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Review and Evaluate the Bioinformatics Analysis Strategies of ATAC-seq and CUT&Tag Data

Genomics, Proteomics & Bioinformatics 2024年第3期22卷 11-27页

作者： Siyuan Cheng benpeng miao Tiandao Li Guoyan Zhao Bo Zhang Department of Developmental Biology Center of Regenerative MedicineWashington University School of MedicineSt.LouisMO 63108USA Department of Genetics Washington University School of MedicineSt.LouisMO 63108USA Department of Neurology Washington University School of MedicineSt.LouisMO 63108USA Department of Pathology and Immunology Washington University School of MedicineSt.LouisMO 63108USA

Efficient and reliable profiling methods are essential to study ***5,one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency,is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and *** on Tn5,the Assay for Transposase-Accessible Chromatin using sequencing(ATAC-seq)and the Cleavage Under Targets and Tagmentation(CUT&Tag)were developed to measure chromatin accessibility and detect DNA–protein *** methodologies can be applied to large amounts of biological samples with low-input levels,such as rare tissues,embryos,and sorted single ***,fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase ***,inappropriate data analysis can generate biased or misleading ***,it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools,many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing(ChIP-seq)***,we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag *** compared the sensitivity,specificity,and peak width distribution for both narrow-type and broad-type peak *** also tested the influence of the availability of control IgG input in CUT&Tag data ***,we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag *** study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies,which were implemented into Docker/Singularity images for streamlined data analysis.

关键词： Tn5 transposase Epigenetic Bioinformatics ATAC-seq CUT&Tag

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AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis

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Genomics, Proteomics & Bioinformatics 2021年第4期19卷 641-651页

作者： Shaopeng Liu Daofeng Li Cheng Lyu Paul MGontarz benpeng miao Pamela A.F.Madden Ting Wang Bo Zhang Department of Developmental Biology Center of Regenerative MedicineWashington University School of MedicineSt.LouisMO 63108USA Department of Genetics Center for Genomic Sciences and Systems BiologyWashington University School of MedicineSt.LouisMO 63108USA Department of Psychiatry Washington University School of MedicineSt.LouisMO 63108USA

Assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq) is a technique widely used to investigate genome-wide chromatin accessibility. The recently published Omni-ATAC-seq protocol substantially improves the signal/noise ratio and reduces the input cell number. High-quality data are critical to ensure accurate *** tools have been developed for assessing sequencing quality and insertion size distribution for ATAC-seq data;however, key quality control(QC) metrics have not yet been established to accurately determine the quality of ATAC-seq data. Here, we optimized the analysis strategy for ATAC-seq and defined a series of QC metrics for ATAC-seq data,including reads under peak ratio(RUPr), background(BG), promoter enrichment(Pro En), subsampling enrichment(Sub En), and other measurements. We incorporated these QC tests into our recently developed ATAC-seq Integrative Analysis Package(AIAP) to provide a complete ATAC-seq analysis system, including quality assurance, improved peak calling, and downstream differential analysis. We demonstrated a significant improvement of sensitivity(20%–60%) in both peak calling and differential analysis by processing paired-end ATAC-seq datasets using AIAP. AIAP is compiled into Docker/Singularity, and it can be executed by one command line to generate a comprehensive QC report. We used ENCODE ATAC-seq data to benchmark and generate QC recommendations, and developed q ATACViewer for the userfriendly interaction with the QC report. The software, source code, and documentation of AIAP are freely available at https://***/Zhang-lab/ATAC-seq_QC_analysis.

关键词： ATAC-seq Quality control Chromatin accessibility Differential analysis Data visualization

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Genome assembly and transcriptome analysis provide insights into the antischistosome mechanism of Microtus fortis

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Journal of Genetics and Genomics 2020年第12期47卷 743-755页

作者： Hong Li Zhen Wang Shumei Chai Xiong Bai Guohui Ding Yuanyuan Li Junyi Li Qingyu Xiao benpeng miao Weili Lin Jie Feng Mingyue Huang Cheng Gao Bin Li Wei Hu Jiaojiao Lin Zhiqiang Fu Jianyun Xie Yixue Li Bio-Med Big Data Center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China Shanghai Veterinary Research Institute Chinese Academy of Agricultural SciencesKey Laboratory of Animal ParasitologyMinistry of AgricultureShanghai 200241China Shanghai Laboratory Animal Research Center Shanghai 201203China Institute for Digital Health International Human Phenome Institutes(Shanghai)Shanghai 200433China Shanghai Center for Bioinformation Technology Shanghai Academy of Science and TechnologyShanghai 201203China School of Computer Science and Technology Harbin Institute of Technology(Shenzhen)ShenzhenGuangdong 518055China Shanghai Institute of Immunology Department of Immunology and MicrobiologyShanghai JiaoTong University School of MedicineShanghai 200025China State Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Contemporary AnthropologyCollaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan UniversityShanghai 200438China Hangzhou Institute for Advanced Study University of Chinese Academy of SciencesHangzhouZhejiang 330106China

Microtus fortis is the only mammalian host that exhibits intrinsic resistance against Schistosoma japonicum ***,the underlying molecular mechanisms of this resistance are not yet ***,we perform the first de novo genome assembly of ***,comprehensive gene annotation analysis,and evolution ***,we compare the recovery rate of schistosomes,pathological changes,and liver transcriptomes between *** and mice at different time points after *** observe that the time and type of immune response in *** are different from those in *** activates immune and inflammatory responses on the 10th day post infection,such as leukocyte extravasation,antibody activation,Fc-gamma receptor-mediated phagocytosis,and the interferon signaling cascade,which play important roles in preventing the development of *** contrast,an intense immune response occurrs in mice at the late stages of infection and could not eliminate *** mice suffer severe pathological injury and continuous decreases in cell cycle,lipid metabolism,and other *** findings offer new insights into the intrinsic resistance mechanism of *** against schistosome *** genome sequence also provides the basis for future studies of other important traits in ***.

关键词： Genome assembly Microtus fortis Schistosome Immune Transcriptome

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Ultrasound:A new strategy for artificial synapses modulation

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InfoMat 2024年第6期6卷 110-120页

作者： Junru Yuan Yi Li Meng Wang Xiaodi Huang Tao Zhang Kan-Hao Xue Junhui Yuan Jun Ou-Yang Xiaofei Yang Xiangshui miao benpeng Zhu School of Integrated Circuits Huazhong University of Science and TechnologyWuhanthe People's Republic of China

Due to its non-invasive nature,ultrasound has been widely used for neuromodulation in biological systems,where its application influences the synaptic weights and the process of neurotransmitter ***,such modulation has not been emulated in physical *** are ideal electrical components for artificial synapses,but up till now they are hardly reported to respond to ultrasound *** we design and fabricate a HfOx-based memristor on 64Y-X LiNbO_(3) single crystal substrate,and successfully realize artificial synapses modulation by shear-horizontal surface acoustic wave(SH-SAW).It is a prominent short-term resistance modulation,where ultrasound has been shown to cause resistance drop for various resistance states,which could fully recover after the ultrasound is shut *** physical mechanism illustrates that ultrasound induced polarization potential in the HfOx dielectric layer acts on the Schottky barrier,leading to the resistance *** emulation of neuron firing frequency modulation through ultrasound signals is ***,the joint application of ultrasound and electric voltage yields fruitful functionalities,such as the enhancement of resistance window and synaptic plasticity through ultrasound *** these promising results provide a new strategy for artificial synapses modulation,and also further advance neuromorphic devices toward system applications.

关键词： artificial synapse memristor neuromodulation ultrasound

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膜下滴灌减量施肥对甘蔗脱毒原种苗田间繁育效率和养分利用率的影响

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热带作物学报 2025年第1期46卷 115-122页

作者：彭李顺曹峥英蔡文伟杨本鹏杨学广西热带农业科学研究院广西崇左532199 中国热带农业科学院热带生物技术研究所/热带作物生物育种全国重点实验室海南海口571101 中国热带农业科学院三亚研究院海南三亚572024 广西久洋禾农业科技有限公司广西崇左532199

本研究探讨不同膜下滴灌减量施肥模式对甘蔗脱毒原种苗生长、繁育效率及肥料利用率的影响,并分析最佳减量施肥模式,旨在为科学指导甘蔗脱毒原种苗田间繁育过程中滴灌施肥技术的应用提供理论依据。在所有对照和处理均配备膜下滴灌系统并... 详细信息

本研究探讨不同膜下滴灌减量施肥模式对甘蔗脱毒原种苗生长、繁育效率及肥料利用率的影响,并分析最佳减量施肥模式,旨在为科学指导甘蔗脱毒原种苗田间繁育过程中滴灌施肥技术的应用提供理论依据。在所有对照和处理均配备膜下滴灌系统并进行水分管理的条件下,以空白对照(CK_(0))、常规施肥(CK_(1))为对照,设置1个膜下滴灌施肥处理T_(100)(施肥量同CK_(1))以及3个膜下滴灌减量施肥处理T_(80)、T_(70)和T_(60)(减量施肥20%、30%和40%),对甘蔗脱毒原种苗繁育过程中主要农艺性状、种茎产量、总芽数、繁育效率及养分利用率等指标进行比较分析。研究结果表明:在各项农艺指标中,2022、2023年T_(100)和T_(80)的平均分蘖率略低于CK_(1),但在成茎率、单株芽数、有效茎数方面较CK_(1)均有显著提升。在繁育总种芽数上,T_(100)和T_(80)最高,年平均分别达到(1480.87×10^(3))/hm^(2)和(1477.87×10^(3))/hm^(2),显著高于CK_(1)的(1302.50×10^(3))/hm^(2);T_(70)与CK_(1)间差异不显著;T_(60)最低仅为(1170.53×10^(3))/hm^(2)。在繁育效率方面,原种苗田间繁育倍数T_(100)和T_(80)最高,分别达到66.64倍和66.50倍;其次为T_(70)和CK_(1),繁育倍数为59.61倍和58.61倍;T_(60)繁育倍数最低,为52.67。在繁育收益方面,相较于CK_(0),T_(100)和T_(80)收益增幅最高,分别达到5.82和5.87万元/hm^(2);其次为T_(70),收益增幅为4.19万元/hm^(2),略高于CK_(1)(3.84万元/hm^(2));T_(60)最低,仅为2.51万元/hm^(2)。在肥料投入产出比方面,T_(80)最高,达到1∶21.89,明显高于T_(100)(1∶17.36);CK_(1)最低,为1∶11.45。在肥料利用率方面,所有施肥处理中,氮、磷、钾肥的利用率均为CK_(1)最低。而T_(80)最高,试验平均氮、磷、钾肥利用率分别达到51.57%、27.37%和67.45%,分别较CK_(1)提高了21.21、10.37和23.13个百分点。综上所述,在中等肥力红壤蔗区,采用T_(80)膜下滴灌减量施肥模式,可以同时获得较理想的甘蔗脱毒原种苗繁育效率和收益。

关键词：甘蔗脱毒种苗膜下滴灌施肥化肥减施繁育效率养分利用率

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Microstructural Characteristics and Heat Transfer of Flattened Millimeter-size Nickel Droplet

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稀有金属材料与工程 2012年第S1期41卷 287-290页

作者： Li Hui Wang benpeng Wei Qi Li Zhuoxin Beijing Univ Technol Coll Mat Sci & Engn Beijing 100124 Peoples R China

The splat is the fundamental unit of thermally sprayed coatings,which has been one of the hottest issues for *** order to study the splat formation,an experiment was designed and conducted,in which a millimeter-size nickel metal droplet fell freely and impacted on aluminum and stainless steel *** microstructural characteristics of the splat and the heat conduction and solidification processes during the flattening process have been studied numerically and *** effect of the droplet temperature,impact velocity as well as the substrate temperature was *** phenomenon of substrate melting was observed after the spreading of nickel droplet,which became more pronounced when the initial substrate temperature *** the impact velocity of droplet resulted in a decrease in the interfacial temperature between droplet and substrate.

关键词： flattening behavior splat heat transfer

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Recent Advancements in Ultrasound Transducer:From Material Strategies to Biomedical Applications

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Biomedical Engineering Frontiers 2022年第1期3卷 188-206页

作者： Jiapu Li Yuqing Ma Tao Zhang KKirk Shung benpeng Zhu Wuhan National Laboratory for Optoelectronics Optics Valley LaboratorySchool of Optical and Electronic InformationHuazhong University of Science and TechnologyWuhanChina 430074 State Key Laboratory of Transducer Technology Chinese Academy of SciencesShanghai 200050China NIH Resource Center for Medical Ultrasonic Transducer Technology Department of Biomedical EngineeringUniversity of Southern CaliforniaLos AngelesCA 90089USA

Ultrasound is extensively studied for biomedical engineering *** the core part of the ultrasonic system,the ultrasound transducer plays a significant *** the purpose of meeting the requirement of precision medicine,the main challenge for the development of ultrasound transducer is to further enhance its *** this article,an overview of recent developments in ultrasound transducer technologies that use a variety of material strategies and device designs based on both the piezoelectric and photoacoustic mechanisms is *** applications are also presented,including ultrasound imaging,ultrasound therapy,particle/cell manipulation,drug delivery,and nerve ***,perspectives and opportunities are also highlighted.

关键词： Transducer piezoelectric Advance

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Immunolocalization of Arabinogalactan Proteins and Pectins in Floral Buds of Cucumber （Cucumis sativus L.） During Sex Determination

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Journal of Integrative Plant Biology 2005年第2期47卷 194-200页

作者： Yi-benpeng ChengZOU Hua-QinGONG Shu-NongBAI Zhi-HongXU Yi-QinLI PekingUniversity-YaleJointResearchCenterofAgriculturalandPlantMolecularBiology CollegeofLifeSciencesPekingUniversityBeijing100871China ProteinScienceLaboratoryoftheMinistryofEducation SchoolofLifeSciencesandEngineeringTsinghuaUniversityBeijing100084China

Abstract: Arabinogalactan proteins (AGPs) and pectins were detected in the floral buds of cucumber (Cucumis sativus L.) during its sex determination using the following monoclonal antibodies: MAC 207 (recognizes AGP epitopes); JIM 8 (recognizes a subset of AGP epitopes); and JIM 5 and JIM 7 (epitopes of pectins esterified to various degrees). In the stem apex meristem (SAM) of the cucumber, epitopes of MAC 207, JIM 7, and JIM 5 were localized in the cells from second to third peripheral layers when the sex organ primodium began to differentiate; epitopes of MAC 207 and JIM 5 were also detected in the ragged edge cells. A very dense labeling signal with MAC 207 was observed in the carpel and pistil primodium. The AGP epitopes recognized by JIM 8 were localized in the anther of the male flower and the anther-like portion of the stagnant stamen of the female flower. This suggests that the AGPs and pectins in the SAM of the cucumber are closely associated with the differentiation of the SAM, from meristematic cells to floral primodium. The subset of AGPs recognized by JIM 8 may play an important role in stamen formation.

关键词： arabinogalactan proteins cucumber (Cucumis sativus L.) floral buds immunolocalization pectins

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A restoration method using dual generate adversarial networks for Chinese ancient characters

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Visual Informatics 2022年第1期6卷 26-34页

作者： benpeng Su Xuxing Liu Weize Gao Ye Yang Shanxiong Chen College of Computer and Information Science Southwest UniversityChongqing 400715China Chongqing Key Lab of Automated Reasoning and Cognition Chongqing Institute of Green and Intelligent TechnologyChinese Academy of SciencesChongqing 400714China

Ancient books that record the history of different periods are precious for human *** the protection of them is facing serious problems such as *** is significant to repair the damaged characters in ancient books and restore their original *** requirement of the restoration of the damaged character is keeping the stroke shape correct and the font style *** order to solve these problems,this paper proposes a new restoration method based on generative adversarial *** use the shape restoration network to complete the stroke shape recovery and the font style *** texture repair network is responsible for reconstructing texture *** order to improve the accuracy of the generator in the shape restoration network,we use the adversarial feature loss(AFL),which can update the generator and discriminator synchronously to replace the traditional perceptual ***,the font style loss is proposed to maintain the stylistic consistency for the whole *** model is evaluated on the datasets Yi and Qing,and shows that it outperforms current state-of-the-art techniques quantitatively and *** particular,the Structural Similarity has increased by 8.0%and 6.7%respectively on the two datasets.

关键词： Stroke shape restoration Texture restoration Calligraphy style

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Ultrashort-time liquid phase sintering of high-performance fine-grain tungsten heavy alloys by laser additive manufacturing

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Journal of Materials Science & Technology 2021年第31期90卷 30-36页

作者： Shangcheng Zhou Yao-Jian Liang Yichao Zhu benpeng Wang Lu Wang Yunfei Xue School of Materials Science and Engineering Beijing Institute of TechnologyBeijing 100081China

Liquid phase sintering(LPS)is a proven technique for preparing large-size tungsten heavy alloys(WHAs).However,for densification,this processing requires that the matrix of WHAs keeps melting for a long time,which simultaneously causes W grain coarsening that degenerates the *** work develops a novel ultrashort-time LPS method to form bulk high-performance fine-grain WHAs based on the principle of laser additive manufacturing(LAM).During LAM,the high-entropy alloy matrix(Al_(0.5)Cr_(0.9)FeNi_(2.5)V_(0.2))and W powders were fed simultaneously but only the matrix was melted by laser and most W particles remained solid,and the melted matrix rapidly solidified with laser moving away,producing an ultrashort-time LPS processing in the melt pool,i.e.,laser ultrashort-time liquid phase sintering(LULPS).The extreme short dwell time in liquid(-1/10,000 of conventional LPS)can effectively suppress W grain growth,obtaining a small size of 1/3 of the size in LPS ***,strong convection in the melt pool of LULPS enables a nearly full densification in such a short sintering *** with LPS WHAs,the LULPS fine-grain WHAs present a 42%higher yield strength,as well as an enhanced susceptibility to adiabatic shear banding(ASB)that is important for strong armor-piercing capability,indicating that LULPS can be a promising pathway for forming high-performance WHAs that surpass those prepared by conventional LPS.

关键词： Tungsten heavy alloy Laser additive manufacturing Liquid phase sintering

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