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

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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 *** process can provide basic support for the automatic construction of knowledge *** contrast to general texts,biomedical texts frequently contain numerous nested entities and local dependencies among these entities,presenting significant challenges to prevailing NER *** 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 *** then incorporates a Bidirectional Long Short-Term Memory network for capturing bidirectional semantic information,effectively addressing the issue of long-distance ***,the Global Pointer model is employed to comprehensively recognize all nested entities in the *** conduct extensive experiments on the Chinese medical dataset CMeEE and the results demonstrate the superior performance of RoBGP over several baseline *** 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

Discrimination of pharmacodynamic components and volatile compounds of Poria cocos cultivated with five different materials based on GC-IMS analysis

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Food Quality and Safety 2024年第1期8卷 135-144页

作者： Yinan Wang Fei Zhou Hui Wang Jinping Zhang Hongxia Xu research institute of Subtropical forestry Chinese Academy of ForestryHangzhouChina Chun‘an County Thousand-island Lake Forest Farm HangzhouChina

Objectives:The chemical constituents of Poria cocos grown with different substrates vary significantly;thus,identifying and comparing their biomarkers are *** and Methods:Herein,the chemical constituents of Poria cocos obtained with five different substrates were assessed using gas chromatography–ion mobility spectrometry(GC-IMS),high-performance liquid chromatography and multivariate statistical ***:The content of moisture,ash,alcohol-soluble matter,and heavy metals,except for those of the miscellaneous wood Poria cocos,conform to the specifications defined in the Chinese Pharmacopoeia(Edition 2020),and the polysaccharide contents are all greater than 57%.Conclusions:Based on GC-IMS and the established fingerprints,87 compounds were detected,70 of which were identified in each *** statistical analysis revealed seven compounds(two esters,three alcohols,and two aldehydes),which could be considered as potential marker compounds for discrimination.

关键词： Poria cocos cultivation material pharmacodynamic component gas chromatography-ion mobility spectrometry(GC-IMS) volatile compound.

Hydrothermal hydrogenation/deoxygenation of palmitic acid to alkanes over Ni/activated carbon catalyst

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Chinese Journal of Chemical Engineering 2024年第2期66卷 8-18页

作者： Min Lin Yuhao Yan Xiaoxian Li Rui Li Yulong Wu MOE Engineering Center of forestry Biomass Materials and Bioenergy Beijing Forestry UniversityBeijing 100083China institute of Nuclear and new Energy technology Tsinghua UniversityBeijing 100084China Key Laboratory of Advanced Reactor Engineering and Safety of Ministry of Education Tsinghua UniversityBeijing 100084China

To produce paraffin from hydrogenation/deoxygenation of palmitic acid,model compound of bio-oil obtained by hydrothermal liquefaction(HTL)of microalgae has been an attractive focus in recent *** order to avoid energy-intensive separation process of water and bio-oil,it is of importance that deoxygenation upgrading of fatty acids under hydrothermal conditions similar to HTL ***,it is the first time to explore the application of activated carbon(AC)-supported non-noble-metal catalysts,such as Ni,Co,and Mo,and so on,in the hydrothermal hydrogenation/deoxygenation of long-chain fatty acids,and the obtained Ni/AC-H(the Ni/AC was further H_(2)pre-reduced)is one of the best *** addition,it is found that the catalytic activity can be further improved by H_(2)pre-reduction of *** results that are more low valences of nickel and oxygen vacancy can be obtained after H_(2)pre-reduction,thus significant promoting the deoxygenation especially the decarbonylation pathway of fatty *** total alkanes yield can reaches 95.9%at optimal conditions(280℃,360 min).This work confirmed that the low-priced AC-supported non-noble-metal catalysts have great potential compared with the noble-metal catalyst,in hydrothermal upgrading of bio-oil.

关键词： Bio-oil Fatty acids Deoxygenation Hydrothermal upgrading

Variability of urban fractional vegetation cover and its driving factors in 328 cities in China

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Science China Earth Sciences 2024年第2期67卷 466-482页

作者： Fei FENG Xin YANG Baoquan JIA Xiaoting LI Xianwen LI Chengyang XU Kaicun WANG research Centre of Urban forestry Key Laboratory for Silviculture and Forest Ecosystem of State Forestry and Grassland AdministrationBeijing Forestry UniversityBeijing100083China State Key Laboratory of Earth Surface Processes and Resource Ecology Beijing Normal UniversityBeijing100875China research institute of forestry Chinese Academy of ForestryBeijing100091China School of Architecture Tsinghua UniversityBeijing100084China College of Urban and Environmental Sciences Sino-French Institute for Earth System ScienceInstitute of Carbon NeutralityPeking UniversityBeijing100871China

Urban green space promotes the health of urban residents,enhances urban ecosystem biodiversity,mitigates environmental pollution,and attenuates urban heat island ***,urban vegetation cover is highly heterogeneous and difficult to *** this study,the variation of urban fractional vegetation cover(FVC)in 328 cities in China from 1990 to2022 was quantified based on Landsat satellite data at a 30-m *** was found that from 1990 to 2005,due to increases in building density and impervious surfaces in cities,the national mean urban vegetation cover decreased from 0.38 to ***2005,urban vegetation cover began to reverse,reaching 0.45 in *** increasing trend was most pronounced in newly built urban *** decrease in average urban vegetation cover before 2005 was mainly due to the expansion of low vegetation cover areas,while the increase in urban vegetation cover after 2005 manifested as the expansion of high vegetation cover *** reversal in the trend of urban vegetation cover change after 2004 is related to the gradual implementation of national policies requiring increased urban green space *** urban gross domestic product(GDP)showed the highest correlation with changes in urban vegetation *** large and medium-sized cities,the top three factors influencing vegetation cover were GDP,urban population,and ***,for cities in arid/semi-arid regions,changes in vegetation cover were more sensitive to climatic factors(such as precipitation).Although the urban vegetation cover in China has substantially increased in recent years,the urban green space in small-sized cities and in the old urban districts of large-sized cities still have room to improve.

关键词： Urban vegetation Urban vegetation cover Urbanization Remote sensing

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

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Plant Diversity 2024年第3期46卷 294-308页

作者： Zhen Yang Lisong Liang Weibo Xiang Lujun Wang Qinghua Ma Zhaoshan Wang Key Laboratory of Tree Breeding and Cultivation National Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091China National Engineering research Center of Eco-Environment Protection for Yangtze River Economic Belt China Three Gorges CorporationBeijing 100083China Rare Plants research institute of Yangtze River China Three Gorges CorporationYichang 443133China research institute of Economic Forest Cultivation and Processing Anhui Academy of ForestryHefei 230031China

Global climate change has increased concerns regarding biodiversity ***,many key conservation issues still required further research,including demographic history,deleterious mutation load,adaptive evolution,and putative *** we generated the first chromosome-level genome of the endangered Chinese hazelnut,Corylus chinensis,and compared the genomic signatures with its sympatric widespread ***-C yunnanensis *** found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in *** genomics revealed that both *** and the *** complex had diverged into two genetic lineages,forming a consistent pattern of southwestern-northern *** size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene,whereas the widespread northern lineages have remained stable(***) or have even recovered from population bottlenecks(*** complex) during the *** with ***-C. yunnanensis complex,*** showed significantly lower genomic diversity and higher inbreeding ***,*** carried significantly fewer deleterious mutations than ***-C. yunnanensis complex,as more effective purging selection reduced the accumulation of homozygous *** also detected signals of positive selection and adaptive introgression in different lineages,which facilitated the accumulation of favorable variants and formation of local ***,both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of ***,our study provides critical insights into lineage differentiation,local adaptation,and the potential for future recovery of endangered trees.

关键词： Conservation genomics Demographic history Inbreeding Genetic load Runs of homozygosity Local adaptation

Nonlinear Registration of Brain Magnetic Resonance Images with Cross Constraints of Intensity and Structure

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Computers, Materials & Continua 2024年第5期79卷 2295-2313页

作者： Han Zhou HongtaoXu Xinyue Chang Wei Zhang Heng Dong Digital Fujian research institute of Big Data forAgriculture and forestry Fujian Agriculture and Forestry UniversityFuzhou350002China College of Computer and Information Science Fujian Agriculture and Forestry UniversityFuzhou350002China

Many deep learning-based registration methods rely on a single-stream encoder-decoder network for computing deformation fields between 3D ***,these methods often lack constraint information and overlook semantic consistency,limiting their *** address these issues,we present a novel approach for medical image registration called theDual-VoxelMorph,featuring a dual-channel cross-constraint *** innovative network utilizes both intensity and segmentation images,which share identical semantic information and feature *** encoder-decoder structures calculate deformation fields for intensity and segmentation images,as generated by the dual-channel cross-constraint *** design facilitates bidirectional communication between grayscale and segmentation information,enabling the model to better learn the corresponding grayscale and segmentation details of the same anatomical *** ensure semantic and directional consistency,we introduce constraints and apply the cosine similarity function to enhance semantic *** on four public datasets demonstrates superior performance compared to the baselinemethod,achieving Dice scores of 79.9%,64.5%,69.9%,and 63.5%for OASIS-1,OASIS-3,LPBA40,and ADNI,respectively.

关键词： Medical image registration cross constraint semantic consistency directional consistency dual-channel

Functional Optical Fiber Sensors Detecting Imperceptible Physical/Chemical Changes for Smart Batteries

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Nano-Micro Letters 2024年第8期16卷 268-308页

作者： Yiding Li Li Wang Youzhi Song Wenwei Wang Cheng Lin Xiangming He institute of Nuclear and new Energy technology Tsinghua UniversityBeijing 100084People’s Republic of China National Engineering research Center of Electric Vehicles Beijing Institute of Technology(BIT)Beijing 100081People’s Republic of China Shenzhen Automotive research institute of BIT(Shenzhen research institute of National Engineering research Center of Electric Vehicles) Shenzhen 518118People’s Republic of China

The battery technology progress has been a contradictory process in which performance improvement and hidden risks *** the battery is still a“black box”,thus requiring a deep understanding of its internal *** battery should“sense its internal physical/chemical conditions”,which puts strict requirements on embedded sensing *** paper summarizes the application of advanced optical fiber sensors in lithium-ion batteries and energy storage technologies that may be mass deployed,focuses on the insights of advanced optical fiber sensors into the processes of one-dimensional nano-micro-level battery material structural phase transition,electrolyte degradation,electrode-electrolyte interface dynamics to three-dimensional macro-safety *** paper contributes to understanding how to use optical fiber sensors to achieve“real”and“embedded”*** the inherent advantages of the advanced optical fiber sensor,it helps clarify the battery internal state and reaction mechanism,aiding in the establishment of more detailed *** advancements can promote the development of smart batteries,with significant importance lying in essentially promoting the improvement of system ***,with the help of smart batteries in the future,the importance of consistency can be weakened or even *** application of advanced optical fiber sensors helps comprehensively improve the battery quality,reliability,and life.

关键词： Smart battery Advanced embedded optical fiber sensor Battery internal physical/chemical state Quality-reliability-life characteristic

2-O-β-D-Glucopyranosyl-L-ascorbic acid,an ascorbic acid derivative isolated from the fruits of Lycium barbarum L.,ameliorates high fructose-induced neuroinflammation in mice:involvement of gut microbiota and leaky gut

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Food Science and Human Wellness 2024年第1期13卷 241-253页

作者： Wei Dong Yujia Peng Guijie Chen Zhiyong Xie Weiqi Xu Wangting Zhou Jia Mi Lu Lu Yi Sun Xiaoxiong Zeng Youlong Cao Yamei Yan College of Food Science and technology Nanjing Agricultural UniversityNanjing 210095China institute of Wolfberry Engineering technology National Wolfberry Engineering Research CenterNingxia Academy of Agriculture and Forestry SciencesYinchuan 750002China

Western diet(rich in highly refined sugar and fat)can induce a range of metabolic dysfunctions in animals and humans,including neuroinflammation and cognitive function *** and cognitive impairment,two critical pathological characteristics of Alzheimer’s disease,have been closely associated with microbial alteration via the gut-brain ***,the present study aimed to investigate the influence of 2-O-β-D-glucopyranosyl-L-ascorbic acid(AA-2βG)isolated from the fruits of Lycium barbarum on preventing the high-fructose diet(HFrD)induced neuroinflammation in *** was found that AA-2βG prevented HFr D-induced cognitive ***-2βG also predominantly enhanced the gut barrier integrity,decreased lipopolysaccharide entry into the circulation,which subsequently countered the activation of glial cells and neuroinflammatory *** beneficial effects were transmissible by horizontal fecal microbiome transplantation,transferring from AA-2βG fed mice to HFr D fed ***,AA-2βG exerted neuroprotective effects involving the enrichment of Lactobacillus and Akkermansia,potentially beneficial intestinal *** present study provided the evidence that AA-2βG could improve indices of cognition and neuroinflammmation via modulating gut dybiosis and preventing leaky *** a potential functional food ingredient,AA-2βG may be applied to attenuate neuroinflammation associated with Western-style diets.

关键词： Neuroinfl ammation Gut microbiota Leaky gut Lipopolysaccharide Fecal microbiome transplantation 2-O-β-D-Glucopyranosyl-L-ascorbic acid

Aboveground carbon sequestration of Cunninghamia lanceolata forests:Magnitude and drivers

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Forest Ecosystems 2024年第1期11卷 32-41页

作者： Chen Wang Shuguang Liu Yu Zhu Andrew R.Smith Ying Ning Deming Deng National Engineering Laboratory for Applied technology of forestry&Ecology in South China Central South University of Forestry and TechnologyChangsha 410004China technology Innovation Center for Ecological Conservation and Restoration in Dongting Lake Basin Ministry of Natural ResourcesChangsha 410007China College of Life Science and technology Central South University of Forestry and TechnologyChangsha 410004China School of Ecology and Environment Hainan UniversityHaikou 570228China School of Natural Sciences Bangor UniversityGwyneddLL572UWUK College of forestry Central South University of Forestry and TechnologyChangsha 410004China Hunan Prospecting Designing&research General institute for Agriculture Forestry&IndustryChangsha 410007China

Understanding the spatial variation,temporal changes,and their underlying driving forces of carbon sequestration in various forests is of great importance for understanding the carbon cycle and carbon management *** carbon density and sequestration in various Cunninghamia lanceolata forests,extensively cultivated for timber production in subtropical China,vary with biodiversity,forest structure,environment,and cultural factors remain poorly explored,presenting a critical knowledge gap for realizing carbon sequestration supply potential through *** on a large-scale database of 449 permanent forest inventory plots,we quantified the spatial-temporal heterogeneity of aboveground carbon densities and carbon accumulation rates in Cunninghamia lanceolate forests in Hunan Province,China,and attributed the contributions of stand structure,environmental,and management factors to the heterogeneity using quantile age-sequence analysis,partial least squares path modeling(PLS-PM),and hot-spot *** results showed lower values of carbon density and sequestration on average,in comparison with other forests in the same climate zone(i.e.,subtropics),with pronounced spatial and temporal ***,quantile regression analysis using carbon accumulation rates along an age sequence showed large differences in carbon sequestration rates among underperformed and outperformed forests(0.50 and 1.80 Mg·ha^(-1)·yr^(-1)).PLS-PM demonstrated that maximum DBH and stand density were the main crucial drivers of aboveground carbon density from young to mature ***,species diversity and geotopographic factors were the significant factors causing the large discrepancy in aboveground carbon density change between low-and high-carbon-bearing *** analysis revealed the importance of culture attributes in shaping the geospatial patterns of carbon *** work highlighted that retaining largesized DBH trees and increasing shade-t

关键词： Carbon density Carbon accumulation rate Forest age Spatial variation Cultural influence