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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 xi.ohui 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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Silencing of early auxin responsive genes MdGH3-2/12 reduces the resistance to Fusarium solani in apple

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Journal of Integrative Agriculture 2024年第9期23卷 3012-3024页

作者： Qianwei Liu shuo Xu Lu Jin xi Yu Chao Yang xi.omin Liu Zhijun Zhang Yusong Liu Chao Li Fengwang Ma State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple College of HorticultureNorthwest A&F UniversityYangling 712100China

Apple replant disease(ARD)has led to severe yield and quality reduction in the apple *** solani(***)has been identified as one of the main microbial pathogens responsible for ***(indole-3-acetic acid,IAA),an endogenous hormone in plants,is involved in almost all plant growth and development processes and plays a role in plant immunity against *** Hagen3(GH3)is one of the early/primary auxin response *** aim of this study was to evaluate the function of MdGH3-2 and MdGH3-12 in the defense response of *** by treating MdGH3-2/12 RNAi plants with *** results show that under *** infection,RNAi of MdGH3-2/12 inhibited plant biomass accumulation and exacerbated root *** inoculation with ***,MdGH3-2/12 RNAi inhibited the biosynthesis of acid-amido *** led to the inhibition of free IAA combining with amino acids,resulting in excessive free IAA *** excessive free IAA altered plant tissue structure,accelerated fungal hyphal invasion,reduced the activity of antioxidant enzymes(SoD,PoD and CAT),increased the reactive oxygen species(RoS)level,and reduced total chlorophyll content and photosynthetic ability,while regulating the expression of PR-related genes including PR1,PR4,PR5 and *** also changed the contents of plant hormones and amino acids,and ultimately reduced the resistance to *** conclusion,these results demonstrate that MdGH3-2 and MdGH3-12 play an important role in apple tolerance to *** and ARD.

关键词： Fusarium solani early auxin responsive gene apple replant disease plant hormone antioxidant

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Comparison-embedded evidence-CNN model for fuzzy assessment of wear severity using multi-dimensional surface images

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Friction 2024年第6期12卷 1098-1118页

作者： Tao SHAo shuo WANG Qinghua WANG Tonghai WU Zhifu HUANG Key Laboratory of Education Ministry for Modern Design and Rotor-Bearing System Xi’an Jiaotong UniversityXi’an 710049China State Key Laboratory for Mechanical Behavior of Materials Xi’an Jiaotong UniversityXi’an 710049China

Wear topography is a significant indicator of tribological behavior for the inspection of machine health *** intelligent in-suit wear assessment method for random topography is here ***-dimension(3D)topography is employed to address the uncertainties in wear ***,3D topography reconstruction from a worn surface is accomplished with photometric stereo vision(PSV).Then,the wear features are identified by a contrastive learning-based extraction network(WSFE-Net)including the relative and temporal prior knowledge of wear ***,the typical wear degrees including mild,moderate,and severe are evaluated by a wear severity assessment network(WSA-Net)for the probability and its associated uncertainty based on subjective *** integrating the evidence information from 2D and 3D-damage surfaces with Dempster–Shafer(D–S)evidence,the uncertainty of severity assessment results is further *** proposed model could constrain the uncertainty below 0.066 in the wear degree evaluation of a continuous wear experiment,which reflects the high credibility of the evaluation result.

关键词： wear severity assessment contrastive learning subjective logic Dempster-Shafer(D-S)evidence theory

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optimized Mask-RCNN model for particle chain segmentation based on improved online ferrograph sensor

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Friction 2024年第6期12卷 1194-1213页

作者： shuo WANG Miao WAN Tonghai WU Zichen BAI Kunpeng WANG Key Laboratory of Education Ministry for Modern Design and Rotor-Bearing System Xi’an Jiaotong UniversityXi’an 710049China

Ferrograph-based wear debris analysis(WDA)provides significant information for wear fault analysis of mechanical *** decades of offline application,this conventional technology is being driven by the online ferrograph sensor for real-time wear state ***,online ferrography has been greatly limited by the low imaging quality and segmentation accuracy of particle chains when analyzing degraded lubricant oils in practical *** address this issue,an integrated optimization method is developed that focuses on two aspects:the structural re-design of the online ferrograph sensor and the intelligent segmentation of particle *** enhancing the imaging quality of wear particles,the magnetic pole of the online ferrograph sensor is optimized to enable the imaging system directly observe wear particles without penetrating ***,a light source simulation model is established based on the light intensity distribution theory,and the LED installation parameters are determined for particle illumination uniformity in the online ferrograph *** this basis,a Mask-RCNN-based segmentation model of particle chains is constructed by specifically establishing the region of interest(RoI)generation layer and the RoI align layer for the irregular particle *** these measures,a new online ferrograph sensor is designed to enhance the image acquisition and information extraction of wear *** verification,the developed sensor is tested to collect particle images from different degraded oils,and the images are further handled with the Mask-RCNN-based model for particle feature *** results reveal that the optimized online ferrography can capture clear particle images even in highly-degraded lubricant oils,and the illumination uniformity reaches 90%in its imaging *** importantly,the statistical accuracy of wear particles has been improved from 67.2%to 94.1%.

关键词： wear particle analysis online ferrography particle image acquisition particle chain segmentation

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Achieving high carrier mobility and low lattice thermal conductivity in GeTe-based alloys by cationic/anionic co-doping

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Rare Metals 2024年第6期43卷 2784-2795页

作者： xi.o-Qiang Wang xi.o-Quan Hu Jun-Yan Lin Chu-Bin Li xi.o-Tong Yu Qi-Yong Chen Li-Li xi Qi-shuo Yang Han Li Ji-Ye Zhang Shuan-Kui Li Kai Guo School of Physics and Materials Science Guangzhou UniversityGuangzhou 510006China Research Center for Advanced Information Materials(CAIM) Huangpu Research&Graduate School of Guangzhou UniversitySino-Singapore Guangzhou Knowledge CityGuangzhou510555China School of Materials Science and Engineering Shanghai UniversityShanghai 200444China Materials Genome Institute Shanghai UniversityShanghai 200444China School of Mechanical and Mining Engineering University of QueenslandBrisbaneQLD 4072Australia Key Laboratory of Si-Based Information Materials&Devices and Integrated Circuits Design Department of Education of Guangdong ProvinceGuangzhou 510006China

TheⅣ-Ⅵcompound GeTe is considered as a promising alternative to the toxic PbTe for high-efficiency mid-temperature thermoelectric ***,pristine GeTe suffers from a high concentration of Ge vacancies,resulting in an excessively high hole concentration(>1×10^(21)cm^(-3)),which greatly limits its thermoelectric *** address this issue,CuBiTe_(2)alloying is introduced to increase the formation energy of Ge vacancies in GeTe,thereby inhibiting the high carrier *** carrier scattering caused by the electronegativity difference between different elements is suppressed due to the similar electronegativity of Cu and Ge atoms.A relatively high hole mobility is obtained,which ultimately leads to a high power ***,by introducing Se as an alloying element at the anionic site in GeTe,dense point defects with mass/strainfield fluctuations are *** contributes to the strengthening of phonon scattering,thereby reducing the lattice thermal conductivity from 1.44 W·m^(-1)·K^(-1)for pristine GeTe to 0.28 W·m^(-1)·K^(-1)for Ge_(0.95)Cu_(0.05)Bi_(0.05)Te_(0.9)Se_(0.15)compound at 623 K.

关键词： GeTe Carrier mobility CuBiTe_(2)alloying Lattice thermal conductivity Thermoelectric properties

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Role of hsa_circ_0007482 in pterygium development: insights into proliferation, apoptosis, and clinical correlations

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International Journal of ophthalmology(English edition) 2024年第8期17卷 1387-1395页

作者： Li-Yun Zhang xin Liu shuo Zheng Wen-Qun xi Xue-Ping Wu Dan-Yao Nie Hui-Ling Hu Jian-Tao Wang xin-Hua Liu Jing Zhang Shenzhen Eye Hospital Jinan UniversityShenzhen Eye InstituteShenzhen 518000Guangdong ProvinceChina

AIM:To investigate the impact of hsa_circ_0007482 on the proliferation and apoptosis of human pterygium fibroblasts(HPFs)and its correlation with the severity grades of ***:Pterygium and normal conjunctival tissues were collected from the superior area of the same patient’s eye(n=33).The correlation between pterygium severity and hsa_circ_0007482 expression using quantitative reversetranscription polymerase chain reaction(RT-qPCR)were *** distinct siRNA sequences targeting hsa_circ_0007482,along with a negative control sequence,were transfected into *** proliferation was assessed using the cell counting *** levels of Ki67,proliferating cell nuclear antigen(PCNA),Cyclin D1,Bax,B-cell lymphoma-2(Bcl-2),and Caspase-3 were measured via *** staining was employed to detect Ki67 and vimentin *** was evaluated using flow ***:Hsa_circ_0007482 expression was significantly higher in pterygium tissues compared to normal conjunctival tissues(Positive correlations were observed between hsa_circ_0007482 expression and pterygium severity,thickness,and vascular *** of hsa_circ_0007482 inhibited cell proliferation,reducing the mRNA expression of Ki67,PCNA,and Cyclin D1 in ***_circ_0007482 knockdown induced apoptosis,increasing mRNA expression levels of Bax and Caspase-3,while decreasing Bcl-2 expression in ***,hsa_circ_0007482 knockdown attenuated vimentin expression in ***:The downregulation of hsa_circ_0007482 effectively hampers cell proliferation and triggers apoptosis in *** are discernible positive correlations detected between the expression of hsa_circ_0007482 and the severity of pterygium.

关键词： hsa_circ_0007482 circular RNA pterygium cell proliferation apoptosis

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Freezing imaginarity of quantum states based onℓ_(1)-norm

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Chinese Physics B 2024年第10期33卷 166-175页

作者： shuo Han Bingke Zheng Zhihua Guo School of Mathematics and Statistics Shaanxi Normal UniversityXi’an 710119China

We discuss freezing of quantum imaginarity based onℓ_(1)-*** properties about a quantity of imaginarity based onℓ_(1)-norm are *** a qubit(2-dimensional)system,we characterize the structure of real quantum operations that allow for freezing the quantity of imaginarity of any ***,we characterize the structure of local real operations which can freeze the quantity of imaginarity of a class of N-qubit quantum states.

关键词： imaginarity freezing ℓ_(1)-norm real operation

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Association of TRMT2B gene variants with juvenile amyotrophic lateral sclerosis

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Frontiers of Medicine 2024年第1期18卷 68-80页

作者： Yanling Liu xi He Yanchun Yuan Bin Li Zhen Liu Wanzhen Li Kaixuan Li shuo Tan Quan Zhu Zhengyan Tang Feng Han Ziqiang Wu Lu Shen Hong Jiang Beisha Tang Jian Qiu Zhengmao Hu Junling Wang Department of Neurology Xiangya HospitalCentral South UniversityJiangxiNational Regional Center for Neurological DiseasesNanchang330038China Provincial Laboratory for Diagnosis and Treatment of Genitourinary System Disease Department of UrologyXiangya HospitalCentral South UniversityChangsha410078China Department of orthopedics The First Affiliated HospitalZhejiang University School of MedicineHangzhou310002China Department of Neurology Xiangya HospitalCentral South UniversityChangsha410078China National Clinical Research Center for Geriatric Diseases Xiangya HospitalCentral South UniversityChangsha410008China Key Laboratory of Hunan Province in Neurodegenerative Disorders Central South UniversityChangsha410008China Center for Medical Genetics School of Life SciencesCentral South UniversityChangsha410008China Engineering Research Center of Hunan Province in Cognitive Impairment Disorders Central South UniversityChangsha410078China Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases Changsha410078China Hunan Key Laboratory of Molecular Precision Medicine Xiangya HospitalCentral South UniversityChangsha410078China

Amyotrophic lateral sclerosis(ALS)is a fatal neurodegenerative disease characterized by progressive degeneration of motor neurons,and it demonstrates high clinical heterogeneity and complex genetic architecture.A variation within TRMT2B(c.1356G>T;p.K452N)was identified to be associated with ALS in a family comprising two patients with juvenile ALS(JALS).Two missense variations and one splicing variation were identified in 10 patients with ALS in a cohort with 910 patients with ALS,and three more variants were identified in a public ALS database including 3317 patients with ALS.A decreased number of mitochondria,swollen mitochondria,lower expression of ND1,decreased mitochondrial complex I activities,lower mitochondrial aerobic respiration,and a high level of RoS were observed functionally in patient-originated lymphoblastoid cell lines and TRMT2B interfering HEK293 ***,TRMT2B variations overexpression cells also displayed decreased *** conclusion,a novel JALS-associated gene called TRMT2B was identified,thus broadening the clinical and genetic spectrum of ALS.

关键词： TRMT2B amyotrophic lateral sclerosis mitochondrial complex I tRNA methylation reactive oxygen species

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Towards high-strength cold spray additive manufactured metals:Methods,mechanisms,and properties

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Journal of Materials Science & Technology 2024年第3期170卷 47-64页

作者： shuo Yin Ningsong Fan Chunjie Huang Yingchun xie Chao Zhang Rocco Lupoi Wenya Li Department of Mechanical Manufacturing&Biomedical EngineeringParsons BuildingTrinity College DublinThe University of DublinDublin 2Ireland Institute of Materials Technology Helmut-Schmidt-University/University of the Federal Armed Forces HamburgHamburg 22043Germany The Key Lab of Guangdong for Modern Surface Engineering Technology National Engineering Laboratory for Modern Materials Surface Engineering TechnologyInstitute of New MaterialsGuangdong Academy of SciencesGuangzhou 510651China College of Mechanical Engineering Yangzhou UniversityYangzhou 225127China State Key Laboratory of Solidification Processing Shaanxi Key Laboratory of Friction Welding TechnologiesNorthwestern Polytechnical UniversityXi’an 720072China

Cold spray,as a solid-state additive manufacturing process,has been attracting increasing attention from both scientific and industrial ***,cold-sprayed deposits generally have unfavorable mechanical properties in their as-fabricated state compared to conventionally manufactured and fusion-based additive-manufactured counterparts due to the inherent microstructural defects in the deposits(e.g.,porosity and incomplete interparticle bonding).This downside reduces its competitiveness and limits its wide applications as an additive manufacturing *** the past years,many strengthening technologies have been developed or introduced to adjust the microstructure and improve the mechanical properties of cold-sprayed *** term“strengthening”in this work specifically refers to improving the mechanical strength,particularly the tensile strength of the cold-sprayed bulk *** to the stage that the strengthening technologies are used in the cold spray process,they can be classified into three categories:pre-process(e.g.,powder heat treatment),in-process(e.g.,powder heating,in-situ micro-forging,laser-assisted cold spray),and post-process(e.g.,post heat treatment,hot isostatic pressing,hot rolling,friction stir processing).Therefore,a comprehensive review of these strengthening technolo-gies is conducted to illuminate the possible correlations between the strengthening mechanisms and the resultant deposit microstructures and mechanical *** review paper aims to help researchers and engineers well understand the different strengthening methods and provide guidance for the cold spray community to develop new strengthening strategies for future high-quality mass production.

关键词： Cold spray Additive manufacturing Strengthening Microstructure Ductility Tensile strength

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Strengthening mechanism and forming control of linear friction welded GH4169 alloy joints

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Chinese Journal of Aeronautics 2024年第4期37卷 609-626页

作者： Yu SU xiawei YANG Tingxi MENG xinyuan HE Dong WU Wenya LI shuo YIN State Key Laboratory of Solidification Processing School of Materials Science and EngineeringNorthwestern Polytechnical UniversityXi’an 710072China Shaanxi Key Laboratory of Friction Welding Technologies School of Materials Science and EngineeringNorthwestern Polytechnical UniversityXi’an 710072China Department of Mechanical Manufacturing and Biomedical EngineeringParsons BuildingTrinity College DublinThe University of DublinDublin 2Ireland

Numerical simulation and experimental research on Linear Friction Welding(LFW) for GH4169 superalloy were carried out. Based on the joint microstructure and mechanical properties,a suitable welding process was determined, which provided an important theoretical basis for the manufacture and repair of aeroengine components such as the superalloy blisk. The results show that the joint strain rate gradually increases with the increase of welding frequency, and the deformation resistance of the thermoplastic metal increases in the welding process, resulting in the interface thermoplastic metal not being extruded in time to form a flash, so the joint shortening amount gradually decreases. The thermoplastic metal in the center of the welding surface is kept at high welding temperature for a long time, resulting in the decrease of the joint strength. The microhardness of the joint shows a “W” distribution perpendicular to the weld, and most of the joints break in the Thermo-Mechanically Affected Zone(TMAZ) with high tensile strength and low *** the welding area is increased without changing the aspect ratio of the welding surface, the interface peak temperature increases gradually, and the joint shortening amount decreases with the increase of the welding interface size.

关键词： Linear Friction Welding(LFW) Microstructure Mechanical properties Numerical simulation Joint shortening amount

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