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

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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

Deciphering Water Oxidation Catalysts: The Dominant Role of Surface Chemistry over Reconstruction Degree in Activity Promotion

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NANO-MICRO LETTERS 2025年第1期17卷 1-15页

作者： An, Li Li, jianyi sun, Yuanmiao Zhu, jiamin Seow, justin Zhu Yeow Zhang, Hong Zhang, Nan Xi, Pinxian Xu, Zhichuan j. Yan, Chun-Hua Lanzhou Univ Frontiers Sci Ctr Rare Isotopes Key Lab Nonferrous Met Chem & Resources Utilizat G State Key Lab Appl Organ ChemColl Chem & Chem Eng Lanzhou 730000 Peoples R China Nanyang Technol Univ Sch Mat Sci & Engn Singapore 639798 Singapore Chinese Acad Sci Fac Mat Sci & Energy Engn Shenzhen Inst Adv Technol Inst Technol Carbon Neutral Shenzhen 518055 Peoples R China Yunnan Univ Natl Ctr Int Res Photoelect & Energy Mat Electron Microscopy Ctr Sch Mat & EnergyKey Lab Electromagnet Mat & Devic Kunming 650091 Peoples R China Baotou Res Inst Rare Earths State Key Lab Baiyunobo Rare Earth Resource Res & Baotou 014030 Peoples R China Peking Univ Beijing Natl Lab Mol Sci State Key Lab Rare Earth Mat Chem & Applicat PKU HKU Joint Lab Rare Earth Mat & Bioinorgan Chem Beijing 100871 Peoples R China

Demonstrate that the key factor to determine the activity of reconstructed surfaces is the surface chemistry, instead of reconstruction degree using the popular perovskite LaNi1-xFexO3 oxides as model *** content can influence both the surface reconstruction degree, the activation degree, and the activity of reconstructed *** oxygen evolution reaction activity of reconstructed catalysts is primarily governed by the chemistry of the reconstructed surface species. Water splitting hinges crucially on the availability of electrocatalysts for the oxygen evolution reaction. The surface reconstruction has been widely observed in perovskite catalysts, and the reconstruction degree has been often correlated with the activity enhancement. Here, a systematic study on the roles of Fe substitution in activation of perovskite LaNiO3 is reported. The substituting Fe content influences both current change tendency and surface reconstruction degree. LaNi0.9Fe0.1O3 is found exhibiting a volcano-peak intrinsic activity in both pristine and reconstructed among all substituted perovskites in the LaNi1-xFexO3 (x = 0.00, 0.10, 0.25, 0.50, 0.75, 1.00) series. The reconstructed LaNi0.9Fe0.1O3 shows a higher intrinsic activity than most reported NiFe-based catalysts. Besides, density functional theory calculations reveal that Fe substitution can lower the O 2p level, which thus stabilize lattice oxygen in LaNi0.9Fe0.1O3 and ensure its long-term stability. Furthermore, it is vital interesting that activity of the reconstructed catalysts relied more on the surface chemistry rather than the reconstruction degree. The effect of Fe on the degree of surface reconstruction of the perovskite is decoupled from that on its activity enhancement after surface reconstruction. This finding showcases the importance to customize the surface chemistry of reconstructed catalysts for water oxidation.

关键词： Oxygen evolution reaction Perovskite oxides Doping Activation and reconstruction

Impact of ocean data assimilation on the seasonal forecast of the 2014/15 marine heatwave in the Northeast Pacific Ocean

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Atmospheric and Oceanic Science Letters 2025年第1期18卷 24-31页

作者： Tiantian Tang jiaying He Huihang sun jingjia Luo Institute for Climate and Application Research(ICAR)/Key Laboratory of Meteorological Disaster Nanjing University of Information Science and TechnologyNanjingChina

A remarkable marine heatwave,known as the“Blob”,occurred in the Northeast Pacific Ocean from late 2013 to early 2016,which displayed strong warm anomalies extending from the surface to a depth of 300 *** study employed two assimilation schemes based on the global Climate Forecast System of Nanjing University of Information Science(NUIST-CFS 1.0)to investigate the impact of ocean data assimilation on the seasonal prediction of this extreme marine *** sea surface temperature(SST)nudging scheme assimilates SST only,while the deterministic ensemble Kalman filter(EnKF)scheme assimilates observations from the surface to the deep *** latter notably improves the forecasting skill for subsurface temperature anomalies,especially at the depth of 100-300 m(the lower layer),outperforming the SST nudging *** excels in predicting both horizontal and vertical heat transport in the lower layer,contributing to improved forecasts of the lower-layer warming during the *** improvements stem from the assimilation of subsurface observational data,which are important in predicting the upper-ocean *** results suggest that assimilating ocean data with the EnKF scheme significantly enhances the accuracy in predicting subsurface temperature anomalies during the Blob and offers better understanding of its underlying mechanisms.

关键词： Seasonal forecast Ocean data assimilation Marine heatwave Subsurface temperature

Boosting bidirectional sulfur conversion enabled by introducing boron-doped atoms and phosphorus vacancies in Ni2P for lithium-sulfur batteries

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journal of Energy Chemistry 2025年第1期100卷 760-769页

作者： Lin Peng Yu Bai Hang Li Meixiu Qu Zhenhua Wang Kening sun Advanced Research Institute of Multidisciplinary Science Beijing Institute of Technology Beijing Key Laboratory of Chemical Power Source and Green Catalysis School of Chemistry and Chemical Engineering Beijing Institute of Technology

Lithium-sulfur （Li-S） batteries have gained great attention due to the high theoretical energy density and low cost,yet their further commercialization has been obstructed by the notorious shuttle effect and sluggish redox ***,we supply a strategy to optimize the electron structure of Ni2P by concurrently introducing B-doped atoms and P vacancies in Ni2P （Vp-B-Ni2P）,thereby enhancing the bidirectional sulfur *** study indicates that the simultaneous introduction of B-doped atoms and P vacancies in Ni2P causes the redistribution of electron around Ni atoms,bringing about the upward shift of d-band center of Ni atoms and effective d-p orbital hybridization between Ni atoms and sulfur species,thus strengthening the chemical anchoring for lithium polysulfides （LiPSs） as well as expediting the bidirectional conversion kinetics of sulfur ***,theoretical calculations reveal that the incorporation of B-doped atoms and P vacancies in Ni2P selectively promotes Li2S dissolution and nucleation ***,the Li-S batteries with Vp-B-Ni2P-separators present outstanding rate ability of 777 m A h g-1at 5 C and high areal capacity of 8.03 mA h cm-2under E/S of 5μL mg-1and sulfur loading of 7.20 mg *** work elucidates that introducing heteroatom and vacancy in metal phosphide collaboratively regulates the electron structure to accelerate bidirectional sulfur conversion.

关键词： Lithium sulfur batteries

Fluorinated poly(p-triphenylene isatin) anion exchange membranes based on hydrophilic hydroxyl side chain modulation for fuel cells

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journal of Energy Chemistry 2025年第1期100卷 702-709页

作者： Yiman Gu Yanchao Zhang Zhanyu Li Yijia Lei Baozeng sun Xiaoyu Yu Zhe Wang College of Chemistry and Life Science Changchun University of Technology College of Chemical Engineering Changchun University of Technology School of Materials Science and Engineering Changchun University of Technology Key Laboratory of Advanced Functional Polymer Membrane Materials of jilin Province

The development of alkaline fuel cells is moving forward at an accelerated pace,and the application of ether-free bonded polymers to anion exchange membranes （AEMs） has been widely ***,the question of the“trade-off”between AEM ionic conductivity and dimensional stability remains *** strategy of inducing microphase separation to improve the performance of AEM has attracted much attention recently,but the design of optimal molecular structures is still being ***,this work introduced different ratios of 3-bromo-1,1,1-trifluoroacetone （x=40,50,and 60） into the main chain of poly（p-terphenylene isatin）.Because fluorinated groups have excellent hydrophobicity,hydrophilic hydroxyl-containing side chains are introduced to jointly adjust the formation of phase separation *** results show that PTI-PTF50-NOH AEM with the appropriate fluorinated group ratio has the best ionic conductivity and alkali stability under the combined effect of *** has an ionic conductivity of 133.83 mS cm-1at 80°*** addition,the OH-conductivity remains at 89%of the initial value at 80°C and 3 M KOH for 1056 h of *** cell polarization curve based on PTI-PTF50-NOH shows a power density of 734.76 mW cm-2at a current density of 1807.7 mA cm-2.

关键词： Anion exchange membranes Poly(p-terphenylene isatin) Hydrophilic-hydrophobic phase separation Fluorinated group

Flexible molecules dedicate to release strain of inverted inorganic perovskite solar cell

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journal of Energy Chemistry 2025年第1期100卷 87-93页

作者： Hongrui sun Sanlong Wang Pengyang Wang Yali Liu Shanshan Qi Biao Shi Ying Zhao Xiaodan Zhang Institute of Photoelectronic Thin Film Devices and Technology Renewable Energy Conversion and Storage Center State Key Laboratory of Photovoltaic Materials and CellsNankai University Key Laboratory of Photoelectronic Thin Film Devices and Technology of Tianjin Haihe Laboratory of Sustainable Chemical Transformations Engineering Research Center of Thin Film Photoelectronic Technology of Ministry of Education Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)

The tensile strain in inorganic perovskite films induced by thermal annealing is one of the primary factors contributing to the inefficiency and instability of inorganic perovskite solar cells （IPSCs）,which reduces the defect formation ***,a flexible molecule 5-maleimidovaleric acid （5-MVA） was introduced as a strain buffer to release the residual strain of *** anhydride and carboxyl groups in 5-MVA interact strongly with the uncoordinated Pb2+through Lewis acid-base reaction,thus tightly“pull”the perovskite *** in-between soft carbon chain increased the structural flexibility of CsPbI2.85Br0.15perovskite materials,which effectively relieved the intrinsic internal strain of CsPbI2.85Br0.15,resisted the corrosion of external strain,and also reduced the formation of defects such as VIand *** addition,the introduction of 5-MVA improved crystal quality,passivated residual defects,and narrowed energy level ***,power conversion efficiency （PCE） of NiOxbased inverted IPSCs increased from 19.25% to 20.82% with the open-circuit voltage enhanced from 1.164 V to 1.230 *** release of strain also improved the stability of CsPbI2.85Br0.15perovskite films and devices.

关键词： Inverted inorganic perovskite solar cells Flexible molecules Strain release Crystallization Energy barrier High PCE

Calcium Phosphate Coating over Silk Fibroin Film by Biomimetic Methods

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journal of Wuhan University of Technology(Materials Science) 2005年第B12期20卷 92-94页

作者：赵勇陈治清 ong j West China College of Stomatology Sichuan University Chengdu 610041 China Department of Biomedical Engineering and Orthopedic Surgery University of Tennessee Health Science Center Memphis 38163USA

To investigate the biomincralization behavior of silk fibroin and to valuate the biodegradation and biocompatibility of the hybrid biomaterial, the calcium phosphate deposits were identified with SEM, EDX, XRD and FTIR. The results reveal that supersaturated calcification solution is an effective method for the mineralization of fibroin film. Enzymatic degradation experiment demonstrates the biodegradability of the composites. Osteoblasts incubation shows an excellent cytocompatibility on the mincralized fibroin films.

关键词： biomineralization degradation apatite fibroin/HAP composite

Application of the improved dung beetle optimizer,muti-head attention and hybrid deep learning algorithms to groundwater depth prediction in the Ningxia area,China

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Atmospheric and Oceanic Science Letters 2025年第1期18卷 18-23页

作者： jiarui Cai Bo sun Huijun Wang Yi Zheng Siyu Zhou Huixin Li Yanyan Huang Peishu Zong Collaborative Innovation Center on forecast and Evaluation of Meteorological Disasters/Key Laboratory of Meteorological Disaster Ministry of Education/Joint International Research Laboratory of Climate and Environment ChangeNanjing University of Information Science and TechnologyNanjingChina Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) ZhuhaiChina China Meteorological Administration Key Laboratory of Transportation MeteorologyNanjingChina jiangsu Meteorological Observatory NanjingChina

Due to the lack of accurate data and complex parameterization,the prediction of groundwater depth is a chal-lenge for numerical *** learning can effectively solve this issue and has been proven useful in the prediction of groundwater depth in many *** this study,two new models are applied to the prediction of groundwater depth in the Ningxia area,*** two models combine the improved dung beetle optimizer(DBO)algorithm with two deep learning models:The Multi-head Attention-Convolution Neural Network-Long Short Term Memory networks(MH-CNN-LSTM)and the Multi-head Attention-Convolution Neural Network-Gated Recurrent Unit(MH-CNN-GRU).The models with DBO show better prediction performance,with larger R(correlation coefficient),RPD(residual prediction deviation),and lower RMSE(root-mean-square error).Com-pared with the models with the original DBO,the R and RPD of models with the improved DBO increase by over 1.5%,and the RMSE decreases by over 1.8%,indicating better prediction *** addition,compared with the multiple linear regression model,a traditional statistical model,deep learning models have better prediction performance.

关键词： Groundwater depth Multi-head attention Improved dung beetle optimizer CNN-LSTM CNN-GRU Ningxia

A bio-inspired optical imaging method for robotic perception in turbid water

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Science China Technological Sciences 2025年第1期 79-81页

作者： Xudong sun Yafeng LI Peng LIN Xiaodi SHANG Xianping FU School of Information Science and Technology Dalian Maritime University College of Computer Science and Technology Qingdao University

In the realm of underwater robotics, optical imaging plays a pivotal role in many scientific researches. Due to the effects of absorption and scattering,images captured in turbid water are severely degraded. Therefore, enhancing the quality of underwater optical images stands paramount in ensuring the continued advancement and efficacy of underwater robots across its multifarious applications.

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