Dongying 257062, china) department of physics University of Petroleum Dongying 257062 China

According to the Bruggeman theory and Maxwell-Garnett theory, the effective dielectric constant of a two-phase random composite with an interfacial shell is presented. The nonlinearity of the theory is obvious. Especially, the theory is suited to study the dielectric properties of two-phase random composites with a spherical interfacial shell. The theoretical results on dielectric properties of polystyrene-barium titanate composites with an interfacial shell are in good agreement with experimental data.

关键词： Zhang Effective-Medium Theory for Two-Phase Random Composites with and Interfacial Shell Wang

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Highly Sensitive Fiber-Optic Faraday-Effect Magnetic Field Sensor Based on Yttrium Iron Garnet

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Journal of Materials Science & Technology 2000年第2期16卷 205-206页

作者： Wenbo FEI (department of physics, Northeastern Universitys Shenyang 110006, china) department of physics Northeastern University Shenyang 110006 China

The principle and performance of a fiber-optic Faraday-effect magnetic-field sensor based on an yttrium iron garnet (YIG) and two flux concentrations are described. A single polarization-maintaining optical fiber links the sensor head to the source and detection system, in which the technique of phase shift cancellation is used to cancel the phase shift that accumulatein the optical fiber. Flux concentrators were exploited to enhance the YIG crystal magneto-optic sensitivity .The sensor system exhibited a noise-equivalent field of 8 pT/√Hz and a 3 dB bandwidth of ～10 MHz.

关键词： YIG Highly Sensitive Fiber-Optic Faraday-Effect Magnetic Field Sensor Based on Yttrium Iron Garnet

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A post-modification strategy to precisely construct dual-atom sites for oxygen reduction electrocatalysis

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Journal of Energy Chemistry 2024年第3期90卷 511-517,I0012页

作者： Juan Wang xinyan Liu Chang-xin Zhao Yun-Wei Song Jia-Ning Liu xi-Yao Li Chen-xi Bi xin Wan Jianglan Shui Hong-Jie Peng Bo-Quan Li Jia-Qi Huang School of Materials Science and engineering Beijing Institute of TechnologyBeijing 100081China Advanced Research Institute of Multidisciplinary Science Beijing Institute of TechnologyBeijing 100081China Beijing Key Laboratory of Green Chemical Reaction engineering and Technology Department of Chemical EngineeringTsinghua UniversityBeijing 100084China Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of ChinaChengdu 611731SichuanChina School of Materials Science and engineering Beihang UniversityBeijing 100191China

Dual-atom catalysts(DACs) afford promising potential for oxygen reduction electrocatalysis due to their high atomic efficiency and high intrinsic ***,precise construction of dual-atom sites remains a *** this work,a post-modification strategy is proposed to precisely fabricate DACs for oxygen reduction ***,a secondary metal precursor is introduced to the primary single-atom sites to introduce direct metal-metal interaction,which ensures the formation of desired atom pair structure during the subsequent pyrolysis process and allows for successful construction of *** as-prepared FeCo-NC DAC exhibits superior oxygen reduction electrocatalytic activity with a half-wave potential of 0,91 V *** hydrogen ***-air batteries equipped with the FeCo-NC DAC demonstrate higher peak power density than those with the Pt/C *** importantly,this post-modification strategy is demonstrated universal to achieve a variety of dual-atom *** work presents an effective synthesis methodology for precise construction of catalytic materials and propels their applications in energy-related devices.

关键词： Dual-atom catalysts Electrocatalysis Oxygen reduction reaction Post-modification Zinc–air batteries

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X-ray spectra induced by ^(129)Xe^(q+) impacting the metal surface

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Science china(physics,Mechanics & Astronomy) 2008年第1期51卷 82-89页

作者： ZHANG xiaoAn 1,2 ,xiAO GuoQing 1 ,YANG ZhiHu 1 ,CHEN xiMeng 3 ,ZHAO YongTao 1 , LI FuLi 4 ,WANG Li 1,2 ,CUI Ying 3 ,ZHANG HongQiang 3 &ZHAN WenLong 1 1Institute of Modern physics,Chinese Academy of Sciences,Lanzhou 730000,china 2department of physics,xianyang Normal University,xianyang 712000,china 3department of Modern physics,Lanzhou University,Lanzhou 730000,china 4department of Applied physics,xi’an Jiaotong University,xi’an 710049,china Institute of Modern physics Chinese Academy of Sciences Lanzhou China department of physics Xianyang Normal University Xianyang China department of Modern physics Lanzhou University Lanzhou China department of Applied physics Xi’an Jiaotong University China

Using the slow highly charged ions 129 Xe q+ (q=25,26,27;initial kinetic T0≤4.65 keV/a.u.)to impact Au surface,the Au atomic Mαcharacteristic X-ray spectrum is *** result shows that as long as the charge state of projectile is high enough,the heavy atomic characteristic X-ray can be effectively excited even though the incident beam is very weak(nA magnitude),and the X-ray yield per ion is in the order of 10-8and increases with the kinetic energy and potential energy of *** measuring the Au Mα-X-ray spectra,Au atomic N-level lifetime is estimated at about 1.33×10-18s based on Heisenberg uncertainty relation.

关键词： slow highly charged ions characteristic X-ray level lifetime

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