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RoBGP:A Chinese Nested Biomedical Named Entity Recognition Model Based on RoBERTa and Global Pointer

Computers, Materials & Continua 2024年第3期78卷 3603-3618页

作者： Xiaohui Cui Chao Song dongmei li Xiaolong Qu Jiao Long Yu Yang Hanchao Zhang School of Information Science and Technology Beijing Forestry UniversityBeijing100083China Engineering Research Center for Forestry-Oriented Intelligent Information Processing of National Forestry and Grassland Administration Beijing100083China Division of Biostatistics Department of Population HealthGrossman School of MedicineNew York UniversityNew York10016USA

Named Entity Recognition(NER)stands as a fundamental task within the field of biomedical text mining,aiming to extract specific types of entities such as genes,proteins,and diseases from complex biomedical texts and categorize them into predefined entity types.This process can provide basic support for the automatic construction of knowledge bases.In contrast to general texts,biomedical texts frequently contain numerous nested entities and local dependencies among these entities,presenting significant challenges to prevailing NER models.To address these issues,we propose a novel Chinese nested biomedical NER model based on RoBERTa and Global Pointer(RoBGP).Our model initially utilizes the RoBERTa-wwm-ext-large pretrained language model to dynamically generate word-level initial vectors.It then incorporates a Bidirectional Long Short-Term Memory network for capturing bidirectional semantic information,effectively addressing the issue of long-distance dependencies.Furthermore,the Global Pointer model is employed to comprehensively recognize all nested entities in the text.We conduct extensive experiments on the Chinese medical dataset CMeEE and the results demonstrate the superior performance of RoBGP over several baseline models.This research confirms the effectiveness of RoBGP in Chinese biomedical NER,providing reliable technical support for biomedical information extraction and knowledge base construction.

关键词： Biomedicine knowledge base named entity recognition pretrained language model global pointer

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Multi-modal knowledge graph inference via media convergence and logic rule

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CAAI Transactions on Intelligence Technology 2024年第1期9卷 211-221页

作者： Feng lin dongmei li Wenbin Zhang Dongsheng Shi Yuanzhou Jiao Qianzhong Chen Yiying lin Wentao Zhu School of Information Science and Technology Beijing Forestry UniversityBeijingChina Engineering Research Center for Forestry-oriented Intelligent Information Processing National Forestry and Grassland AdministrationBeijingChina Michigan Technological University HoughtonMichiganUSA

Media convergence works by processing information from different modalities and applying them to different domains.It is difficult for the conventional knowledge graph to utilise multi-media features because the introduction of a large amount of information from other modalities reduces the effectiveness of representation learning and makes knowledge graph inference less effective.To address the issue,an inference method based on Media Convergence and Rule-guided Joint Inference model(MCRJI)has been pro-posed.The authors not only converge multi-media features of entities but also introduce logic rules to improve the accuracy and interpretability of link prediction.First,a multi-headed self-attention approach is used to obtain the attention of different media features of entities during semantic synthesis.Second,logic rules of different lengths are mined from knowledge graph to learn new entity representations.Finally,knowledge graph inference is performed based on representing entities that converge multi-media features.Numerous experimental results show that MCRJI outperforms other advanced baselines in using multi-media features and knowledge graph inference,demonstrating that MCRJI provides an excellent approach for knowledge graph inference with converged multi-media features.

关键词： logic rule media convergence multi-modal knowledge graph inference representation learning

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Resistance index and browning mechanism of apple peel under high temperature stress

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Horticultural Plant Journal 2024年第2期10卷 305-317页

作者： Hui Wang Shuhui Zhang Zidun Wang dongmei li Leiyu Yan Yifeng Feng Xiaojie liu Rongxin Chen Wenmin Fan Lulong Sun Zhengyang Zhao College of Horticulture Northwest A&F UniversityYanglingShaanxi 712100China College of Horticultural Science and Engineering Shandong Agricultural University State Key Laboratory of Crop BiologyTai'anShandong 271018China

Apples are one of the most important economic crops worldwide.Because of global warming and an aggravation of environmental,abnormally high temperatures occur frequently in fruit-growing season and seriously affect normal fruit growth and reduce fruit quality and yield.We took five-year-old Ruixue’(Qinfu 1×Pink Lady;CNA20151469.1) fruits as test materials,and the ambient temperature during fruit development was monitored.The results showed that during the fruit-growing season,especially during the rapid growth stage (July to August),the maximum daily temperature exceeded 30℃ and lasted for more than 40 days.To determine the effects of high temperature stress on the apple fruit resistance,we treated expanding,veraison,and maturity-period fruits at different temperatures.It was found that the fruits of the expanding period showed strong resistance to high temperature stress,whereas during veraison and maturity,fruit resistance to high temperature stress decreased,and the fruit peel browning phenotype appeared.Meanwhile,the content of malonaldehyde (MDA),hydrogen peroxide (H_(2)O_(2)),and superoxide anion (O._(2)^(-)) in the peel gradually increased with increasing temperature.The content of total phenols,flavanol,and flavonoids in the peel decreased substantially at 45℃.Moreover,it was found that polyphenol oxidase gene (MdPPO1) was most sensitive to high temperature stress in apple.Furthermore,transient and stable MdPPO1 overexpression significantly promoted peel browning.The transgenic materials were more sensitive to high temperatures,and browning was more severe compared to non-genetically modified organism (WT).Stable MdPPO1 knockout calli obtained via clustered regularly interspersed short palindromic repeats (CRISPR/Cas9) gene knockout technology reduced the browning phenotype,and the resultant fruits were not sensitive to the effects of high temperature stress.Thus,MdPPO1 expression may be a key factor of high temperature-related changes observed in the browning phenotype that provides a scientific theoreti

关键词： Malus domestica Borkh High temperature stress Peel Browning MdPPO1

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Belowground Bud Bank Is Insensitive to Short-Term Nutrient Addition in the Meadow Steppe of Inner Mongolia

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Phyton-International Journal of Experimental Botany 2024年第6期93卷 1129-1141页

作者： Jin Tao Jiatai Tian dongmei li Jinlei Zhu Qun Ma Zhiming Zhang Jungang Chen Yipeng liu Jianqiang Qian College of Forestry Henan Agricultural UniversityZhengzhou450002China Institute of Ecological Conservation and Restoration Chinese Academy of ForestryBeijing100093China Institute of Applied Ecology Chinese Academy of SciencesShenyang110164China Institute of Botany Chinese Academy of SciencesBeijing100093China liaoning Metallurgical Geological Exploration Research Institute Co. Anshan114038China

Human activities and industrialization have signiﬁcantly increased soil nutrients,such as nitrogen(N)and phos-phorus(P),profoundly impacting the composition and structure of plant community,as well as the ecosystem functions,especially in nutrient-limited ecosystems.However,as the key propagule pool of perennial grasslands,how belowground bud bank and its relationship with aboveground vegetation respond to short-term changes in soil nutrients was still unclear.In this study,we conducted a short-term(2021–2022)soil fertilization experiment with N addition(10 g N m^(-2) yr^(-1))and P addition(5 g N m^(-2) yr^(-1))in the meadow steppe of Inner Mongolia,China,to explore the responses of belowground bud bank,aboveground shoot population and their relationships(represented by the ratio of bud to shoot density-meristem limitation index(Mli))for the whole community and three plant functional groups(perennial rhizomatous grasses-PR,perennial bunchgrasses-PB,and perennial forbs-PF)to nutrient addition.The short-term nutrient addition had no signiﬁcant inﬂuences on belowground bud density,aboveground shoot density,and Mli of the whole plant community.Plant functional groups showed different responses to soil fertilization.Speciﬁcally,N addition signiﬁcantly increased the bud density and shoot density of PR,especially in combination with P addition.N addition reduced the shoot density of PF but had no inﬂuence on its bud density and Mli.Nutrient addition had signiﬁcant effects on the three indicators of PB.Our study indicates that the belowground bud bank and its relationship with aboveground vegetation in temperate meadow steppe are insensitive to short-term soil fertilization,but plant functional groups exhibit speciﬁc responses in terms of population regeneration,which implies that plant community composition and ecosystem functions will be changed under the ongoing global change.

关键词： Clonal trait population regeneration community dynamics soil resource availability nitrogen addition

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MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non-small cell lung cancer

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Cancer Innovation 2024年第3期3卷 33-48页

作者： Jing Chen Jing Yang Yufang liu Xu Zhao Juanjuan Zhao lin Tang Mengmeng Guo Ya Zhou Chao Chen dongmei li Zhenke Wen Guiyou liang lin Xu Special Key Laboratory of Gene Detection&Therapy of Guizhou Province ZunyiGuizhouChina Department of Immunology Zunyi Medical UniversityZunyiGuizhouChina Department of Medical Physics Zunyi Medical UniversityZunyiGuizhouChina Institute of Biomedical Soochow UniversitySuzhouJiangsuChina Department of Cardiovascular Surgery Affiliated Hospital of Guizhou Medical UniversityGuiyangGuizhouChina

Background:Angiogenesis plays an important role in the occurrence and development of non-small cell lung cancer(NSCLC).The atypical mitogen-activated protein kinase 4(MAPK4)has been shown to be involved in the pathogenesis of various diseases.However,the potential role of MAPK4 in the tumor angiogenesis of NSCLC remains unclear.Methods:Adult male C57BL/6 wild-type mice were randomly divided into the control group and p-siMAPK4 intervention group,respectively.The cell proliferation was analyzed with flow cytometry and immunofluorescence staining.The vascular density in tumor mass was analyzed by immuno-fluorescence staining.The expressions of MAPK4 and related signaling molecules were detected by western blot analysis and immunofluorescence staining,and so on.Results:We found that the expression of MAPK4,which was dominantly expressed in local endothelial cells(ECs),was correlated with tumor angiogenesis of NSCLC.Furthermore,MAPK4 silencing inhibited the proliferation and migration abilities of human umbilical vein ECs(HUVECs).QKHZC-2020-4Y156,QKH-JC-2018-1428,QKH-RC-2019-5612;Collaborative Innovation Center of Chinese Ministry of Education,Grant/Award Number:2020-39;Program for Science and Technology Joint Fund Project in Zunyi Science and Technology Bureau and Zunyi Medical University,Grant/Award Numbers:ZSKH-RPT-2020-6,ZSKH-HZ-2021-193;Graduate Research Fund of Zunyi Medical University,Grant/Award Number:2023-ZYK-171 Global gene analysis showed that MAPK4 silencing altered the expression of multiple genes related to cell cycle and angiogenesis pathways,and that MAPK4 silencing increased transduction of the extracellular regulated protein kinases 1/2(ERK1/2)pathway but not Akt and c-Jun n-terminal kinase pathways.Further analysis showed that MAPK4 silencing inhibited the proliferation and migration abilities of HUVECs cultured in tumor cell supernatant,which was accompanied with increased transduction of the ERK1/2 pathway.Clinical data analysis suggested that the higher expression of MAPK4 and CD34 were associa

关键词： angiogenesis endothelial cell MAPK4 NSCLC p-ERK1/2

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Synergistically enhanced dielectric, insulating and thermally conductive performances of sandwich PMMA based dielectric films

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Progress in Natural Science:Materials International 2024年第3期34卷 591-597页

作者： dongmei Zhang Yufan li Yuchao li Zhonggui Sun Hanxue Zhu Lujia Yang Yanhu Zhan Yankai li Shi Wang Jun-Wei Zha School of Mathematical Sciences Liaocheng University School of Materials Science and Engineering Liaocheng University State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM) Nanjing University of Posts & Telecommunications School of Chemistry and Biological Engineering University of Science and Technology Beijing

A tri-layered(B-G-B) dielectric films were simply prepared by alternatively spin-coating boron nitride/polymethylmethacrylate(BN/PMMA, B) and graphene nanosheets(GNS/PMMA, G) compound solutions. The structure, morphology, thermal conductivity, and particularly the dielectric and relaxation behaviors were systematically studied. Results showed that a good exfoliation and dispersion of BN and GNS can be simply achieved through intensive mechanical compounding with PMMA in the internal mixer. The dielectric constant and breakdown strength of the obtained 1-3-1(B-G-B) sandwich composite film reached 4.3(@1 kHz) and 458.6kV/mm, being 119 % and 113 % higher than that of pure PMMA, respectively. Furthermore, the overall thermal conductivity of sandwich 1-3-1 composite increased by 112 % due to the addition of thermally conductive BN and GNS. The sandwich design strategy provided an effective way of achieving good permittivity, high insulation, and improved thermal conductivity simultaneously, showing potential applications in the miniaturization and integration of electronic devices.

关键词： Breakdown strength Composites Dielectric constant Sandwich structure Thermal conductivity

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Pd cluster decorated free standing flexible cathode for high performance li-oxygen batteries

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Nano Research 2024年第4期17卷 2678-2686页

作者： liang Guo Guoliang Zhang Ruonan Yang dongmei Zhang Xiuqi Zhang Han Yu Xia li Feng Dang Key Laboratory for liquid-Solid Structure Evolution and Processing of Materials Ministry of EducationShandong UniversityJinan 250061China

As a promising candidate for the next generation energy storage system,rechargeable lithium-oxygen batteries(LOBs)still face substantial challenges caused by insulating discharge products that preclude their practical application.Exploring highly efficient cathode catalysts capable of facilitating formation/decomposition of discharge products is considered as an essential approach towards high performance LOBs.Herein,Pd decorated Te nanowires(Pd@Te NWs)were synthesized as advanced catalyst in LOBs to maximize Pd utilization and achieve synergistic effect,in which Pd clusters were uniformly grown on Te substrate though regulating the Pd:Te ratio.Meanwhile,Pd@Te nanowires assembled into an interpenetrating network-like structure by vacuum filtration and employed as flexible cathode,enabling LOBs achieved an ultralong 190 cycles stability and a superior specific capacity of 3.35 mAh·cm^(-2).Experimental studies and density functional theory(DFT)calculations reveal the excellent catalytic ability of Pd@Te and synergistic catalytic mechanism of Pd and Te,in which uniform electron distribution,extensive electron exchange,and large adsorption distance between Pd cluster and discharge products promote homogeneous adsorption/desorption of discharge products,while the high adsorption energy of Te substrate for li species reduces the initial dynamical energy barrier during discharging process.The current work provides viable strategy to design composite catalysts for flexible cathode of LOBs with synergistic catalytic effects.

关键词： flexible lithium-oxygen batteries Pd@Te synergistic catalysis cathode catalysts density functional theory(DFT)calculation

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Assimilating FY-4A AGRI Radiances with a Channel-Sensitive Cloud Detection Scheme for the Analysis and Forecasting of Multiple Typhoons

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Advances in Atmospheric Sciences 2024年第5期41卷 937-958页

作者： Feifei SHEN Aiqing SHU Zhiquan liU Hong li lipeng JIANG Tao ZHANG dongmei XU Key Laboratory of Meteorological Disaster Ministry of Education(KLME)/Joint International Research Laboratory of Climate and Environment Change(ILCEC)/Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters(CIC-FEMD)Nanjing University of Information Science&TechnologyNanjing 210044China Shanghai Typhoon Institute China Meteorological AdministrationShanghai 200030China China Meteorological Administration Basin Heavy Rainfall Key Laboratory/Hubei Key Laboratory for Heavy Rain Monitoring and Warning Research Institute of Heavy RainChina Meteorological AdministrationWuhan 430205China National Center for Atmospheric Research Boulder 80307COUSA State Key Laboratory of Severe Weather Chinese Academy of Meteorological SciencesBeijing 100081China National Meteorological Information Center Beijing 100081China Fujian Key Laboratory of Severe Weather and Key Laboratory of Straits Severe Weather China Meteorological AdministrationFuzhou 350001China

This paper presents an attempt at assimilating clear-sky FY-4A Advanced Geosynchronous Radiation Imager(AGRI)radiances from two water vapor channels for the prediction of three landfalling typhoon events over the West Pacific Ocean using the 3DVar data assimilation(DA)method along with the WRF model.A channel-sensitive cloud detection scheme based on the particle filter(PF)algorithm is developed and examined against a cloud detection scheme using the multivariate and minimum residual(MMR)algorithm and another traditional cloud mask–dependent cloud detection scheme.Results show that both channel-sensitive cloud detection schemes are effective,while the PF scheme is able to reserve more pixels than the MMR scheme for the same channel.In general,the added value of AGRI radiances is confirmed when comparing with the control experiment without AGRI radiances.Moreover,it is found that the analysis fields of the PF experiment are mostly improved in terms of better depicting the typhoon,including the temperature,moisture,and dynamical conditions.The typhoon track forecast skill is improved with AGRI radiance DA,which could be explained by better simulating the upper trough.The impact of assimilating AGRI radiances on typhoon intensity forecasts is small.On the other hand,improved rainfall forecasts from AGRI DA experiments are found along with reduced errors for both the thermodynamic and moisture fields,albeit the improvements are limited.

关键词： FY-4A AGRI radiance particle filter multiple typhoons data assimilation numerical weather prediction

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Protective mechanism of Coprinus comatus polysaccharide on acute alcoholic liver injury in mice,the metabolomics and gut microbiota investigation

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Food Science and Human Wellness 2024年第1期13卷 401-413页

作者： Jinyan Yu Jianguang Sun Min Sun Weidong li dongmei Qi Yongqing Zhang Chunchao Han School of Pharmacy Shandong University of Traditional Chinese MedicineJinan 250355China Hepatology Department of Affiliated Hospital of Shandong University of Traditional Chinese Medicine Jinan 250355China Experimental center Shandong University of Traditional Chinese MedicineJinan 250355China

Coprinus comatus polysaccharide(CCP)has significant hepatoprotective effect.To explore hepatoprotective mechanism of CCP,the study analyzed preventive effect of CCP on acute alcoholic liver injury in mice by histopathological examination and biochemical analysis.Simultaneously,hepatoprotective mechanism was also analyzed in conjunction with metabolomics and proliferation of gut microbiota.The results showed that CCP significantly decreased alanine aminotransferase(ALT),aspartate aminotransferase(AST)and triglyceride(TG)levels in serum of alcoholic liver disease(ALD)mice.Histopathological examination showed that CCP can significantly improve liver damage.Metabolomics results showed that there were significant differences in the level of metabolites in liver tissue of control group,ALD group and CCP group,including taurine,xanthosine,fumaric acid and arachidonic acid,among others.Metabolites pathways analysis showed that hepatoprotective effect of CCP was related to energy metabolism,biosynthesis of unsaturated fatty acids,amino acids metabolism and lipid metabolism.Additionally,CCP inhibited an increase in the number of Clostridium perfringens,Enterobacteriaceae and Enterococcus,and a decrease in the number of Lactobacillus and Bifidobacterium in the gut of ALD mice.All these findings suggested that CCP treatment reversed the phenotype of ethanol-induced liver injury and the associated metabolites pathways.

关键词： Coprinus comatus Polysaccharide Alcoholic liver disease Metabolomics Gut microbiota

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Toward Improved Accuracy in Quasi-Static Elastography Using Deep Learning

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Computer Modeling in Engineering & Sciences 2024年第4期139卷 911-935页

作者： Yue Mei Jianwei Deng dongmei Zhao Changjiang Xiao Tianhang Wang li Dong Xuefeng Zhu Department of Engineering Mechanics State Key Laboratory of Structural Analysis for Industrial EquipmentDalian University of TechnologyDalian116023China International Research Center for Computational Mechanics Dalian University of TechnologyDalian116023China DUT-BSU Joint Institute Dalian University of TechnologyDalian116023China Department of Automotive Engineering Tongji UniversityShanghai201804China *** SeattleWA98109USA School of Automotive Engineering Dalian University of TechnologyDalian116023China

Elastography is a non-invasive medical imaging technique to map the spatial variation of elastic properties of soft tissues.The quality of reconstruction results in elastography is highly sensitive to the noise induced by imaging measurements and processing.To address this issue,we propose a deep learning(DL)model based on conditional Generative Adversarial Networks(cGANs)to improve the quality of nonhomogeneous shear modulus reconstruction.To train this model,we generated a synthetic displacement field with finite element simulation under known nonhomogeneous shear modulus distribution.Both the simulated and experimental displacement fields are used to validate the proposed method.The reconstructed results demonstrate that the DL model with synthetic training data is able to improve the quality of the reconstruction compared with the well-established optimization method.Moreover,we emphasize that our DL model is only trained on synthetic data.This might provide a way to alleviate the challenge of obtaining clinical or experimental data in elastography.Overall,this work addresses several fatal issues in applying the DL technique into elastography,and the proposed method has shown great potential in improving the accuracy of the disease diagnosis in clinical medicine.

关键词： Nonhomogeneous elastic property distribution reconstruction deep learning finite element method inverse problem elastography conditional generative adversarial network

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