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BioTreasury:a community-based repository enabling indexing and rating of bioinformatics tools

Science China(Life Sciences) 2024年第2期67卷 221-229页

作者： qi Zhao Xin Zhou Jingxing Wu Jieyi Cai Xiaoqiong Bao Lin tang Chaoye Wang Chunlei Liu Yukai Wang Yuyan Teng Mohan Zheng Weiping Mu Zhixiang Zuo Yubin Xie Xiaotong Luo Jian Ren School of Life Sciences State Key Laboratory of Oncology in South ChinaCancer CenterGuangdong Provincial Clinical Research Center for CancerSun Yat-sen UniversityGuangzhou 510060China Institute of Precision Medicine The First Affiliated HospitalSun Yat-sen UniversityGuangzhou 510080China Guangdong Institute of Gastroenterology Department of General SurgeryGuangdong Provincial Key Laboratory of Colorectal and Pelvic Floor DiseasesThe Sixth Affiliated HospitalSun Yat-sen UniversityGuangzhou 510275China

The exponential growth of bioinformatics tools in recent years has posed challenges for scientists in selecting the most suitable one for their data analysis ***,to aid scientists in making informed choices,a community-based platform that indexes and rates bioinformatics tools is urgently *** this study,we introduce Bio Treasury(http://***),an integrated communitybased repository that provides an interactive platform for users and developers to share their experiences in various bioinformatics *** Treasury offers a comprehensive collection of well-indexed bioinformatics software,tools,and databases,totaling over 10,000 *** the past two years,we have continuously improved and maintained Bio Treasury,adding several exciting features,including creating structured homepages for every tool and user,a hierarchical category of bioinformatics tools and classifying tools using large language model(LLM).Bio Treasury streamlines the tool submission process with intelligent ***,Bio Treasury provides a wide range of social features,for example,enabling users to participate in interactive discussions,rate tools,build and share tool collections for the *** believe Bio Treasury can be a valuable resource and knowledge-sharing platform for the biomedical *** empowers researchers to effectively discover and evaluate bioinformatics tools,fostering collaboration and advancing bioinformatics research.

关键词： bioinformatics tools index tool database rating system large language model tool collections shari

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Credible and Facile Fluorometric Detection of Soybean Trypsin Inhibitor Activity with a Water-Soluble Poly(diphenylacetylene) Derivative

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Transactions of Tianjin University 2024年第4期30卷 305-313页

作者： Jiao tang Xiao tang Jiaxiang tang Wei qi qianwei Pan Jinhong Zeng Housheng Xia Jianping Zhou Zhongyi Sheng Junfeng Niu Zhejiang Tiantai Xianghe Industrial Co. Ltd.Taizhou 317200China Zhejiang Xianghe Track Fastener Research Institute Taizhou 317200China Shaoxing Institute for Food and Drug Control Shaoxing 312000China Key Laboratory of Chemical and Biological Processing Technology for Farm Products of Zhejiang Province School of Biological and Chemical EngineeringZhejiang University of Science and TechnologyHangzhou 310023China

Herein,a novel method for fl uorometric detection of soybean trypsin inhibitor(SBTI)activity based on a water-soluble poly(diphenylacetylene)derivative was *** quenching of the polymer via p-nitroaniline,produced from the trypsin-catalyzed decomposition of N-benzoyl-DL-arginine-4-nitroanilide hydrochloride(L-BAPA),was well described using the Stern-Volmer *** activity was quantitatively assessed based on changes in the fl uorescence intensity of the *** strategy has several advantages,such as high sensitivity and ease of ***,its applicability to other biochemical analyses is promising.

关键词： Fluorometric detection Soybean trypsin inhibitor Inhibition activity Fluorescence quenching

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融合实体信息的古汉语关系分类研究

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数据分析与知识发现 2024年第1期8卷 114-124页

作者：唐雪梅苏祺王军北京大学信息管理系北京100871 北京大学数字人文研究中心北京100871 北京大学外国语学院北京100871

【目的】将实体信息与预训练语言模型结合应用到古汉语关系分类任务中,构建古汉语关系分类模型。【方法】首先,在预训练模型输入层中使用特殊标记标出实体对的位置,同时在原关系句之后拼接实体类型描述句;其次,在预练语言模型的输出中... 详细信息

【目的】将实体信息与预训练语言模型结合应用到古汉语关系分类任务中,构建古汉语关系分类模型。【方法】首先,在预训练模型输入层中使用特殊标记标出实体对的位置,同时在原关系句之后拼接实体类型描述句;其次,在预练语言模型的输出中进一步提取实体语义信息;然后,通过CNN将每个字符相对于首尾实体的位置信息融入模型中;最后,将句表示、实体语义表示以及CNN输出拼接经过分类器得到关系标签。【结果】相较于仅使用预训练语言模型,本文模型在Macro F1指标上平均有3.5个百分点的提升。【局限】通过分析混淆矩阵发现本文模型在有相同实体类型组合的关系上容易出现预测错误。【结论】在预训练语言模型中结合实体信息能够提高古汉语关系分类的效果,且实验结果证明本文融合实体信息的方法是有效的。

关键词：古汉语关系抽取关系分类预训练语言模型实体信息

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Phage-displayed heptapeptide sequence conjugation significantly improves the specific targeting ability of antimicrobial peptides against Staphylococcus aureus

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mLife 2024年第2期3卷 251-268页

作者： Tao Wang Peng Tan qi tang Chenlong Zhou Yakun Ding Shenrui Xu Mengda Song Huiyang Fu Yucheng Zhang Xiaohui Zhang Yueyu Bai Zhihong Sun Xi Ma State Key Laboratory of Animal Nutrition and Feeding College of Animal Science and TechnologyChina Agricultural UniversityBeijingChina Luoyang Key Laboratory of Animal Genetic and Breeding College of Animal ScienceHenan University of Science and TechnologyLuoyangChina Key Laboratory of Innovative Utilization of Indigenous Cattle and Sheep Germplasm Resources(Co‐construction by Ministry and Province) Ministry of Agriculture and Rural AffairsZhengzhou UniversityZhengzhouChina Animal Health Supervision in Henan Province ZhengzhouChina Laboratory for Bio‐Feed and Molecular Nutrition Department of Animal Science and TechnologySouthwest UniversityChongqingChina

Broad-spectrum antibacterial drugs often lack specificity,leading to indiscriminate bactericidal activity,which can disrupt the normal microbial balance of the host flora and cause unnecessary cytotoxicity during systemic *** this study,we constructed a specifically targeted antimicrobial peptide against Staphylococcus aureus by introducing a phage-displayed peptide onto a broad-spectrum antimicrobial peptide and explored its structure–function relationship through one-factor ***2 obtained by screening based on the selectivity index and the targeting index showed specific killing ability against ***,SFK2 showed excellent biocompatibility in mice and piglet,and demonstrated significant therapeutic efficacy against *** *** conclusion,our screening of phage-derived heptapeptides effectively enhances the specific bactericidal ability of the antimicrobial peptides against ***,providing a theoretical basis for developing targeted antimicrobial peptides.

关键词： antimicrobial peptides membrane disruption mechanism microbial infection phage display technology Staphylococcus aureus

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农业大灾保险与粮食安全——基于农业大灾保险试点的准自然实验

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农业技术经济 2024年第4期 4-17页

作者：黄少安唐琦山东大学经济研究院济南250199

本文以农业大灾保险试点作为准自然实验,首先基于特征事实进行理论分析,提出研究假说:农业大灾保险试点显著提高粮食产量,且存在区域异质性。然后基于2013—2019年山东省县域面板数据,采用渐进双重差分法实证分析试点对粮食产量的影响,... 详细信息

本文以农业大灾保险试点作为准自然实验,首先基于特征事实进行理论分析,提出研究假说:农业大灾保险试点显著提高粮食产量,且存在区域异质性。然后基于2013—2019年山东省县域面板数据,采用渐进双重差分法实证分析试点对粮食产量的影响,而且进一步识别和验证试点政策在提高粮食产量时,通过促进农业规模化经营程度发挥了中介效应,通过影响农户投保积极性发挥了调节效应。本文认为应继续提高粮食作物保险保障水平,加快农业保险向收入险转变。同时,要持续提升农业规模化经营水平,培养农民保险意识,发挥农业保险在保障粮食安全等方面的积极作用。

关键词：农业大灾保险试点粮食产量规模经营渐进双重差分法

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先进优质生产要素赋能新质生产力的实践路径研究

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浙江工商大学学报 2024年第4期 98-110页

作者：唐琦张辉北京大学医学人文学院北京100191 北京大学经济与人类发展研究中心北京100871 北京大学经济学院北京100871

生产要素的质效提升和结合方式变化是新质生产力的重要特质,其创新性配置和顺畅流动能够高效赋能新质生产力的培育和发展。优质生产要素的先进性体现为要素对产业发展带动作用的创新式突破,优质性体现为要素之间结合方式的颠覆性发展及... 详细信息

生产要素的质效提升和结合方式变化是新质生产力的重要特质,其创新性配置和顺畅流动能够高效赋能新质生产力的培育和发展。优质生产要素的先进性体现为要素对产业发展带动作用的创新式突破,优质性体现为要素之间结合方式的颠覆性发展及要素生产效率的大幅提高。当前,为创新生产要素配置方式,应采取建设高标准生产要素市场、探索生产要素结合新方式、协同现代化产业体系建设的措施;为推动先进优质生产要素顺畅流动,应深化经济体制、科技体制改革,打通束缚发展的堵点卡点,用好两个市场两种资源。通过优化生产要素配置、发挥新型要素的纽带作用、推动科技成果加快转化,能够有效促进全要素生产率的大幅提升。

关键词：先进优质生产要素新质生产力实践路径全要素生产率

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Broadband and fabrication-tolerant 3-dB couplers with topological valley edge modes

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Light(Science & Applications) 2024年第8期13卷 1623-1630页

作者： Guo-Jing tang Xiao-Dong Chen Lu Sun Chao-Heng Guo Meng-Yu Li Zhong-Tao Tian Hou-Hong Chen Hong-Wei Wang qi-Yao Sun Ying-Di Pan Xin-Tao He Yi-Kai Su Jian-Wen Dong School of Physics&State Key Laboratory of Optoelectronic Materials and Technologies Sun Yat-sen UniversityGuangzhou 510275China State Key Laboratory of Advanced Optical Communication Systems and Networks Department of Electronic EngineeringShanghai Jiao Tong UniversityShanghai 200240China

3-dB couplers,which are commonly used in photonic integrated circuits for on-chip information processing,precision measurement,and quantum computing,face challenges in achieving robust performance due to their limited 3-dB bandwidths and sensitivity to fabrication *** address this,we introduce topological physics to nanophotonics,developing a framework for topological 3-dB *** couplers exhibit broad working wavelength range and robustness against fabrication dimensional *** leveraging valley-Hall topology and mirror symmetry,the photonic-crystal-slab couplers achieve ideal 3-dB splitting characterized by a wavelength-insensitive scattering *** analysis confirms the superiority on broad bandwidth of 48 nm and robust splitting against dimensional errors of 20 *** further propose a topological interferometer for on-chip distance measurement,which also exhibits robustness against dimensional *** extension of topological principles to the fields of interferometers,may open up new possibilities for constructing robust wavelength division multiplexing,temperature-drift-insensitive sensing,and optical coherence tomography applications.

关键词： topological splitting insensitive

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因地制宜发展新质生产力的重要原则研究

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教学与研究 2024年第9期 16-30页

作者：张辉唐琦北京大学经济学院北京大学医学人文学院

新质生产力是符合新发展理念的先进生产力质态，因地制宜是推动其发展的重要原则。为此，应确立“先立后破、因地制宜、分类指导”的发展方略，通过改造提升传统产业、培育壮大新兴产业、超前布局未来产业而完善现代化产业体系；根据各... 详细信息

新质生产力是符合新发展理念的先进生产力质态，因地制宜是推动其发展的重要原则。为此，应确立“先立后破、因地制宜、分类指导”的发展方略，通过改造提升传统产业、培育壮大新兴产业、超前布局未来产业而完善现代化产业体系；根据各地的资源禀赋、产业基础、科研条件找准比较优势，进而促使各地有选择地推动新产业、新模式、新动能的发展以统筹推进新型工业化。因地制宜是在坚持稳中求进工作总基调下，基于各地传统优势与发展规划，推动生产要素有序流转与高效集聚，协调推进科技创新和产业创新，实现劳动者、劳动资料、劳动对象优化组合和生产力跃升的重要方略。

关键词：新质生产力高质量发展先立后破因地制宜分类指导

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AGV Scheduling Optimization of Automated Port Based on Disruption Management

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Journal of Transportation Technologies 2024年第3期14卷 423-444页

作者： Ching-Kuei Kao qi-Er Ke King-Zoo tang Peng-Jung Lin Key Laboratory of LNG Industry Chain Fujian University of Technology Fuzhou China Department of Logistics Management Fujian University of Technology Fuzhou China Department of Information Management Taiwan Chung Cheng University Chiayi Metaverse and New Media College Yango University Fuzhou China

The recent rapid development of China’s foreign trade has led to the significant increase in waterway transportation and automated container ports. Automated terminals can significantly improve the loading and unloading efficiency of container terminals. These terminals can also increase the port’s transportation volume while ensuring the quality of cargo loading and unloading, which has become an inevitable trend in the future development of ports. However, the continuous growth of the port’s transportation volume has increased the horizontal transportation pressure on the automated terminal, and the problems of route conflicts and road locks faced by automated guided vehicles (AGV) have become increasingly prominent. Accordingly, this work takes Xiamen Yuanhai automated container terminal as an example. This work focuses on analyzing the interference problem of path conflict in its horizontal transportation AGV scheduling. Results show that path conflict, the most prominent interference factor, will cause AGV scheduling to be unable to execute the original plan. Consequently, the disruption management was used to establish a disturbance recovery model, and the Dijkstra algorithm for combining with time windows is adopted to plan a conflict-free path. Based on the comparison with the rescheduling method, the research obtains that the deviation of the transportation path and the deviation degree of the transportation path under the disruption management method are much lower than those of the rescheduling method. The transportation path deviation degree of the disruption management method is only 5.56%. Meanwhile, the deviation degree of the transportation path under the rescheduling method is 44.44%.

关键词： Automated Port Disruption Management Automated Guided Vehicle Scheduling Dijkstra Algorithm

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Synchronization and firing mode transition of two neurons in a bilateral auditory system driven by a high–low frequency signal

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Chinese Physics B 2024年第5期33卷 722-735页

作者： Charles Omotomide Apata 唐浥瑞周祎凡蒋龙裴启明 School of Physics and Optoelectronic Engineering Yangtze UniversityJingzhou 434023China

The FitzHugh–Nagumo neuron circuit integrates a piezoelectric ceramic to form a piezoelectric sensing neuron,which can capture external sound signals and simulate the auditory neuron *** piezoelectric sensing neurons are coupled by a parallel circuit consisting of a Josephson junction and a linear resistor,and a binaural auditory system is *** the non-singleness of external sound sources,the high–low frequency signal is used as the input signal to study the firing mode transition and synchronization of this *** is found that the angular frequency of the high–low frequency signal is a key factor in determining whether the dynamic behaviors of two coupled neurons are *** they are in synchronization at a specific angular frequency,the changes in physical parameters of the input signal and the coupling strength between them will not destroy their *** addition,the firing mode of two coupled auditory neurons in synchronization is affected by the characteristic parameters of the high–low frequency signal rather than the coupling *** asynchronous dynamic behavior and variations in firing modes will harm the auditory *** findings could help determine the causes of hearing loss and devise functional assistive devices for patients.

关键词： piezoelectric ceramic Josephson junction auditory neuron synchronization

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