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GenBase: A Nucleotide Sequence Database

Genomics, Proteomics & Bioinformatics 2024年第3期22卷 107-112页

作者： Congfan Bu Xinchang Zheng Xuetong Zhao Tianyi Xu Xue Bai Yaokai Jia Meili Chen Lili Hao Jingfa Xiao Zhang Zhang Wenming Zhao Bixia Tang Yiming Bao national Genomics Data center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key Laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China human genome Sequencing {2. Baylor College of MedicineHoustonTX 77030USA University of chinese Academy of Sciences Beijing 100049China

The rapid advancement of sequencing technologies poses challenges in managing the large volume and exponential growth of sequence data efficiently and on *** address this issue,we present GenBase(https://***/genbase),an open-access data repository that follows the International Nucleotide Sequence Database Collaboration(INSDC)data standards and structures,for efficient nucleotide sequence archiving,searching,and *** a core resource within the national Genomics Data {2.(NGDC)of the China national {2. for Bioinformation(CNCB;https://***),GenBase offers bilingual submission pipeline and services,as well as local submission assistance in *** also provides a unique Excel format for metadata description and feature annotation of nucleotide sequences,along with a real-time data validation system to streamline sequence *** of April 2.,2.2.,GenBase received 68,2.1 nucleotide sequences and 689,574 annotated protein sequences across 414 species from 2.19 *** of these,63,614(93%)nucleotide sequences and 62.,640(90%)annotated protein sequences have been released and are publicly accessible through GenBase’s web search system,File Transfer Protocol(FTP),and Application Programming Interface(API).Additionally,in collaboration with INSDC,GenBase has constructed an effective data exchange mechanism with GenBank and started sharing released nucleotide ***,GenBase integrates all sequences from GenBank with daily updates,demonstrating its commitment to actively contributing to global sequence data management and sharing.

关键词： Nucleotide sequence Database GenBase GenBank INSDC

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Traditional chinese medicine for the treatment of immune-related nephropathy:A review

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Acta Pharmaceutica Sinica B 2024年第1期14卷 38-66页

作者： Pu Jiang Changliang Yao De-an Guo School of Pharmacy Nanjing University of Chinese MedicineNanjing 210023China shanghai Research center for Modernization of Traditional {2. Medicine National Engineering Research Center of TCM Standardization TechnologyShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China

Immune-related nephropathy(IRN)refers to immune-response-mediated glomerulonephritis and is the main cause of end-stage renal *** pathogenesis of IRN is not fully understood;therefore,treatment is *** chinese medicines(TCMs)have potent clinical effects in the treatment of the IRN conditions immunoglobulin A nephropathy,lupus nephropathy,and diabetic *** underlying mechanisms mainly include its inhibition of inflammation;improvements to renal interstitial fibrosis,oxidative stress,autophagy,apoptosis;and regulation of *** this review,we summarize the clinical symptoms of the three IRN subtypes and the use of TCM prescriptions,herbs,and bioactive compounds in treating IRN,as well as the potential mechanisms,intending to provide a reference for the future study of TCM as IRN treatments.

关键词： IgA nephropathy Diabetic nephropathy Lupus nephritis Traditional chinese medicine Immunity Pathogenesis Mechanism Pathophysiology

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Medcheck:A novel software for automated de-formulation of traditional chinese medicine(TCM)prescriptions by liquid chromatography-mass spectrometry

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Journal of Pharmaceutical Analysis 2024年第6期14卷 930-932页

作者： Xiao-lan Li Jian-qing Zhang Yun Li Xuan-jing Shen Huan-ya Yang Lin Yang Meng Xu Qi-rui Bi Chang-liang Yao De-an Guo shanghai Research center for Modernization of Traditional {2. Medicine National Engineering Research Center of TCM Standardization TechnologyShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203China b University of chinese Academy of Sciences Beijing100049China

Prescriptions are the main clinical application of traditional chinese medicines(TCMs).Common forms include chinese patent medicines,Kampo formulas,and hospital decoctions.A new pre-scription called“famous classical formulas”is recently developed and expected to boom in the *** constituent me-dicinal plants in prescriptions is critical for new drug development and quality control[1],which could avoid safety issues from adulteration or substandard ingredients,as seen in the notorious Longdan Xiegan Pill event.

关键词： medicines formulation prescription

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Digitization of Astronomical Photographic Plates of China and Astrometric Measurement of Single-exposure Plates

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Research in Astronomy and Astrophysics 2024年第5期24卷 103-116页

作者：商正君于涌王亮亮杨美婷杨静沈世银刘敏徐权峰崔辰州樊东卫唐正宏赵建海 shanghai Astronomical Observatory Chinese Academy of SciencesShanghai 200030China University of chinese Academy of Sciences Beijing 100049China Key Lab for Astrophysics Shanghai200234China national Astronomical Observatories Chinese Academy of SciencesBeijing 100101China national Astronomical Data center Chinese Academy of SciencesBeijing 100101China

From the mid-19th century to the end of the 2.th century, photographic plates served as the primary detectors for astronomical observations. Astronomical photographic observations in China began in 1901, and over a century, a total of approximately 30,000 astronomical photographic plates were captured. These historical plates play an irreplaceable role in conducting long-term, time-domain astronomical research. To preserve and explore these valuable original astronomical observational data, shanghai Astronomical Observatory has organized the transportation of plates, taken during nighttime observations from various stations across the country, to the Sheshan Plate Archive for centralized preservation. For the first time, plate information statistics were calculated. On this basis, the plates were cleaned and digitally scanned, and finally digitized images were acquired for 2.,314 plates. In this study, using Gaia DR2.as the reference star catalog, astrometric processing was carried out successfully on 15,696 single-exposure plates, including object extraction, stellar identification,and plate model computation. As a result, for long focal length telescopes, such as the 40 cm double-tube refractor telescope, the 1.56 m reflector telescope at shanghai Astronomical Observatory, and the 1m reflecting telescope at Yunnan Astronomical Observatory, the astrometric accuracy obtained for their plates is approximately 0."1–0."3. The distribution of astrometric accuracy for medium and short focal length telescopes ranges from 0."3 to 1."0. The relevant data of this batch of plates, including digitized images and a stellar catalog of the plates, are archived and released by the {2. Astronomical Data center. Users can access and download plate data based on keywords such as station, telescope, observation year, and observed celestial coordinates.

关键词： methods data analysis-techniques image processing-astronomical databases miscellaneous-astrometry

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Plant genomic resources at national Genomics Data center:assisting in data-driven breeding applications

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aBIOTECH 2024年第1期5卷 94-106页

作者： Dongmei Tian Tianyi Xu Hailong Kang Hong Luo Yanqing Wang Meili Chen Rujiao Li Lina Ma Zhonghuang Wang Lili Hao Bixia Tang Dong Zou Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang Shuhui Song national Genomics Data center Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China CAS Key Laboratory of genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China University of chinese Academy of Sciences Beijing 100049China

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among *** various efforts in genomic data archiving,integrative analysis and value-added curation,the national Genomics Data center(NGDC),which is a part of the China national center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database *** dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research ***,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application *** intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

关键词： Plant-omics data Data repositories Data integration Knowledgebase Plant genomics

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In silico optimization of actuation performance in dielectric elastomercomposites via integrated finite element modeling and deep learning

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Theoretical & Applied Mechanics Letters 2024年第1期14卷 48-56页

作者： Jiaxuan Ma Sheng Sun Materials genome Institute Shanghai UniversityShanghai 200444China Zhejiang Laboratory Hangzhou 311100China shanghai Frontier Science center of Mechanoinformatics Shanghai UniversityShanghai 200444China

Dielectric elastomers(DEs)require balanced electric actuation performance and mechanical integrity under applied *** high dielectric particles as fillers provides extensive design space to optimize concentration,morphology,and distribution for improved actuation performance and material *** study presents an integrated framework combining finite element modeling(FEM)and deep learning to optimize the microstructure of DE *** first calculates actuation performance and the effective modulus across varied filler combinations,with these data used to train a convolutional neural network(CNN).Integrating the CNN into a multi-objective genetic algorithm generates designs with enhanced actuation performance and material modulus compared to the conventional optimization approach based on FEM approach within the same *** framework harnesses artificial intelligence to navigate vast design possibilities,enabling optimized microstructures for high-performance DE composites.

关键词： Dielectric elastomer composites Multi-objective optimization Finite element modeling Convolutional neural network

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On-surface photo-induced dechlorination

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chinese Chemical Letters 2024年第9期35卷 198-201页

作者： Yu He Hao Jiang Shaoxuan Yuan Jiayi Lu Qiang Sun Materials genome Institute Shanghai UniversityShanghai 200444China

On-surface Ullmann-type reaction,or the dehalogenated coupling,is arguably the most pivotal reaction in on-surface synthesis for the fabrications of carbon ***,the vast majority of works rely on activating the C-Br bond of aryl bromide which has a moderate bond dissociation *** C-Cl bond of aryl chloride has a higher dissociation energy and requires much higher thermal energy to break the *** this study,we have explored the on-surface photo-induced dechlorination and achieved the activation of three distinct aryl chlorines on the Au(111)surface with mild *** work enriches our understanding of on-surface photo-induced reactions and highlights the potential of photochemistry in realizing unconventional reactions.

关键词： On-surface synthesis Scanning probe microscopy On-surface photochemistry Dechlorination reaction

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How plants sense and respond to osmotic stress

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Journal of Integrative Plant Biology 2024年第3期66卷 394-423页

作者： Bo Yu Dai-Yin Chao Yang Zhao shanghai center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesThe Chinese Academy of SciencesShanghai 200032China Key Laboratory of Plant Carbon Capture The Chinese Academy of SciencesShanghai 200032China national Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyThe Chinese Academy of SciencesShanghai 200032China University of chinese Academy of Sciences Beijing 100049China

Drought is one of the most serious abiotic stresses to land *** sense and respond to drought stress to survive under water *** have studied how plants sense drought stress,or osmotic stress caused by drought,ever since Charles Darwin,and gradually obtained clues about osmotic stress sensing and signaling in *** stress is a physical stimulus that triggers many physiological changes at the cellular level,including changes in turgor,cell wall stiffness and integrity,membrane tension,and cell fluid volume,and plants may sense some of these stimuli and trigger downstream *** this review,we emphasized water potential and movements in organisms,compared putative signal inputs in cell wall-containing and cell wall-free organisms,prospected how plants sense changes in turgor,membrane tension,and cell fluid volume under osmotic stress according to advances in plants,animals,yeasts,and bacteria,summarized multilevel biochemical and physiological signal outputs,such as plasma membrane nanodomain formation,membrane water permeability,root hydrotropism,root halotropism,Casparian strip and suberin lamellae,and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple *** also discussed the core scientific questions,provided perspective about the future directions in this field,and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.

关键词： cell volume drought membrane tension osmotic stress turgor

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Rapid and chemoselective imidation of sulfides in aqueous buffer enabled by a novel guanidine-derived N-O reagent

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Science China Chemistry 2024年第6期67卷 1929-1934页

作者： Hanzheng Li Long Xu Jiajia Dong Key Laboratory of Organofluorine Chemistry Center for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200032China Institute of Translational Medicine National Facility for Translational Medicine(Shanghai)Shanghai Jiao Tong UniversityShanghai200240China School of Chemistry and Chemical Engineering Zhangjiang Institute for Advanced StudyShanghai Jiao Tong UniversityShanghai200240China shanghai Artificial Intelligence Laboratory Shanghai200232China

Herein we report the facile synthesis of a series of novel N-O reagents and identify N′-di-Boc-N′′-[(mesitylsulfonyl)oxy]-guanidine as an efficient imidating *** reagent is synthetically scalable and bench-stable,yet it shows unprecedented reactivity and chemoselectivity towards S(II)in buffer/hexafluoroisopropanol(HFIP)system,to generate a new class of Nguanyl *** transformation of N-guanyl sulfilimines to N-guanyl sulfoximines provides us a chance to investigate these rarely reached compounds,which are shown to be versatile precursors to a variety of N-heterocyclic and *** work provides an addition to the tool box of both sulfur imidation and guanidine synthesis,especially for the need of rapid and selective modifications of sulfur(II)center under biocompatible conditions.

关键词： sulfur imidation N-O reagent

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Improving flangeability of multiphase steel by increasing microstructural homogeneity

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Journal of Iron and Steel Research International 2024年第7期31卷 1736-1745页

作者： Xiao-yu Yang Yong-gang Yang Xing Fang Han-long Zhang Zhen-li Mi Beijing Advanced Innovation center for Materials genome Engineering Institute of Engineering TechnologyUniversity of Science and Technology BeijingBeijing 100083China shanghai Baosteel Group Corp.Technology center Shanghai 201900China

Multiphase microstructure significantly increases the strength,usually at the expense of flangeability because of lacking microstructure *** further improve the strength-flangeability of multiphase steel,the microstructural homogeneity was advanced by adjusting the hard martensite/austenite(M/A)*** strength-flangeability was measured via uniaxial tensile tests and hole expansion *** microstructures were characterized using a scanning electron microscope equipped with an electron backscatter diffraction detector and a transmission electron *** tests were supplementally used to quantitatively reveal the microstructural homogeneity of the *** show that the adjusted multiphase steel achieves an excellent ultimate tensile strength(~800 MPa)and flangeability(~135%hole expansion ratio).A promising homogeneous multiphase microstructure was obtained by controlling undercooled austenite transformed at about 600℃.This microstructure consists of soft polygonal ferrite,blocky bainitic ferrite,and hard M/A *** volume fraction of M/A islands is around 5%,and the average size is less than l *** nanoindentation analysis indicated that the participation of M/A islands impressively influenced the microstructural *** strain partition and better mechanical compatibility were present in the adjusted multiphase steel since the plasticity initiation started late,which resulted in a positive ***,avoiding M/A islands distributed in the chain along the rolling direction on the matrix hindered the possibility of voids coalescing into cracks and stabilized the flanging performance.

关键词： Multiphase steel Flangeability Martensite/austenite island-Microstructural homogeneity-Microstructure Compact strip production process

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