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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 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

Pre-combustion mercury removal with co-production of hydrogen via coal electrolysis

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Journal of Environmental Sciences 2024年第2期136卷 382-389页

作者： Xiang Lyu Runming Tao Tianyu Zhang Chemical and Biomolecular Engineering Department Ohio University165 Stocker CenterAthensOH45701USA Electrification and Energy Infrastructures division Oak Ridge National LaboratoryOak RidgeTN37831USA Beijing Key Lab for Source Control Technology of Water Pollution College of Environmental Science and EngineeringBeijing Forestry UniversityBeijing 100083China Engineering Research Center for Water Pollution Source Control&Eco-remediation College of Environmental Science and EngineeringBeijing Forestry UniversityBeijing 100083China

Pre-combustion mercury removal via coal electrolysis was performed and investigated on a bench-scale coal electrolytic cell(CEC)systemically,and factorial design was used to determine the effect of different operating conditions(coal particle size,operating temperature,operating cell voltage,and flow rate of slurry)on the percentage of mercury removal,percentage of ash removal,and dry heating value change.The results showed that the operating cell voltage,as well as the interaction between operating cell voltage and coal particle size,are significant factors in the percentage of mercury removal.There is no significant factor in the percentage of ash removal and the dry heating value change,but the coal could be purified while keeping the dry heating value almost constant after electrolysis.A co-product of hydrogen could be produced during coal electrolysis with 50%lower energy consumption compared with water electrolysis.Meanwhile,a mechanism for mercury removal in coal was proposed.The facts indicate that coal electrolysis is a promising method for precombustion mercury removal.

关键词： Pre-combustion mercury removal Coal electrolysis Ash removal Dry heating value Hydrogen production

Rice ONAC016 promotes leaf senescence through abscisic acid signaling pathway involving OsNAP

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The Crop Journal 2024年第3期12卷 709-720页

作者： Eunji Gi Sung-Hwan Cho Suk-Hwan Kim Kiyoon Kang Nam-Chon Paek Department of Agriculture Forestry and BioresourcesPlant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea division of Life Sciences Incheon National UniversityIncheon 22012Republic of Korea

Senescence-induced NAC(senNAC)TFs play a crucial role in senescence during the final stage of leaf development.In this study,we identified a rice senNAC,ONAC016,which functions as a positive regulator of leaf senescence.The expression of ONAC016 increased rapidly in rice leaves during the progression of dark-induced and natural senescence.The onac016-1 knockout mutant showed a delayed leaf yellowing phenotype,whereas the overexpression of ONAC016 accelerated leaf senescence.Notably,ONAC016 expression was upregulated by abscisic acid(ABA),and thus detached leaves of the onac016-1 mutant remained green much longer under ABA treatment.Quantitative RT-PCR analysis showed that ONAC016 upregulates the genes associated with chlorophyll degradation,senescence,and ABA signaling.Yeast one-hybrid and dual-luciferase assays revealed that ONAC016 binds directly to the promoter regions of OsNAP,a key gene involved in chlorophyll degradation and ABA-induced senescence.Taken together,these results suggest that ONAC016 plays an important role in promoting leaf senescence through the ABA signaling pathway involving OsNAP.

关键词： Rice ONAC016 OsNAP Leaf senescence Abscisic acid signaling

Long-term grape powder feed attenuates experimental ischemic stroke by altering gut microbiota and metabolome

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Food Science and Human Wellness 2024年

作者： Haojie Jin Decao Yang Jia Guo Baohui Xu Yu Fu Lixiang Xue Yan Wang The Key Laboratory for Silviculture and Conservation of Ministry of Education The College of forestry Beijing forestry University Institute of Medical Innovation and Research Peking University Third Hospital Department of Neurology Peking University Third Hospital Centre of Hypertension Care Shanxi Medical University First Hospital Medical Research Centre Peking University Third Hospital Department of Surgery division of Vascular Surgery Stanford University School of Medicine Stanford

Increasing evidence indicates that a healthy diet plays a protective role against ischemic stroke injury. As an antioxidant food， grape powder has been shown to have a neuroprotective function after ischemic injury. In the current research， we aimed to determine whether regular grape powder (GP) feeding before brain damage plays a protective role against ischemic damage and its potential mechanism. Mice had grape powder in drinking water for 4 weeks. Then， fecal samples were collected for 16S RNA analysis and metabolite profiling. Ischemic stroke was triggered using GP prefeed mice by MCAo (middle cerebral artery occlusion) to compare the stroke-induced infarction size to the drinking water (DW) group. The data showed that 4 weeks of GP pretreatment significantly decreased the ischemic infarct size. Meanwhile， GP treatment altered the gut microbiota by enriching the population of Lachnospiraceae and enhancing a gut metabolite called fiestin， which belongs to the flavonoid group. Mechanistically， we demonstrated that fiestin could inhibit LPS-induced proinflammatory macrophage polarization in vitro. We also showed that regular grape power feed could decrease stroke-induced neuroinflammation in vivo. In conclusion， our study demonstrated that 4 weeks of GP feeding attenuates experimental ischemic stroke via the gut-brain-immune axis.

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Is the Sundarbans of Bangladesh in a State of Pollution?

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Open Journal of forestry 2024年第1期14卷 19-41页

作者： Mahmood Hossain Chameli Saha Sanjoy Saha Hawlader Mohammed Nurul Islam Mushfiq Ahmed Tanvir Ahmed Abdul Halim Farhad Sikder Md. Mutasim Billah forestry and Wood Technology Discipline Khulna University Khulna Bangladesh Institute for Integrated Studies on the Sundarbans and Coastal Ecosystems (IISSCE) Khulna University Khulna Bangla-desh Ecology Forestry and Biodiversity Division Center for Environmental and Geographic Information Services (CEGIS) Dhaka Bangladesh

The Sundarbans is the world’s most extensive natural mangrove forest and home to various natural resources. The population in the vicinity has increased, causing more dependency on the resources of the Sundarbans. The increasing industrialization, urbanization, aquaculture, intensive agricultural practices, seaports, tourism facilities, and so on in the peripheral areas of the Sundarbans have made significant changes in the surrounding and upstream land uses of the Sundarbans. This situation may have detrimental influences on the ecosystem components of the Sundarbans. Therefore, it is highly demanded to prepare a piece of baseline information or database of different sources of pollution and their present status in the various components of the Sundarbans. This effort helps to identify issues and concerns, determine the key elements of the ecosystem to monitor the level or overall quality of the Sundarbans ecosystem. The present study systematically collects the potential sources of pollution, types, and current levels in the ecosystem components of the Sundarbans using academic databases, libraries, and online resources. Discharge of industrial waste into water, soil and air, heavy metal pollution, use of agrochemicals, oil (refined and crude) pollution, plastic materials from urban areas, and tourism are the major issues and concerns related to the sustainability of the Sundarbans ecosystem. The air quality of the Sundarbans is in good condition with 0 - 50 AQI of Bangladesh. While BOD, COD, TDS, TSS varied from 2.0 to 3.8 mg/L, 21.6 to 416 mg/L, 146.9 to 24,100 mg/L and 54 to 155 mg/L, respectively. Soil EC, organic carbon, total nitrogen, and total phosphorus ranged from 3.01 - 5.82 mS/cm, 1.41% - 2.69%, 0.51 - 1.05 mg/g, and 0.32 - 0.51 mg/g respectively. The air, water and soil quality parameters varied with the sites and seasons and not much at the state of contamination. Indeed, we must pay much attention to the Sundarbans’ air, water and soil quality with the massive and progressive change of the nearby

关键词： Ecosystem Mangroves Monitoring Pollution Soil Sundarbans

When Fleeing Matters:Differences in Escape Behaviours of Three Northeast Asian Anurans

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Asian Herpetological Research 2024年第1期15卷 41-48页

作者： Yoonjung YI Zoljargal PUREVDORJ Irina MASLOVA Yikweon JANG Amaël BORZÉE Laboratory of Animal Behaviour and Conservation College of Life SciencesNanjing Forestry UniversityNanjing 210037JiangsuChina division of EcoScience and Department of Life Sciences Ewha Womans UniversitySeoul 03760Republic of Korea Department of Biology School of MathematicsMongolian State University of EducationUlaanbaatar 210648Mongolia Department of Forest and Environmental Resources Chungnam National UniversityDaejeon 34134Republic of Korea Federal Scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of Russian Academy of SciencesVladivostok 690022Russia

Prey species may have their own optimal escape strategy to balance predation risks and the energetic cost of fleeing.Some species have an advantage when maintaining a short fleeing distance,while others may favour an earlier escape based on microhabitat,size,or body condition.Here,we examined the escape behaviour of the three syntopic Northeast Asian anuran species:Mongolian toads(Strauchbufo raddei),Amur brown frogs(Rana amurensis),and Japanese treefrogs(Dryophytes japonicus)in Mongolia,Russia,China and DPR Korea.We examined flight initiation distance(FID;the distance from a potential predator to the point when the individual starts to flee)and distance fled(DF;distance between flight initiation and flight termination points)of each species and the effects of microhabitat,sex,and body size.Strauchbufo raddei and R.amurensis had a longer FID than D.japonicus,and S.raddei also had a longer DF than D.japonicus.These trends remained similar when dividing FID and DF by a size proxy(snout-vent length)for all individuals.This suggests that the treefrog D.japonicus used a strategy to stay immobile even when they were detected,and the toad S.raddei reacted quicker and more sensitively to predators despite the presence of toxin.Female S.raddei had a significantly longer FID than males suggesting that females are more sensitive to predation risk in this species,but body size was not significant for any of the three species.Our results indicate that the three sympatric species have different escaping strategies,likely related to differences in physiology and crypticity.

关键词： amphibian distance fled escape behaviour flight initiation distance predation

Salt-assisted vapor-liquid-solid growth of high-quality ultrathin nickel oxide flakes for artificial synapses in image recognition applications

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Nano Research 2024年第5期17卷 4622-4630页

作者： Hui Zhang Zongjie Shen Alei Li Lin Wang Qinan Wang Yunfei Li Yunlei Zhong Juntong Zhu Yong Zhang Mengjiao Han Dan Tian Chun Zhao Lixing Kang Qingwen Li School of Physical Science and Technology Shanghai Tech UniversityShanghai 201210China division of Advanced Materials Suzhou Institute of Nano-Tech and Nano-BionicsChinese Academy of SciencesSuzhou 215123China College of Energy Soochow Institute for Energy and Materials Innovationsand Key Laboratory of Advanced Carbon Materials and Wearable Energy Technologies of Jiangsu ProvinceSoochow UniversitySuzhou 215123China Songshan Lake Materials Laboratory Dongguan 523808China School of Advanced Technology Xi’an Jiaotong-Liverpool UniversitySuzhou 215123China College of Materials Science and Engineering Co-Innovation Center of Efficient Processing and Utilization of Forest ResourcesNanjing Forestry UniversityNanjing 210037China

Transition metal oxides have attracted intense interest owing to their abundant physical and chemical properties.The controlled preparation of large-area,high-quality two-dimensional crystals is essential for revealing their inherent properties and realizing high-performance devices.However,fabricating two-dimensional(2D)transition metal oxides using a general approach still presents substantial challenges.Herein,we successfully achieve highly crystalline nickel oxide(NiO)flakes with a thickness as thin as 3.3 nm through the salt-assisted vapor-liquid-solid(VLS)growth method,which demonstrated exceptional stability under ambient conditions.To explore the great potential of the NiO crystal in this work,an artificial synapse based on the NiO-flake resistive switching(RS)layer is investigated.Short-term and long-term synaptic behaviors are obtained with external stimuli.The artificial synaptic performance provides the foundation of the neuromorphic application,including handwriting number recognition based on artificial neuron network(ANN)and the virtually unsupervised learning capability based on generative adversarial network(GAN).This pioneering work not only paves new paths for the synthesis of 2D oxides in the future but also demonstrates the substantial potential of oxides in the field of neuromorphic computing.

关键词： nickel oxide(NiO)flakes vapor-liquid-solid(VLS)growth memristor synapse generative adversarial network(GAN)

Influence of edaphic factors on distribution and condition of Himalayan silver birch(Betula utilis D.Don)communities in the northwestern Indian Himalayas

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Journal of Mountain Science 2024年第2期21卷 590-606页

作者： Khashti DASILA Renu RAWAL Tanay BARMAN Sher Singh SAMANT Anita PANDEY Veena PANDE G.B.Pant National Institute of Himalayan Environment Almora 263643India Centre of Excellence on Sustainable Land Management Indian Council of Forestry Research and EducationDehradun 248006India Uttarakhand State Council for Science&Technology Dehradun 248015India Department of Biotechnology Graphic Era(Deemed to be University)Dehradun 248002India Department of Biotechnology Kumaun UniversityNainital 263136India

The basic concept of phytosociology is crucial for the assessment of species composition and dynamic ecological succession of forests supporting ecological services,functions,disturbance,and resilience that lead to the development of integrated areas such as ecological niche modeling and contribute to identifying the valuable bio-indicators which can be used in framing conservation and management planning.B.utilis is one of the most dominant tree species of treeline ecotone in the Himalayan Region.The species is also considered as indicator species for monitoring the past and recent climate change impact.The current study was carried out in the natural populations of B.utilis from the sub-alpine zone of North-western Indian Himalaya.The birch dominated forest harbors a total of 305 plant species comprising Angiosperms(51 families,160 genera and 277 species),Gymnosperms(03 families,05 genera and 07 species)and Pteridophytes(07 families,11 genera and 21 species)with Asteraceae,Ranunculaceae and Rosaceae as dominant family.Birch forests are found dominant in shady moist habitat and North West aspect.Geographical characteristics,anthropogenic and developmental activities affect the population structure of B.utilis and associated species.However,the species has fair regeneration status in the study area.The acidic nature of soil pH and spatial variation in edaphic characteristics may be due to geographical differences,rooting patterns and litter accumulation of below and above-ground vegetation.Biomass estimation of a representative population of B.utilis from each site showed that TAGBD,TCD and TBD were found maximum in ST3(Hamta Pass II site).The CCA analysis determined that environmental variables such as altitude,organic matter,available phosphorous,organic carbon,available nitrogen,and electrical conductivity played a significant role in determining tree species composition and distribution in B.utilis dominated forests.

关键词： Species composition Indicator species Biomass North-western Indian Himalaya Regeneration Environmental variables

Model development to estimate site index values for six major tree species in North Korea

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Journal of forestry Research 2023年第2期34卷 387-400页

作者： Sohee Park A-Ram Yang Eun-hee Kim Joongbin Lim division of global forestry Department of Future Forest StrategyNational Institute of Forest ScienceSeoul 02455Republic of Korea Forest ICT Research Center National Institute of Forest ScienceSeoul 02455Republic of Korea

Due to considerable deforestation in North Korea,there is a need to plan forest restoration programs based on scientific forest management.In this study,a methodology was developed for estimating the site index values of six major tree species and the forest productivity potential.The site index values of these tree species were derived in South Korea using the Chapman-Richards equation.These values were used with data from the 6th National Forest Inventory,which included 20 types of edaphic,topographic,and climatic factors,and random forest analysis—a widely used machine learning technique for spatial prediction—to develop a new model for estimating the site index values of these species across South Korea.The prediction accuracy of this model was evaluated using the root mean square error.The results show that the prediction accuracy was high,with a root mean square error of~1m.Moreover,the importance of the variables related to climate and geography was generally high.The proposed site index estimation model for six tree species was applied across North Korea,and its effectiveness tested by comparing the estimated values with those reported in literature from North Korea.The differences between the model outputs and recorded data in the northern alpine regions were presumably due to the lack of data for high-altitude regions in South Korea.This model is based on the determination of the suitability of tree species in restoration efforts.Therefore,it can contribute to the evaluation of forest productivity in North Korea and may help plan efficient forest restoration programs.

关键词： Environmental factors Forest productivity Machine learning North Korea Random forest Site index