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Urdnet:A Cryo-EM Particle Automatic Picking Method

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Computers, Materials & Continua 2022年第7期72卷 1593-1610页

作者： Jianquan Ouyang Yue Zhang Kun Fang Tianming Liu xiangyu pan School of Computer Science&School of Cyberspace Science Xiangtan UniversityXiangtan411105China Hunan Meteorological Information Center Hunan Meteorological BureauChangshaHunan410118China Department of Computer Science The University of GeorgiaAthensGeorgiaUSA

Cryo-Electron Microscopy(Cryo-EM)images are characterized by the low signal-to-noise ratio,low contrast,serious background noise,more impurities,less data,difficult data labeling,simpler image semantics,and relatively fixed structure,while U-Net obtains low resolution when downsampling rate information to complete object category recognition,obtains highresolution information during upsampling to complete precise segmentation and positioning,fills in the underlying information through skip connection to improve the accuracy of image segmentation,and has advantages in biological image processing like Cryo-EM image.This article proposes A U-Net based residual intensive neural network(Urdnet),which combines point-level and pixel-level tags,used to accurately and automatically locate particles from cryo-electron microscopy images,and solve the bottleneck that cryo-EM Single-particle biologicalmacromolecule reconstruction requires tens of thousands of automatically picked particles.The 80S ribosome,HCN1 channel and TcdA1 toxin subunits,and other public protein datasets have been trained and tested on Urdnet.The experimental results show that Urdnet could reach the same excellent particle picking performances as the mainstream methods of RELION,DeepPicker,and acquire the 3Dstructure of picked particleswith higher resolution.

关键词： Deep learning convolutional neural network particle picking cryo-electron microscopy single-particle reconstruction

High temperature electrochemical discharge performance of LaFeO3 coated with C/Ni as anode material for NiMH batteries

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Progress in Natural Science:Materials International 2022年第6期32卷 684-692页

作者： Kailiang Ren Jiajia Miao Wenzhuo Shen Huanhuan Su Yunpeng pan Jiajin Zhao xiangyu pan Yuan Li Yaokun Fu Lu Zhang Shumin Han State Key Laboratory of Metastable Materials Science and Technology Yanshan University School of Environmental and Chemical Engineering Yanshan University

Perovskite LaFeO3is considered as a promising new anode material for nickel/metal hydride batteries due to its low cost,environmental friendliness and high temperature resistance.However,the poor conductivity of LaFeO3material restricts the discharge ability,which is problematic for its future widespread application.To solve the above issue,in this study,we prepared C/Ni-coated LaFeO3composite in view of the excellent electrical conductivity of carbon and nickel metal.Results show that the C/Ni-coated LaFeO3composite delivers remarkably increased discharge capacity of ～345 mAh g-1at 60℃ in contrast to ～267 mAh g-1for pure LaFeO3.Furthermore,the carbon and nickel not only increase the electrical conductivity of the LaFeO3but also reduces the agglomeration of the LaFeO3,therefore,the C/Ni-coated LaFeO3composite serves superior long cycle-life,which maintains 60.9% after 100 cycles(52.9% for the LaFeO3sample).In overall,the electrochemical behavior of the C/Ni-coated LaFeO3composite confirms its high potential as nickel/metal hydride batteries for energy storage applications.

关键词： Energy storage Perovskite-type oxide Nickel metal hydride batteries LaFeO 3 Electrochemical performance

CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 632-648页

作者： xiangyu pan Zhaoxia Ma Xinqi Sun Hui Li Tingting Zhang Chen Zhao Nini Wang Rasmus Heller Wing Hung Wong Wen Wang Yu Jiang Yong Wang Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangling 712100China Department of Medical Research Guangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Guangdong Cardiovascular Institute Guangdong Provincial People’s HospitalGuangdong Academy of Medical SciencesGuangzhou 510080China Academy of Mathematics and Systems Science Chinese Academy of SciencesBeijing 100190China School of Mathematics University of Chinese Academy of SciencesBeijing 100049China State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of Animal Science and TechnologyGuangxi UniversityNanning 530005China Section for Computational and RNA Biology Department of BiologyUniversity of CopenhagenCopenhagen DK-2100Denmark Department of Statistics Department of Biomedical Data ScienceBio-X ProgramStanford UniversityStanfordCA 94305USA Center for Ecological and Environmental Sciences Northwestern Polytechnical UniversityXi’an 710072China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China Key Laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China

The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach innovation.We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.

关键词： Trait innovation Gene regulatory network Conserved non-coding element Toolkit transcription factor Ruminant

Allele-specific expression and splicing provide insight into the phenotypic differences between thin- and fat-tailed sheep breeds

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Journal of Genetics and Genomics 2022年第6期49卷 583-586页

作者： Fei Wang Junjie Shao Sangang He Yingwei Guo xiangyu pan Yu Wang Hojjat Asadollahpour Nanaei Lei Chen Ran Li Han Xu Zhirui Yang Mingjun Liu Yu Jiang Key Laboratory of Ruminant Genetics Breeding&ReproductionMinistry of AgricultureChina Key Laboratory of Animal Biotechnology of Xinjiang Institute of BiotechnologyXinjiang Academy of Animal ScienceUrumqiXinjiang 830026China Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi 712100China

The sheep(Ovis aries) was one of the first grazing animals to be domesticated approximately 11,000 years ago in the Fertile Crescent(Chessa et al., 2009). Since domestication, a wide variety of sheep breeds with different production traitsand morphological characteristics have been shaped under the influence of natural and artificial selection. According to the fat content in tail, sheep can be mainly classified into two groups: thin-and fat-tailed breeds.

关键词： sheep artificial shaped

Nanophase precipitation and strengthening in a dual-phase Al_(0.5)CoCrFeNi high-entropy alloy

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Journal of Materials Science & Technology 2021年第13期72卷 1-7页

作者： Haoxue Yang Jinshan Li xiangyu pan William Yi Wang Hongchao Kou Jun Wang State Key Laboratory of Solidification Processing Northwestern Polytechnical UniversityXi’an 710072China

Precipitation-hardening in fcc-based high-entro py alloys(HEAs)have usually been realized by introducing complex intermetallic compounds.In this study,enhanced strength is ascribed to the existence of L1_(2) precipitates and B2/bcc conjoint phases in the fcc matrix.The nano-size particles in the Al_(0.5)CoCrFeNi HEA are produced by cold-rolling,followed by intermediate-temperature-annealing at 650℃.For L1_(2) ordering,the initial granular structure has transformed into lamella structure and then kept stable when the holding time prolonged to 200 h.The formation of this conjoint B2/bcc driven by the concentration profiles takes place when the diffusion process of elements is sufficient after long-time aging.Based on the microstructure analysis,changes in mechanical properties are associated with the shape,size scale and volume fraction of the precipitates.The peak ultimate tensile stress reaches 1221.5 MPa,1.97 times compared with the as-cast alloy,remaining plasticity of 21.3%.

关键词： High-entropy alloy L12 phase B2 phase Precipitation strengthening

Identifying a confused cell identity for esophageal squamous cell carcinoma

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Signal Transduction and Targeted Therapy 2022年第5期7卷 1692-1702页

作者： xiangyu pan Jian Wang Linjie Guo Feifei Na Jiajia Du Xuelan Chen Ailing Zhong Lei Zhao Lu Zhang Mengsha Zhang Xudong Wan Manli Wang Hongyu Liu Siqi Dai Ping Tan Jingyao Chen Yu Liu Bing Hu Chong Chen Department of Gastroenterology State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuanChina Department of Thoracic Oncology State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengdu 610041 SichuanChina Dpartment of Urology Institute of UrologyWest China HospitalSichuan UniversityChengduChina

The cell identity of malignant cells and how they acquire it are fundamental for our understanding of cancer.Here,we report that esophageal squamous cell carcinoma(ESCC)cells display molecular features equally similar but distinct to all three types of normal esophageal epithelial cells,which we term as confused cell identity(CCI).CCI is an independent prognostic marker associated with poor prognosis in ESCC.Further,we identify tropomyosin 4(TPM4)as a critical CCI gene that promotes the aggressiveness of ESCC in vitro and in vivo.And TPM4 creates CCI through activating the Jak/STAT-SOX2 pathway.Thus,our study suggests an unrecognized feature of ESCC cells,which might be of value for clinic prognosis and potential interference.

关键词： esophageal SOX2 squamous

Epigenetic drug library screening identified an LSD1 inhibitor to target UTX-deficient cells for differentiation therapy

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Signal Transduction and Targeted Therapy 2019年第1期4卷 566-575页

作者： Baohong Wu xiangyu pan Xuelan Chen Mei Chen Kaidou Shi Jing Xu Jianan Zheng Ting Niu Chong Chen Xiao Shuai Yu Liu Department of Hematology State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University610041 ChengduSichuanChina

UTX(also known as KDM6A),a histone 3 lysine 27 demethylase,is among the most frequently mutated epigenetic regulators in myelodysplastic syndrome(MDS)and acute myeloid leukemia(AML).Recent studies have suggested that UTX mutations promote MDS and AML by blocking the differentiation of hematopoietic stem and progenitor cells(HSPCs).Here,we performed an epigenetic drug library screening for small molecules able to release the differentiation block on HSPCs induced by UTX deficiency.We found that SP2509,a selective inhibitor of LSD1,specifically promoted the differentiation of Utx-null HSPCs while sparing wild-type HSPCs.Transcriptome profiling showed that Utx loss reduced the expression of differentiation-related and tumor suppressor genes,correlating with their potential roles in HSPC self-renewal and leukemogenesis.In contrast,SP2509 treatment reversed these changes in gene expression in Utx-null HSPCs.Accordingly,Utx loss decreased H3K4 methylation level probably through the COMPASS-like complex,while LSD1 inhibition by SP2509 partially reversed the reduction of H3K4 methylation in Utx-deficient HSPCs.Further,SP2509 promoted the differentiation of Utx-null AML cells in vitro and in vivo and,therefore,extended the survival of these leukemic mice.Thus,our study identified a novel strategy to specifically target both premalignant and malignant cells with Utx deficiency for differentiation therapy and provided insights into the molecular mechanisms underlying the role of Utx in regulating HSPCs and related diseases.

关键词： reversed deficient promoted

Spontaneous apoptosis of cells in therapeutic stem cell preparation exert immunomodulatory effects through release of phosphatidylserine

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Signal Transduction and Targeted Therapy 2021年第8期6卷 2536-2549页

作者： Xuemei He Weiqi Hong Jingyun Yang Hong Lei Tianqi Lu Cai He Zhenfei Bi xiangyu pan Yu Liu Lunzhi Dai Wei Wang Canhua Huang Hongxin Deng Xiawei Wei Laboratory of Aging Research and Cancer Drug Target State Key Laboratory of Biotherapy and Cancer CenterNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduSichuanPeople’s Republic of China Experimental Medicine Center the Affiliated Hospital of Southwest Medical UniversityLuzhouSichuanPeople’s Republic of China

Mesenchymal stem cell(MSC)-mediated immunomodulation has been harnessed for the treatment of human diseases,but its underlying mechanism has not been fully understood.Dead cells,including apoptotic cells have immunomodulatory properties.It has been repeatedly reported that the proportion of nonviable MSCs in a MSC therapeutic preparation varied from 5-50%in the ongoing clinical trials.It is conceivable that the nonviable cells in a MSC therapeutic preparation may play a role in the therapeutic effects of MSCs.We found that the MSC therapeutic preparation in the present study had about 5%dead MSCs(DMSCs),characterized by apoptotic cells.Namely,1×10^(6) MSCs in the preparation contained about 5×10^(4) DMSCs.We found that the treatment with even 5×10^(4) DMSCs alone had the equal therapeutic effects as with 1×10^(6) MSCs.This protective effect of the dead MSCs alone was confirmed in four mouse models,including concanavalin A(ConA)-and carbon tetrachloride(CCI4)-induced acute liver injury,LPS-induced lung injury and spinal cord injury.We also found that the infused MSCs died by apoptosis in vivo.Furthermore,the therapeutic effect was attributed to the elevated level of phosphatidylserine(PS)upon the injection of MSCs or DMSCs.The direct administration of PS liposomes(PSLs)mimic apoptotic cell fragments also exerted the protective effects as MSCs and DMSCs.The Mer tyrosine kinase(MerTK)deficiency or the knockout of chemokine receptor C-C motif chemokine receptor 2(CCR2)reversed these protective effects of MSCs or DMSCs.These results revealed that DMSCs alone in the therapeutic stem cell preparation or the apoptotic cells induced in vivo may exert the same immunomodulatory property as the'living MSCs preparation"through releasing PS,which was further recognized by MerTK and participated in modulating immune cells.

关键词： therapeutic protective preparation

乙二胺-N-丙基改性硅胶的可控键合制备及其在银杏酸脱除中的应用研究

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山东科学 2024年第1期37卷 51-58页

作者：潘翔宇靳钊关彤陈贝怡青岛科技大学高分子科学与工程学院山东青岛266045

优化了乙二胺-N-丙基键合硅胶(PSA)键合量可控的制备工艺,考察了PSA制备的批次重复性,并进行PSA制备的中试放大实验。采用红外光谱、元素分析及电位滴定法对所制备的PSA进行性能评价,结果表明:在3460 cm^(-1)处出现了N—H伸缩振动峰,在2... 详细信息

优化了乙二胺-N-丙基键合硅胶(PSA)键合量可控的制备工艺,考察了PSA制备的批次重复性,并进行PSA制备的中试放大实验。采用红外光谱、元素分析及电位滴定法对所制备的PSA进行性能评价,结果表明:在3460 cm^(-1)处出现了N—H伸缩振动峰,在2960 cm^(-1)和2860 cm^(-1)处出现了—CH的不对称和对称伸缩振动峰,708 cm^(-1)处出现了—NH2的变形振动吸收峰,表明乙二胺-N-丙基成功接枝到硅胶表面;随着制备体系中硅烷化试剂比例的增加,碳、氮和氢元素的含量以及电位滴定法得到的离子交换容量均呈现上升趋势,说明乙二胺-N-丙基官能团的键合量逐渐增加。将制备的PSA填充成分离纯化小柱,考察了不同键合量PSA对银杏叶提取物中银杏酸的脱除效率,结果表明:PSA对银杏酸有强吸附能力,可应用于银杏叶提取物中银杏酸的脱除,2^(#)、3^(#)、4^(#)和5^(#)PSA分离纯化柱的最大上样体积分别为21、22、23、24 mL,且脱除效率随乙二胺-N-丙基键合量的增加而升高。

关键词：乙二胺-N-丙基改性硅胶键合量银杏酸脱除