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Pindel-TD:A Tandem Duplication Detector Based on A Pattern Growth Approach

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Genomics, Proteomics & Bioinformatics 2024年第1期22卷 99-104页

作者： xiaofei yang Gaoyang Zheng Peng Jia Songbo Wang Kai Ye School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Center for Mathematical Medical the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Genome Institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China Faculty of Science Leiden UniversityLeiden 2311 EZNetherland

Tandem duplication(TD)is a major type of structural variations(SVs)that plays an important role in novel gene formation and human ***,TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational ***,we developed a TD detection module for the Pindel tool,referred to as Pindel-TD,based on a TD-specific pattern growth ***-TD is capable of detecting TDs with a wide size range at single nucleotide *** simulated and real read data from HG002,we demonstrated that Pindel-TD outperforms other leading methods in terms of precision,recall,F1-score,and ***,by applying Pindel-TD to data generated from the K562 cancer cell line,we identified a TD located at the seventh exon of SAGE1,providing an explanation for its high ***-TD is available for non-commercial use at https://***/xjtu-omics/pindel.

关键词： Tandem duplication Pattern growth Short-read sequencing Structural variation SAGE1

SEI/dead Li-turning capacity loss for high-performance anode-free solid-state lithium batteries

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Journal of Energy Chemistry 2024年第9期96卷 145-152页

作者： Qianwen Yin Tianyu Li Hongzhang Zhang Guiming Zhong xiaofei yang Xianfeng Li Division of Energy Storage Dalian National Laboratory for Clean EnergyDalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023LiaoningChina University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Long-Duration and Large-Scale Energy Storage Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023LiaoningChina Laboratory of Advanced Spectro-Electrochemistry and Lithium-Ion Batteries Dalian National Laboratory for Clean EnergyDalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023LiaoningChina

Anode-free solid-state lithium metal batteries(AF-SSLBs)have the potential to deliver higher energy density and improved safety beyond lithium-metal ***,the unclear mechanism for the fast capacity decay in AF-SSLBs,either determined by dead Li or solid electrolyte interface(SEI),limits the proposal of effective strategies to prolong cycling *** clarify the underlying mechanism,herein,the evolution of SEI and dead Li is quantitatively analyzed by a solid-state nuclear magnetic resonance(ss-NMR)technology in a typical LiPF6-based polymer *** results show that the initial capacity loss is attributed to the formation of SEI,while the dead Li dominates the following capacity loss and the growth rate is 0.141 mA h cm^(−2)cycle−*** reduce the active Li loss,the combination of inorganic-rich SEI and self-healing electrostatic shield effect is proposed to improve the reversibility of Li deposition/dissolution behavior,which reduces the capacity loss rate for the initial SEI and following dead Li generation by 2.3 and 20.1 folds,*** a result,the initial Coulombic efficiency(ICE)and stable CE increase by 15.1%and 15.3%in Li-Cu cells,which guides the rational design of high-performance AF-SSLBs.

关键词： Solid-state lithium batteries Solid-state NMR Anode-free SEI Dead Li

Two birds with one stone:Functionalized wood composites for efficient photocatalytic hydrogen production and solar water evaporation

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Chinese Chemical Letters 2024年第9期35卷 392-397页

作者： Deqi Fan Yicheng Tang Yemei Liao Yan Mi Yi Lu xiaofei yang College of Chemical Engineering Nanjing Forestry UniversityNanjing 210037China Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources International Innovation Center for Forest Chemicals and MaterialsCollege of ScienceNanjing Forestry UniversityNanjing 210037China Key Laboratory of Chemistry and Engineering of Forest Products State Ethnic Affairs CommissionGuangxi Key Laboratory of Chemistry and Engineering of Forest ProductsGuangxi Minzu UniversityNanning 530006China

Maximizing solar energy utilization is a persistent challenge in photo catalysis,which determines sustainable solar-driven photocatalytic *** thermal-coupled photo catalysis is considered as a promising solution to tackle the issues of sustainable energy scarcity and environmental pollution by harvesting the full-spectrum solar ***,a highly efficient photo thermal-accelerated photo catalysis system is elaborately established,in which the assembled carbonized stick/Nb_(2)C MXene evaporator can heat water into vapor and the integrated g-C_(3)N_(4)photocatalyst further enables high-efficiency photocatalytic hydrogen *** designed hyperboloid wood-based architecture possesses a multiphase interface of water steam/catalyst/hydrogen to reduce the transport resistance of hydrogen gas in liquid and ultimately maximize the output of hydrogen ***,this coupled photothermal-photocatalytic system achieves a stable solar evaporation rate of 2.16 kg m^(-1)h^(-1)under one sun irradiation and highly efficient hydrogen-evolving rate of 3096μmol g^(-1)h^(-1).This work paves a way to explore the improvement of photocatalytic hydrogen production by synergic photothermal effect for potential applications in renewable solar energy utilization and hydrogen production.

关键词： Photocatalysis Photothermal Nb_(2)C MXene g-C_(3)N_(4) Wood

A Self-Healing Optoacoustic Patch with High Damage Threshold and Conversion Efficiency for Biomedical Applications

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Nano-Micro Letters 2024年第7期16卷 31-45页

作者： Tao Zhang Cheng-Hui Li Wenbo Li Zhen Wang Zhongya Gu Jiapu Li Junru Yuan Jun Ou-yang xiaofei yang Benpeng Zhu School of Integrated Circuit Wuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan 430074People’s Republic of China State Key Laboratory of Coordination Chemistry Collaborative Innovation Center of Advanced MicrostructuresSchool of Chemistry and Chemical EngineeringNanjing UniversityNanjing 210093People’s Republic of China National Institute of Dental and Craniofacial Research(NIDCR) National Institutes of Health(NIH)35A Convent DriveBethesdaMD 20892USA Department of Neurology Tongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030People’s Republic of China

Compared with traditional piezoelectric ultrasonic devices,optoacoustic devices have unique advantages such as a simple preparation process,anti-electromagnetic interference,and wireless long-distance power ***,current optoacoustic devices remain limited due to a low damage threshold and energy conversion efficiency,which seriously hinder their widespread *** this study,using a self-healing polydimethylsiloxane(PDMS,Fe-Hpdca-PDMS)and carbon nanotube composite,a flexible optoacoustic patch is developed,which possesses the self-healing capability at room temperature,and can even recover from damage induced by cutting or laser ***,this patch can generate high-intensity ultrasound(>25 MPa)without the focusing *** laser damage threshold is greater than 183.44 mJ cm^(-2),and the optoacoustic energy conversion efficiency reaches a major achievement at 10.66×10^(-3),compared with other carbon-based nanomaterials and PDMS *** patch is also been successfully examined in the application of acoustic flow,thrombolysis,and wireless energy *** findings in this study provides new insight into designing and fabricating of novel ultrasound devices for biomedical applications.

关键词： Optoacoustic Self-healing PDMS Acoustic flow Thrombolytic Wireless energy harvesting

Long-lifespan thin Li anode achieved by dead Li rejuvenation and Li dendrite suppression for all-solid-state lithium batteries

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Chinese Chemical Letters 2024年第10期35卷 530-536页

作者： Xuejie Gao Xinyang Chen Ming Jiang Hanyan Wu Wenfeng Ren xiaofei yang Runcang Sun Center for Lignocellulosic Chemistry and Biomaterials College of Light Industry and Chemical EngineeringDalian Polytechnic UniversityDalian 116034China Division of Energy Storage Dalian National Laboratoryfor Clean EnergyDalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023 China Institute of Physical Science and Information Technology Anhui UniversityHefei 230601China

Solid polymer electrolytes(SPEs)are considered to be one of the most promising systems applied in all-solid-state lithium metal batteries(ASSLMBs)on account of their chemical and electrochemical ro bustness,mechanical stability,cost-effective and scalable manufacturing ***,significant en deavors have been directed towards mitigating the formation of the Li dendrite in SPE-based ASSLMBs while research on the inactive lithium in the forms of the solid-electrolyte interface has been rarely re ***,a bi-functional GaI3additive is developed for in-situ generating Li_(3)Ga alloy for suppressing Li dendrite growth,as well as I3-in recovering dead *** on the density functional theory(DFT)results,the Li atom prefers to deposit on the Li_(3)Ga surface and then guide uniform Li deposi tion,while the I3species features a relatively lower lowest unoccupied molecular orbital(LUMO)energy level(-2.12 e V),meaning a higher electron affinity,which is beneficial for reviving inactive lithium to counterbalance the loss of *** a result,in comparison to cells employing pure PEGDME-based electrolytes,the Li-Li symmetric cells utilizing GaI3-containing solid-state electrolyte exhibited a cycling life nearly 30 times longer at a current density/capacity of 0.2 mA/cm^(2),0.2 mAh/cm^(2).The full batterie of LFP//1%GaI3-SPE//40μm Li delivered a noteworthy capacity retention of 82%after 1300 cycles at a rate of 1 C.

关键词： Synergistic effect In-situ Li Ga alloy Suppress Lidendrite Dead lithium regeneration All-solid-state lithium metal batteries

An optimized method of culturing neurons based on polyacrylamide gel

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Biophysics Reports 2024年第1期10卷 41-47页

作者： Yongjing Qiao Jihong Gong Ziqi Jin Yiting Tu xiaofei yang Key Laboratory of Cognitive Science Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment Laboratory of Membrane Ion Channels and Medicine College of Biomedical Engineering SouthCentral Minzu University

Substrate stiffness is a microenvironment with a certain stiffness constructed by the extracellular matrix and adjacent cells, which plays an important role in the growth and development of cells and tissue formation. Studies have indicated that the stiffness of the brain is about 0.1–1 kPa. The physiological and pathological processes of the nervous system are mediated by the substrate stiffness that the neurons suffer. However, how substrate stiffness regulates these processes remains to be studied. Culturing neurons on substrates with different stiffness in vitro is one of the best methods to study the role of stiffness in regulating neuronal development and activity. In this study, by changing the preparation time and the activation time of polyacrylamide gel, we provide an improved method that achieves a low toxic substrate environment for better primary neuron adhesion and development. Hope that this method is convenient for those studying the role of substrate stiffness in neurons.

关键词： Polyacrylamide gel Neuron culture Cell adhesion Neural cell development

Research on High-Velocity Impact Damage Monitoring Method of CFRP Based on Guided Wave

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Transactions of Nanjing University of Aeronautics and Astronautics 2024年第S1期41卷 60-69页

作者： WANG yang yang xiaofei QIU Lei YUAN Shenfang State Key Laboratory of Mechanics and Control for Aerospace Structures Research Center of Structural Health Monitoring and PrognosisNanjing University of Aeronautics and AstronauticsNanjing 210016P.R.China

Carbon fiber-reinforced polymer(CFRP)is widely used in aerospace *** kind of material may face the threat of high-velocity impact in the process of dedicated service,and the relevant research mainly considers the impact resistance of the material,and lacks the high-velocity impact damage monitoring research of *** solve this problem,a real high-velocity impact damage experiment and structural health monitoring(SHM)method of CFRP plate based on piezoelectric guided wave is *** results show that CFRP has obvious perforation damage and fiber breakage when high-velocity impact *** is also proved that guided wave SHM technology can be effectively used in the monitoring of such damage,and the damage can be reflected by quantifying the signal changes and damage index(DI).It provides a reference for further research on guided wave structure monitoring of high/hyper-velocity impact damage of CFRP.

关键词： guided waves structural health monitoring(SHM) carbon fiber reinforced polymer(CFRP) high-velocity impact

荷兰应用科学大学专业博士学位项目改革及启示

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学位与研究生教育 2024年第2期 86-93页

作者：武学超杨晓斐河南理工大学教育研究所/应急管理学院焦作454003 河南理工大学外国语学院焦作454003

为加快高层次职业人才培养,提升应用科学大学战略地位,荷兰政府积极推进应用科学大学学位体制改革,授权在应用科学大学设立专业博士学位项目。荷兰专业博士学位项目以欧洲博士学位通用能力标准为依据,明确规定了不同于专业硕士和工程博... 详细信息

为加快高层次职业人才培养,提升应用科学大学战略地位,荷兰政府积极推进应用科学大学学位体制改革,授权在应用科学大学设立专业博士学位项目。荷兰专业博士学位项目以欧洲博士学位通用能力标准为依据,明确规定了不同于专业硕士和工程博士的专业博士能力标准,注重通过产科教协同机制和实践研究反哺机制培养博士生解决复杂实践问题的能力,强化教授团队对博士生的专业指导,以三级质量保障机制监测博士生学习质量。荷兰应用科学大学专业博士学位项目具有较强的赋能社会增值和职教高质量发展的价值,对我国加快推进高层次现代职业教育体系建设具有重要借鉴价值。

关键词：荷兰应用科学大学专业博士职业教育学位

黔中地区蔡家坝铝土矿床富锂铝土岩地球化学特征及沉积环境研究

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地质与勘探 2024年第4期60卷 735-746页

作者：朱尤青罗朝坤杨晓飞刘江贵州省有色金属和核工业地质勘查局一总队贵州贵阳551400 贵州大学资源与环境工程学院贵州贵阳550025

贵州清镇蔡家坝铝土矿床是近年来在黔中铝土矿成矿区内新发现的铝土矿床之一,铝土矿体呈层状及似层状产于下石炭统九架炉组地层中。本研究通过对蔡家坝铝土矿床中以铝土岩为主的含铝岩系钻孔岩心剖面开展详细的矿物学和地球化学研究,发... 详细信息

贵州清镇蔡家坝铝土矿床是近年来在黔中铝土矿成矿区内新发现的铝土矿床之一,铝土矿体呈层状及似层状产于下石炭统九架炉组地层中。本研究通过对蔡家坝铝土矿床中以铝土岩为主的含铝岩系钻孔岩心剖面开展详细的矿物学和地球化学研究,发现含铝岩系中的铝土岩明显具有Li超富集的现象。研究结果表明,含铝岩系的所有样品中均富含高浓度的Li(210~2480)×10^(-6);其中,10件铝土岩的Li含量为(210~2480)×10^(-6)(平均1198.9×10^(-6)),3件铝土矿石的Li含量为(412~1440)×10^(-6)(平均980.7×10^(-6)),表现出明显超富集的特征。光学显微镜和XRD分析显示,富锂铝土岩主要由伊利石、高岭石和绿泥石组成,以及少量的硬水铝石、勃姆石、黄铁矿、锐钛矿等。结合矿物学和地球化学证据,研究区铝土岩中的Li主要赋存在高岭石和伊利石等粘土矿物中,当铝土岩中Al_(2)O_(3)含量介于30%~40%之间以及Al_(2)O_(3)/SiO_(2)比值介于1~1.5时,铝土岩中的Li最为富集。元素地球化学分析表明,研究区内的富锂铝土岩形成于温暖潮湿和相对氧化的陆相淡水环境。

关键词：铝土矿富锂铝土岩九架炉组赋存状态沉积环境蔡家坝黔中地区