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Single-cell omics: experimental workflow, data analyses and applications

Science China Life Sciences 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent Computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome,proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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SensFL:Privacy-Preserving Vertical Federated Learning with Sensitive Regularization

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Computer Modeling in Engineering & Sciences 2025年第1期142卷 385-404页

作者： Chongzhen Zhang Zhichen Liu Xiangrui Xu Fuqiang Hu Jiao Dai Baigen Cai Wei wang School of Automation and Intelligence Beijing Jiaotong UniversityBeijing100044China Shuohuang Railway Development Co. Ltd.National Energy GroupCangzhou062350China Beijing Key Laboratory of Security and Privacy in Intelligent Transportation School of Computer Science and TechnologyBeijing Jiaotong UniversityBeijing100044China

In the realm of Intelligent Railway Transportation Systems,effective multi-party collaboration is crucial due to concerns over privacy and data *** Federated Learning(VFL)has emerged as a promising approach to facilitate such collaboration,allowing diverse entities to collectively enhance machine learning models without the need to share sensitive training ***,existing works have highlighted VFL’s susceptibility to privacy inference attacks,where an honest but curious server could potentially reconstruct a client’s raw data from embeddings uploaded by the *** vulnerability poses a significant threat to VFL-based intelligent railway transportation *** this paper,we introduce SensFL,a novel privacy-enhancing method to against privacy inference attacks in ***,SensFL integrates regularization of the sensitivity of embeddings to the original data into the model training process,effectively limiting the information contained in shared *** reducing the sensitivity of embeddings to the original data,SensFL can effectively resist reverse privacy attacks and prevent the reconstruction of the original data from the *** experiments were conducted on four distinct datasets and three different models to demonstrate the efficacy of *** results show that SensFL can effectively mitigate privacy inference attacks while maintaining the accuracy of the primary learning *** results underscore SensFL’s potential to advance privacy protection technologies within VFL-based intelligent railway systems,addressing critical security concerns in collaborative learning environments.

关键词： Vertical federated learning privacy defenses

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Prediction and optimization of flue pressure in sintering process based on SHAP

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International Journal of Minerals,Metallurgy and Materials 2025年第2期32卷 346-359页

作者： Mingyu wang Jue Tang Mansheng Chu Quan Shi Zhen Zhang School of Metallurgy Northeastern UniversityShenyang 110819China Liaoning Low-Carbon Steelmaking Technology Engineering Research Center Northeastern UniversityShenyang 110819China Engineering Research Center of Frontier Technologies for Low-Carbon Steelmaking(Ministry of Education) Shenyang 110819China

Sinter is the core raw material for blast *** pressure,which is an important state parameter,affects sinter *** this paper,flue pressure prediction and optimization were studied based on the shapley additive explanation(SHAP)to predict the flue pressure and take targeted adjustment ***,the sintering process data were collected and processed.A flue pressure prediction model was then constructed after comparing different feature selection methods and model algorithms using SHAP+extremely random-ized trees(ET).The prediction accuracy of the model within the error range of±0.25 kPa was 92.63%.SHAP analysis was employed to improve the interpretability of the prediction *** effects of various sintering operation parameters on flue pressure,the relation-ship between the numerical range of key operation parameters and flue pressure,the effect of operation parameter combinations on flue pressure,and the prediction process of the flue pressure prediction model on a single sample were analyzed.A flue pressure optimization module was also constructed and analyzed when the prediction satisfied the judgment *** operating parameter combination was then *** flue pressure was increased by 5.87%during the verification process,achieving a good optimization effect.

关键词： sintering process flue pressure shapley additive explanation prediction optimization

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An investigation on the wind profiles and gravity wave dynamics in MLT region based on the meteor radars from the Meridian Project

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Earth and Planetary Physics 2025年第1期9卷 29-38页

作者： Tai Liu Zhe wang MengXi Shi Willie Soon ShiCan Qiu Department of Geophysics College of the Geology Engineering and GeomaticsChang’an UniversityXi’an 710054China Center for Environmental Research and Earth Sciences(CERES) SalemMA 01970USA Institute of Earth Physics and Space Science(ELKH EPSS) 9400SopronHungary

The meteor radar can detect the zenith angle,azimuth,radial velocity,and altitude of meteor trails so that one can invert the wind profiles in the mesosphere and low thermosphere(MLT)region,based on the Interferometric and Doppler *** this paper,the horizontal wind field,gravity wave(GW)disturbance variance,and GW fluxes are analyzed through the meteor radar observation from 2012−2022,at Mohe(53.5°N,122.4°E)and Zuoling(30.5°N,114.6°E)stations of the(Chinese)Meridian *** Lomb−Scargle periodogram method has been utilized to analyze the periodic variations for time series with observational data *** results show that the zonal winds at both stations are eastward dominated,while the meridional winds are southward *** variance of GW disturbances in the zonal and meridional directions increases gradually with height,and there is a strong pattern of annual *** zonal momentum flux of GW changes little with height,showing weak annual *** meridional GW flux varies gradually from northward to southward with height,and the annual periodicity is *** both stations,the maximum values of zonal and meridional wind occur close to the peak heights of GW flux,with opposite *** observational evidence is consistent with the filtering *** horizontal wind velocity,GW flux,and disturbance variance of the GW at Mohe are overall smaller than those at Zuoling,indicating weaker activities in the MLT at *** power spectral density(PSD)calculated by the Lomb−Scargle periodogram shows that there are 12-month period and 6-month period in horizontal wind field,GW disturbance variance and GW flux at both stations,and especially there is also a 4-month cycle in the disturbance *** PSD of the 12-month and 6-month cycles exhibits maximum values below 88 km and above 94 km.

关键词： meteor radar wind field gravity wave Lomb−Scargle method

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Statistical analysis on the validity of the cold plasma approximation for chorus waves based on Van Allen Probe observations and their effects on radiation belt electrons

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Earth and Planetary Physics 2025年第1期9卷 159-170页

作者： AoJun Ren Jiang Yu Jing wang ZuZheng Chen XiaoMan Liu Planetary Environmental and Astrobiological Research Laboratory(PEARL) School of Atmospheric SciencesSun Yat-sen UniversityZhuhai Guangdong 519000China

Theoretical analysis has demonstrated that the dispersion relation of chorus waves plays an essential role in the resonant interaction and energy transformation between the waves and magnetospheric *** quantitative analyses often simplified the chorus dispersion relation by using the cold plasma ***,the applicability of the cold plasma assumption is doubtful,especially during geomagnetic *** here present a systematic statistical analysis on the validity of the cold plasma dispersion relation of chorus waves based on observations from the Van Allen Probes over the period from 2012 to *** statistical results show that the observed magnetic field intensities deviate substantially from those calculated from the cold plasma dispersion relation and that they become more pronounced with an increase in geomagnetic activity or a decrease in background plasma *** region with large deviations is mainly concentrated in the nightside and expands in both the radial and azimuthal directions as the geomagnetic activity increases or the background plasma density *** addition,the bounce-averaged electron scattering rates are computed by using the observed and cold plasma dispersion relation of chorus *** with usage of the cold plasma dispersion relation,usage of the observed dispersion relation considerably lowers the minimum resonant energy of electrons and lowers the scattering rates of electrons above tens of kiloelectronvolts but enhances those ***,these differences are more pronounced with the enhancement of geomagnetic activity or the decrease in background plasma density.

关键词： chorus waves cold plasma approximation dispersion relations scattering rates

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Preparation and applications of calcium ferrite as a functional material:A review

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International Journal of Minerals,Metallurgy and Materials 2025年第2期32卷 292-310页

作者： Xiuli Han Bowen Duan Lei Liu Shilong Fang Weiwei wang College of Mining Engineering North China University of Science and TechnologyTangshan 063210China Collaborative Innovation Center of Green Development and Ecological Restoration of Mineral Resources of Hebei Province Tangshan 063210China Key Laboratory of Mining Development and Security Technology of Hebei Province Tangshan 063210China

Calcium ferrite(CF)is recognized as a potential green and efficient functional material because of its advantages of magnetism,electrochemistry,catalysis,and biocompatibility in the fields of materials chemistry,environmental engineering,and ***-fore,the obtained research results need to be systematically summarized,and new perspectives on CF and its composite materials need to be *** on the presented studies of CF and its composite materials,the types and structures of the crystal are *** addition,the current application technologies and theoretical mechanisms with various properties in different fields are ***,the various preparation methods of CF and its composite materials are elaborated in *** importantly,the advantages and disadvantages of the synthesis methods of CF and its composite materials are discussed,and the existing problems and emerging challenges in practical production are ***,the key future research directions of CF and its composite materials have been prospected from the potential application technologies to provide references for its synthesis and efficient utilization.

关键词： calcium ferrite mineral functional materials preparation application perspectives

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An embedded electron current layer observed at the edge of the plasma sheet in the Earth’s magnetotail

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Earth and Planetary Physics 2025年第1期9卷 148-158页

作者： ChenChen Zhan RongSheng wang QuanMing Lu San Lu XinMin Li Deep Space Exploration Laboratory/School of Earth and Space Sciences University of Science and Technology of ChinaHefei 230026China Chinese Academy of Sciences(CAS)Center for Excellence in Comparative Planetology/CAS Key Laboratory of Geospace Environment/Anhui Mengcheng National Geophysical Observatory University of Science and Technology of ChinaHefei 230026China Collaborative Innovation Center of Astronautical Science and Technology Harbin 150001China

The formation of an embedded electron current sheet within the magnetotail plasma sheet has been poorly *** this article,we present an electron current layer detected at the edge of the magnetotail plasma *** ions were demagnetized inside the electron current layer,but the electrons were still frozen in with the magnetic field ***,this decoupling of ions and electrons gave rise to a strong Hall electric field,which could be the reason for the formation of the embedded thin current *** magnetized electrons,the absence of the nongyrotropic electron distribution,and negligible energy dissipation in the layer indicate that magnetic reconnection had not been triggered within the embedded thin current *** highly asymmetric plasma on the two sides of the current layer and low magnetic shear across it could suppress magnetic *** observations indicate that the embedded electric current layer,probably generated by the Hall electric field,even down to electron scale,is not a sufficient condition for magnetic reconnection.

关键词： magnetotail plasma sheet magnetic reconnection

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Mimicking aneurysm in a patient with chronic occlusion of the left middle cerebral artery

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World Journal of Clinical Cases 2025年第3期13卷 20-23页

作者： Xue-Jian wang Department of Neurosurgery Affiliated Hospital 2 of Nantong UniversityNantong 226000Jiangsu ProvinceChina

The chronic occlusion of intracranial arteries generally has no or mild clinical symptoms,and the clinical symptoms of acute cerebral artery occlusion are mostly manifested as severe cerebral infarction symptoms,which often make early diagnosis difficult,thus losing the best treatment *** cerebral infarction occurs,the consequences are difficult to *** is also an important reason for the high misdiagnosis rate and mortality of this *** this paper,the characteristics of the disease were analyzed to provide clinical reference.

关键词： Chronic occlusion Misdiagnose Arterial occlusion Middle cerebral artery occlusion Aneurysm

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Unraveling brain aging through the lens of oral microbiota

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Neural Regeneration Research 2025年第7期20卷 1930-1943页

作者： Qinchao Hu Si wang Weiqi Zhang Jing Qu Guang-Hui Liu State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijingChina Hospital of Stomatology Guanghua School of StomatologyGuangdong Provincial Key Laboratory of StomatologySun Yat-sen UniversityGuangzhouGuangdong ProvinceChina Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders Xuanwu HospitalCapital Medical UniversityBeijingChina Aging Translational Medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijingChina CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina University of Chinese Academy of Sciences BeijingChina Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijingChina Aging Biomarker Consortium BeijingChina State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijingChina Beijing Institute for Stem Cell and Regenerative Medicine BeijingChina

The oral cavity is a complex physiological community encompassing a wide range of *** of oral microbiota can lead to various oral infectious diseases,such as periodontitis and tooth decay,and even affect systemic health,including brain aging and neurodegenerative *** studies have highlighted how oral microbes might be involved in brain aging and neurodegeneration,indicating potential avenues for intervention *** this review,we summarize clinical evidence demonstrating a link between oral microbes/oral infectious diseases and brain aging/neurodegenerative diseases,and dissect potential mechanisms by which oral microbes contribute to brain aging and *** also highlight advances in therapeutic development grounded in the realm of oral microbes,with the goal of advancing brain health and promoting healthy aging.

关键词： Alzheimer's disease brain aging multiple sclerosis neurodegeneration neurodegenerative diseases oral microbiota Parkinson's disease periodontitis bacteria Porphyromonas gingivalis

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CNKSR2 interactome analysis indicates its association with the centrosome/microtubule system

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Neural Regeneration Research 2025年第8期20卷 2420-2432页

作者： Lin Yin Yalan Xu Jie Mu Yu Leng Lei Ma Yu Zheng Ruizhi Li Yin wang Peifeng Li Hai Zhu Dong wang Jing Li Institute for Translational Medicine The Affiliated Hospital of Qingdao UniversityMedical CollegeQingdao UniversityQingdaoShandong ProvinceChina School of Basic Medicine Qingdao UniversityQingdaoShandong ProvinceChina College of Life Sciences and School of PharmacyMedical CollegeQingdao UniversityQingdaoShandong ProvinceChina Department of Urology Qingdao Municipal Hospital Affiliated to Qingdao UniversityQingdaoShandong ProvinceChina

The protein connector enhancer of kinase suppressor of Ras 2(CNKSR2),present in both the postsynaptic density and cytoplasm of neurons,is a scaffolding protein with several protein-binding *** of the CNKSR2 gene have been implicated in neurodevelopmental disorders,particularly intellectual disability,although the precise mechanism involved has not yet been fully *** has demonstrated that CNKSR2 plays a role in facilitating the localization of postsynaptic density protein complexes to the membrane,thereby influencing synaptic signaling and the morphogenesis of dendritic ***,the function of CNKSR2 in the cytoplasm remains to be *** this study,we used immunoprecipitation and high-resolution liquid chromatography-mass spectrometry to identify the interactors of *** a combination of bioinformatic analysis and cytological experiments,we found that the CNKSR2 interactors were significantly enriched in the proteome of the *** also showed that CNKSR2 interacted with the microtubule protein DYNC1H1 and with the centrosome marker *** colocalization analysis confirmed the centrosomal localization of *** we downregulated CNKSR2 expression in mouse neuroblastoma cells(Neuro 2A),we observed significant changes in the expression of numerous centrosomal *** manipulation also affected centrosome-related functions,including cell size and shape,cell proliferation,and ***,we found that CNKSR2 interactors were highly enriched in de novo variants associated with intellectual disability and autism spectrum *** findings establish a connection between CNKSR2 and the centrosome,and offer new insights into the underlying mechanisms of neurodevelopmental disorders.

关键词： autism spectrum disorder centrosome CNKSR2 intellectual disability interactome mass spectrometry microtubule neurodevelopmental disease protein complexes protein-protein interactions

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