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Haplotype-resolved chromosome-level genome of hexaploid Jerusalem artichoke provides insights into its origin,evolution,and inulin metabolism

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Plant Communications 2024年第3期5卷 77-92页

作者： Sen Wang Anqi Wang Rong Chen dong xu Hengchao Wang Fan Jiang Hangwei Liu Wanqiang Qian Wei Fan Guangdong Laboratory for Lingnan Modern Agriculture(Shenzhen Branch) Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518120China Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization Agro-Biological Gene Research CenterGuangdong Academy of Agricultural SciencesGuangzhou 510640China College of Agronomy Qingdao Agricultural UniversityQingdao 266109China

Jerusalem artichoke(Helianthus tuberosus)is a global multifunctional *** has wide applications in the food,health,feed,and biofuel industries and in ecological protection;it also serves as a germplasm pool for breeding of the global oil crop common sunflower(Helianthus annuus).However,biological studies of Je-rusalem artichoke have been hindered by a lack of genome sequences,and its high polyploidy and large genome size have posed challenges to genome ***,we report a 21-Gb chromosome-level as-sembly of the hexaploid Jerusalem artichoke genome,which comprises 17 homologous groups,each with 6 *** found multiple large-scale chromosome rearrangements between Jerusalem artichoke and common sunflower,and our results show that the hexaploid genome of Jerusalem artichoke was formed by a hybridization event between a tetraploid and a diploid Helianthus species,followed by chromosome doubling of the hybrid,which occurred approximately 2 million years ***,we iden-tied more copies of actively expressed genes involved in inulin metabolism and showed that these genes may still be undergoing loss of function or sub-or *** genomic resources will pro-mote further biological studies,breeding improvement,and industrial utilization of Helianthus crops.

关键词： Helianthus tuberosus hexaploid genome hybridization origin chromosome rearrangement inulin metabolism genes

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Amplifying protection against acute lung injury:Targeting both inflammasome and cGAS-STING pathway by Lonicerae Japonicae Flos-Forsythiae Fructus drug pair

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Chinese Herbal Medicines 2024年第3期16卷 422-434页

作者： Junjie Li Ming dong Qing Yao xu dong Yuanyuan Chen Jincai Wen Yingjie xu Zhixin Wu Xiaomei Zhao Ye Xiu Xiaoyan Zhan Zhaofang Bai Xiaohe Xiao Chengde Medical University Chengde 067000China Department of Hepatology The Fifth Medical Center of PLA General HospitalBeijing 100039China China Military Institute of Chinese Materia Fifth Medical Center of Chinese PLA General HospitalBeijing 100039China National Key Laboratory of Kidney Diseases The Fifth Medical Center of PLA General HospitalBeijing 100039China School of Stomatology Heilongjiang Key Lab of Oral Biomedicine Materials and Clinical Application&Experimental Center for Stomatology EngineeringJiamusi UniversityJiamusi 154007China Southern Medical University Guangzhou 510515China

Objective:Acute lung injury(ALI)is characterized by inflammation and currently lacks an efficacious pharmacological *** medicine combination of Lonicerae Japonicae Flos(LJF)and Forsythiae Fructus(FF)demonstrates combined properties in its anti-infective,anti-inflammatory,and therapeutic effects,particularly in alleviating respiratory *** previous studies,Chinese medicine has shown promising efficacy in lipopolysaccharides(LPS)-induced ***,there have been no reports of LJF and FF pairing for lung *** aim of this study is to compare the efficacy of herb pair Lonicerae Japonicae Flos-Forsythiae Fructus(LF)with LJF or FF alone in the treatment of ALI,and to explore whether LJF and FF have a combined effect in the treatment of lung injury,along with the underlying mechanism ***:A total of 36 mice were divided into six groups(control,model,LJF,FF,LF,dexamethasone)based on the treatments they received after undergoing sham-operation/LPS tracheal instillation.H&E staining and pulmonary edema indexes were used to evaluate lung injury *** exudate cells(AECs)were counted based on cell count in bronchoalveolar lavage fluid(BALF),and neutrophil percentage in BALF was measured using flow ***(MPO)activity in BALF was measured using enzyme-linked immunosorbent assay(ELISA),while the production of IL-1β,TNF-α,and IL-6 in the lung and secretion level of them in BALF were detected by quantitative polymerase chain reaction(qPCR)and *** effect of LJF,FF,and LF on the expression of Caspase-1 and IL-1βproteins in bone marrow derived macrophages(BMDMs)supernatant was assessed using Western blot method under various inflammasome activation *** addition,the concentration of IL-1βand changes in lactatedehydrogenase(LDH)release levels in BMDMs supernatant after LJF,FF,and LF administration,respectively,were measured using ***,the effects of LJF,FF and LF on STING and IRF3 phosphor

关键词： acute lung injury BMDMS inflammasomes Lonicerae Japonicae Flos-Forsythia Fructus drug pair STING

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Optimal proportioning of iron ore in sintering process based on improved multi-objective beluga whale optimisation algorithm

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Journal of Iron and Steel Research International 2024年第7期31卷 1597-1609页

作者： Zong-ping Li xu-dong Li xue-tong Yan Wu Wen Xiao-xin Zeng Rong-jia Zhu Ya-hui Wang Ling-zhi Yi Zhongye Changtian International Engineering Co. Ltd.Changsha 410205HunanChina College of Automation and Electronic Information Xiangtan UniversityXiangtan 411105HunanChina College of Electrical and Information Engineering Hunan UniversityChangsha 410082HunanChina

Proportioning is an important part of sintering,as it affects the cost of sintering and the quality of sintered *** address the problems posed by the complex raw material information and numerous constraints in the sintering process,a multi-objective optimisation model for sintering proportioning was established,which takes the proportioning cost and TFe as the optimisation ***,an improved multi-objective beluga whale optimisation(IMOBWO)algorithm was proposed to solve the nonlinear,multi-constrained multi-objective optimisation *** algorithm uses the con-strained non-dominance criterion to deal with the constraint problem in the ***,the algorithm employs an opposite learning strategy and a population guidance mechanism based on angular competition and two-population competition strategy to enhance convergence and population *** actual proportioning of a steel plant indicates that the IMOBWO algorithm applied to the ore proportioning process has good convergence and obtains the uniformly distributed Pareto ***,compared with the actual proportioning scheme,the proportioning cost is reduced by 4.3361¥/t,and the TFe content in the mixture is increased by 0.0367%in the optimal compromise ***,the proposed method effectively balances the cost and total iron,facilitating the comprehensive utilisation of sintered iron ore resources while ensuring quality assurance.

关键词： Sintering process Proportioning Iron ore Multi-objective beluga whale optimisation algorithm Proportioning cost

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Construction of RuO2-Ru/MoO2@carbon cloth bifunctional electrocatalyst for efficient overall water splitting

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Rare Metals 2024年第10期43卷 5095-5104页

作者： Jia-Lin Cai Jing-Yi Fan xu-dong Zhang Xin Xie Wan-Yu Tian Xin-Gang Zhang Jie Ding Yu-Shan Liu College of Material Henan Key Laboratory of Aeronautical Materials and Application TechnologyZhengzhou University of Aeronautics The Green Catalysis Center and College of ChemistryZhengzhou University

Efficient bifunction electrocatalyst is extremely interesting for electrochemical overall water splitting （OWS）.Herein,a new RuO2-Ru/MoO2@CC（RRM/CC） bifunctional electrocatalyst was prepared via a solid phase reaction *** obtain a suitable precursor for SPR,MoS2nanosheets and RuO2nanoparticles （NPs）were sequentially loaded onto carbon cloth conductive ***,the prepared RuO2/MoS2/CC precursor was sealed in a furnace and annealed in Ar to trigger the redox *** SPR,active RuO2-Ru/MoO2units containing metal–metal oxide interfaces were formed on CC substrate *** optimized RRM/CC sample annealed at 400℃ exhibited a overpotential of 13 m V for hydrogen evolution reaction （HER） and 231 mV for oxygen evolution reaction （OER） at 10 mA·cm-2under alkaline condition,respectively,which can be deduced to the modulated electronic structure and unique hierarchica *** addition,a low cell voltage of 1.48 V for OWS was required at 10 mA·cm-2under alkaline condition Meanwhile,RRM/CC exhibited excellent pH-independent durability.

关键词： Bifunctional Electrocatalyst Overall water splitting Ru RuO2

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Construction and performance test of charged particle detector array for MATE

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Nuclear Science and Techniques 2024年第8期35卷 92-100页

作者： Xiao‑Bin Li Long‑Hui Ru Zhi‑Chao Zhang Bing‑Feng Lv Ning‑Tao Zhang Jin‑Long Zhang Chen‑Gui Lu Bing‑Shui Gao Jun‑Bing Ma Fu‑Shuai Shi Satoru Terashima Xiao‑dong xu Zhen Bai Shi‑Wei xu Yan‑Yun Yang Hooi‑Jin Ong Xiao‑dong Tang Institute of Modern Physics(IMP) Chinese Academy of SciencesLanzhou 730000China School of Nuclear Science and Technology University of Chinese Academy of SciencesBeijing 100049China Research Center for Nuclear Physics Osaka UniversityIbarakiOsaka 567‑0047Japan RIKEN Nishina Center WakoSaitama 351‑0198Japan Joint Department for Nuclear Physics Lanzhou University and Institute of Modern PhysicsChinese Academy of SciencesLanzhou 730000China

A charged particle array named MATE-PA,which serves as an auxiliary detector system for a Multi-purpose Active-target Time projection chamber used in nuclear astrophysical and exotic beam Experiments(MATE),was *** array comprised of 20 single-sided strip-silicon detectors covering approximately 10%of the solid *** detectors facilitated the detection of reaction-induced charged particles that penetrate the active volume of the *** performance of MATE-PA has been experimentally studied using an alpha source and a 36-MeV 14 N beam injected into the MATE chamber on the radioactive ion beam line in Lanzhou(RIBLL).The chamber was filled with a gas mixture of 95%4 He and 5%CO_(2) at a pressure of 500 *** results indicated good separation of light-charged particles using the forward double-layer silicon detectors of *** energy resolution of the Si detectors was deduced to be approximately 1%(σ)for an energy loss of approximately 10 MeV caused by theα*** inclusion of MATE-PA improves particle identification and increases the dynamic range of the kinetic energy of charged particles,particularly that of theαparticles,up to approximately 15 MeV.

关键词： Silicon detector array Active target Time projection chamber

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CentIER:Accurate centromere identification for plant genomes

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Plant Communications 2024年第10期5卷 12-15页

作者： dong xu Jinbao Yang Huaming Wen Wenle Feng Xiaohui Zhang Xingqi Hui Junyang Yue Yun xu Fei Chen Weihua Pan Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China Rubber Research Institute Chinese Academy of Tropical Agricultural ScienceHaikouHainan 571101China School of Computer Science and Technology University of Science and Technology of ChinaHefeiAnhui 230026China College of Informatics Huazhong Agricultural UniversityWuhanHubei 430070China School of Horticulture Anhui Agricultural UniversityHefeiAnhui 230026China Nan Fan College Hainan UniversitySanyaHainan 572000China

Dear Editor,Centromeres,the basis for cell division,offer essential insights into cell dynamics,genome stability,and evolutionary processes(McKinley and Cheeseman,2016).Because of ultra-high complexity,high-quality sequences of centromeric regions have long been difficult to obtain,hindering studies of centromere function,evolution,and variation.

关键词： hinder insight stability

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Inferring the Effects of Protein Variants on Protein-Protein Interactions with Interpretable Transformer Representations

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Research 2024年第2期2023卷 473-489页

作者： Zhe Liu Wei Qian Wenxiang Cai Weichen Song Weidi Wang Dhruba Tara Maharjan Wenhong Cheng Jue Chen Han Wang dong xu Guan Ning Lin Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina Shanghai Key Laboratory of Psychotic Disorders ShanghaiChina School of Information Science and Technology Institute of Computational BiologyNortheast Normal UniversityChangchunChina Department of Electrical Engineering and Computer Science University of MissouriColumbiaMO 65211USA Christopher S.Bond Life Sciences Center University of MissouriColumbiaMO 65211USA

Identifying pathogenetic variants and inferring their impact on protein-protein interactions sheds light on their functional consequences on *** by the availability of experimental data on the consequences of protein interaction,most existing methods focus on building models to predict changes in protein binding ***,we introduced MIPPI,an end-to-end,interpretable transformer-based deep learning model that learns features directly from sequences by leveraging the interaction data from *** was specifically trained to determine the types of variant impact(increasing,decreasing,disrupting,and no effect)on protein-protein *** demonstrate the accuracy of MIPPI and provide interpretation through the analysis of learned attention weights,which exhibit correlations with the amino acids interacting with the ***,we showed the practicality of MIPPI in prioritizing de novo mutations associated with complex neurodevelopmental disorders and the potential to determine the pathogenic and driving ***,we experimentally validated the functional impact of several variants identified in patients with such ***,MIPPI emerges as a versatile,robust,and interpretable model,capable of effectively predicting mutation impacts on protein-protein interactions and facilitating the discovery of clinically actionable variants.

关键词： consequences weights versatile

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Mechanical characteristics and reservoir stimulation mechanisms of the Gulong shale oil reservoirs, the northern Songliao Basin

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Petroleum Science 2024年第3期21卷 2023-2036页

作者： Si-Wei Meng Jia-Ping Tao Tian-Jiao Li dong-xu Li Su-Ling Wang Liu Yang Xin Liu Li-Hao Liang He Liu PetroChina Research Institute of Petroleum Exploration Development Beijing100083China National Key Laboratory of Continental Shale Oil Daqing 163002HeilongjiangChina Dalian University of Technology Dalian116024LiaoningChina PetroChina Daqing Oilfield Co.Ltd. Daqing163002HeilongjiangChina Northeast Petroleum University Daqing163002HeilongjiangChina China University of Mining and Technology(Beijing) Beijing100083China

Shale oil of the Qingshankou Formation of the Gulong Sag,the northern Songliao Basin,represents the first attempt at large-scale development of pure-shale-type shale oil in *** integrating the multiscale refined reservoir characterization with macro-micro-scale mechanical testing,it is clarified that the Gulong shale is characterized by high clay mineral content,high rock plasticity,highly-developed bedding,and prominent mechanical anisotropy.A three-dimensional(3D)fracture propagation model of hydraulic fracturing was built for the Gulong shale,which fully captures the hydraulic fracture distribution pattern affected by the high bedding density,in-situ stress,and fracturing treatment *** research showed that due to influences of bedding,hydraulic fracturing in the Gulong shale forms a complex fracture morphology featuring the main fracture with multiple perpendicular branches that have different lengths(like the outdoor directional TV antenna);however,the vertical propagation of fractures is inhibited,and the fracture height is commonly less than 10 *** limited stimulated reservoir volume(SRV)is the main problem facing the fracturing stimulation of the Gulong shale *** density has vital effects on fracture morphology,so case-specific fracturing designs shall be developed for shale intervals with different bedding development *** reservoirs with welldeveloped bedding,it is suggested to properly increase the perforation cluster spacing and raise the volume and proportions of viscous fluids of the pad,so as to effectively promote vertical fracture propagation and improve reservoir stimulation *** study integrates multi-scale fine reservoir characterization and macro-micro-scale mechanical testing,as well as the construction and numerical simulation of hydraulic fracturing models for high-density layered shale reservoirs,providing a new approach and methodological framework for the fracturing research of high-density layer

关键词： Shale oil Hydraulic fracturing High bedding density Fracture propagation model

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The hard X-ray nanoprobe beamline at the SSRF

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Nuclear Science and Techniques 2024年第7期35卷 79-88页

作者： Yan He Hui Jiang dong-xu Liang Zhi-Sen Jiang Huai-Na Yu Hua Wang Cheng-Wen Mao Jia-Nan Xie Ai-Guo Li Shanghai Advanced Research Institute Chinese Academy of SciencesShanghai201210China

The hard X-ray nanoprobe beamline BL13U is a phase-Ⅱ beamline project at the Shanghai Synchrotron Radiation *** beamline aims to enable comprehensive experiments at high spatial resolutions ranging from 50 to 10 nm. The X-ray energy range of the beamline, 5–25 keV, can detect most elements in the periodic table. Two operating modes were designed to accommodate the experimental requirements of high-energy resolution or high photon flux, respectively. X-ray nanofluorescence, nanodiffraction, and coherent diffraction imaging are developed as the main experimental techniques for BL13U. This paper describes the beamline optics, end station configurations, experimental methods under development, and preliminary test results. This comprehensive overview aims to provide a clear understanding of the beamline capabilities and potential applications.

关键词： Shanghai synchrotron radiation facility Hard X-ray nanoprobe X-ray nanofocusing

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Key genes and regulatory networks for diabetic retinopathy based on hypoxia-related genes:a bioinformatics analysis

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International Journal of Ophthalmology(English edition) 2024年第8期17卷 1411-1417页

作者： Cai-Han Yu Cai-Xia Wu Dai Li Lan-Lan Gong xu-dong Lyu Jie Yang Department of Ophthalmology Xianning Central HospitalThe First Affiliated Hospital of Hubei University of Science and TechnologyXianning 437100Hubei ProvinceChina School of Pharmacy Xianning Medical CollegeHubei University of Science and TechnologyXianning 437100Hubei ProvinceChina School of Optometry Hubei University of Science and TechnologyXianning 430071Hubei ProvinceChina

AIM:To prevent neovascularization in diabetic retinopathy(DR)patients and partially control disease ***:Hypoxia-related differentially expressed genes(DEGs)were identified from the GSE60436 and GSE102485 datasets,followed by gene ontology(GO)functional annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment *** candidate drugs were screened using the CMap ***,a protein-protein interaction(PPI)network was constructed to identify hypoxia-related hub genes.A nomogram was generated using the rms R package,and the correlation of hub genes was analyzed using the Hmisc R *** clinical significance of hub genes was validated by comparing their expression levels between disease and normal groups and constructing receiver operating characteristic curve(ROC)***,a hypoxia-related miRNA-transcription factor(TF)-Hub gene network was constructed using the NetworkAnalyst online ***:Totally 48 hypoxia-related DEGs and screened 10 potential candidate drugs with interaction relationships to upregulated hypoxia-related genes were identified,such as ruxolitinib,meprylcaine,and *** addition,8 hub genes were also identified:glycogen phosphorylase muscle associated(PYGM),glyceraldehyde-3-phosphate dehydrogenase spermatogenic(GAPDHS),enolase 3(ENO3),aldolase fructose-bisphosphate C(ALDOC),phosphoglucomutase 2(PGM2),enolase 2(ENO2),phosphoglycerate mutase 2(PGAM2),and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3(PFKFB3).Based on hub gene predictions,the miRNA-TF-Hub gene network revealed complex interactions between 163 miRNAs,77 TFs,and hub *** results of ROC showed that the except for GAPDHS,the area under curve(AUC)values of the other 7 hub genes were greater than 0.758,indicating their favorable diagnostic ***:PYGM,GAPDHS,ENO3,ALDOC,PGM2,ENO2,PGAM2,and PFKFB3 are hub genes in DR,and hypoxia-related hub genes exhibited favorable diagnostic perform

关键词： diabetic retinopathy hypoxia-related genes hub genes miRNA-TF-Hub gene drug prediction

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