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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 assignments.Therefore,to aid scientists in making informed choices,a community-based platform that indexes and rates bioinformatics tools is urgently needed.In 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 tools.Bio Treasury offers a comprehensive collection of well-indexed bioinformatics software,tools,and databases,totaling over 10,000 entries.In 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 auto-completion.Additionally,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 public.We believe Bio Treasury can be a valuable resource and knowledge-sharing platform for the biomedical community.It 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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Newcastle disease virus suppresses antigen presentation via inhibiting IL-12 expression in dendritic cells

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第3期25卷 254-270页

作者： Fulong NAN Wenlong NAN Xin YAN Hui WANG Shasha JIANG Shuyun ZHANG Zhongjie YU Xianjuan ZHANG Fengjun liu Jun LI xiaoqiong ZHOU Delei NIU Yiquan LI Wei WANG Ning SHI Ningyi JIN Changzhan XIE Xiaoni CUI He ZHANG Bin WANG Huijun LU Department of Special Medicine Department of Pathogenic BiologySchool of Basic MedicineQingdao UniversityQingdao 266071China China Animal Health and Epidemiology Center Qingdao 266032China Academician Workstation of Jilin Province Changchun University of Chinese MedicineChangchun 130117China Institute of Virology Wenzhou UniversityWenzhou 325035China College of Veterinary Medicine Jilin UniversityChangchun 130012China Changchun Veterinary Research Institute Chinese Academy of Agricultural SciencesChangchun 130122China Sino-Cell Biomed Co. Ltd.Qingdao 266000China

As a potential vectored vaccine,Newcastle disease virus(NDV)has been subject to various studies for vaccine development,while relatively little research has outlined the immunomodulatory effect of the virus in antigen presentation.To elucidate the key inhibitory factor in regulating the interaction of infected dendritic cells(DCs)and T cells,DCs were pretreated with the NDV vaccine strain LaSota as an inhibitor and stimulated with lipopolysaccharide(LPS)for further detection by enzyme-linked immunosorbent assay(ELISA),flow cytometry,immunoblotting,and quantitative real-time polymerase chain reaction(qRT-PCR).The results revealed that NDV infection resulted in the inhibition of interleukin(IL)-12p40 in DCs through a p38 mitogen-activated protein kinase(MAPK)-dependent manner,thus inhibiting the synthesis of IL-12p70,leading to the reduction in T cell proliferation and the secretion of interferon-(IFN-),tumor necrosis factor-α(TNF-α),and IL-6 induced by DCs.Consequently,downregulated cytokines accelerated the infection and viral transmission from DCs to T cells.Furthermore,several other strains of NDV also exhibited inhibitory activity.The current study reveals that NDV can modulate the intensity of the innate-adaptive immune cell crosstalk critically toward viral invasion improvement,highlighting a novel mechanism of virus-induced immunosuppression and providing new perspectives on the improvement of NDV-vectored vaccine.

关键词： Newcastle disease virus Dendritic cells Interleukin-12(IL-12) T cells Immunosuppression

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Pollination Biology of the Endangered Herbal Medicines Dendrobium chrysotoxum(Orchidaceae)

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Phyton-International Journal of Experimental Botany 2023年第7期92卷 1975-1986页

作者： Kai Luo Yanbing Bai Yan Jiang Guiling Li Min Jia Yongguo He Zhijun Yao Ziwei Xiao xiaoqiong liu Wenjie liu Shanshan Yin Zesheng Li Medicinal Plant Research Center Dehong Tropical Agriculture Research Institute of YunnanRuili678600China Human Resources Management Office The People’s Hospital of XiangyunXiangyun672100China

Pollination biology studies of the endangered herbal medicines Dendrobium chrysotoxum were conducted in natural pollination conditions using flower observation,pollinator observation and artificial pollination experiments.Populations of D.chrysotoxum with fragrance and nectar were pollinated by Ctenoplectra davidi Valhalla(Hymenoptera:Apidae)species.The floral structure of D.chrysotoxum adapted precisely to its pollinators.Flowers had a low capsule setting(0.17%)under natural conditions.However,compared to open pollination,artificial pollination experiments showed a significant increase in capsule setting,and D.chrysotoxum was cross-compatible and self-compatible,but there was pollinator limitation also.This study will provide important information for the preservation of this endangered species.

关键词： Breeding system Dendrobium chrysotoxum pollination pollination biology

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中药单体及复方干预Wnt信号通路调控骨代谢的研究进展

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中国药房 2024年第5期35卷 623-628页

作者：李婷张小琼刘梅王琴重庆医科大学药学院重庆400016 重庆中医药学院附属第一医院/重庆市中医院药剂科重庆400021

骨代谢是指骨骼重塑过程中发生的分解合成代谢,其平衡由骨吸收和骨形成调控。这种平衡稍有偏差就会导致各种骨骼疾病,如骨质疏松症、肾性骨病等。中药单体和复方在治疗骨代谢疾病方面具有一定优势。Wnt信号通路包括依赖β-连环蛋白(β-c... 详细信息

骨代谢是指骨骼重塑过程中发生的分解合成代谢,其平衡由骨吸收和骨形成调控。这种平衡稍有偏差就会导致各种骨骼疾病,如骨质疏松症、肾性骨病等。中药单体和复方在治疗骨代谢疾病方面具有一定优势。Wnt信号通路包括依赖β-连环蛋白(β-catenin)的经典Wnt信号通路和不依赖β-catenin的非经典Wnt信号通路,且2种通路均可通过调控骨形成和骨吸收来维持骨代谢平衡,对骨骼发育、骨量维持和骨重塑至关重要。近年来,多种中药单体(如芍药内酯苷、梓醇、淫羊藿苷)以及中药复方(如左归丸、益肾固骨方、杜仲健骨方等)被证实可通过激活Wnt信号通路,促进骨髓间充质干细胞成骨分化、成骨细胞增殖和分化来修复骨损伤和治疗骨质疏松症。基于此,本文总结了中药单体及复方干预Wnt信号通路调控骨代谢的研究进展,以期为中药防治骨代谢疾病的临床应用及新药研发提供思路。

关键词：中药单体中药复方骨代谢 Wnt信号通路骨形成骨吸收

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A Highly Selective and Turn-on Fluorescent Probe for Fe^(3+) Ion Based on Perylene Tetracarboxylic Diimide

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Chinese Journal of Chemistry 2014年第11期32卷 1116-1120页

作者： Jinbin Lin Chunhui Zhu xiaoqiong liu Bo Chen Yiyang Zhang Jinping Xue Jianyong liu Fujian Engineering Research Center for Photodynamic Therapy and Photodynamic Diagnoses&College of Chemistry Fuzhou UniversityFuzhouFujian 350108China

We have demonstrated a turn-on fluorescent sensor 6 for detection of Fe^(3+) based on photo-induced electron transfer(PET)mechanism.The probe comprises a perylene tetracarboxylic diimide(PDI)fluorophore and two bis((1,2,3-triazol-4-yl)methyl)amine(DTA)moieties as the metal ion receptors.It exhibits high selectivity toward Fe^(3+) over various other metal ions in CH_(3)CN/H_(2)O(1∶1,V/V).The binding stoichiometry for 6-Fe^(3+) complexes has been determined to be 1∶2 by a Job plot of fluorescence.The association constant between 6 and Fe^(3+) was estimated to be 1.04×10^(10)(mol/L)^(−2) by Benesi-Hildebrand equation.

关键词： fluorescent sensor perylene tetracarboxylic diimide Fe^(3+) photo-induced electron transfer fluorophore

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面向资源转化的中国传统村落分类振兴研究——基于“人-业-位”要素视角

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干旱区资源与环境 2024年第1期38卷 87-95页

作者：芮旸罗飞王玲孙玮鸿刘晓琼西北大学城市与环境学院西安710127 陕西省地表系统与环境承载力重点实验室西安710127

不同于一般村落,传统村落兼具社区、遗产和资源三重属性,资源属性的转化在其振兴中发挥着纽带作用。面向资源转化,选取4221个国家级传统村落为研究样本,开展传统村落分类振兴的理论和实证研究。结果表明:1)传统村落资源转化的核心要素... 详细信息

不同于一般村落,传统村落兼具社区、遗产和资源三重属性,资源属性的转化在其振兴中发挥着纽带作用。面向资源转化,选取4221个国家级传统村落为研究样本,开展传统村落分类振兴的理论和实证研究。结果表明:1)传统村落资源转化的核心要素是人口、产业和区位,其中“人”是主体、“业”是基础、“位”是条件,三者缺一不可。2)传统村落按单要素的优劣性分为人口空心村与实心村、产业一般村与示范村、区位不优村与优势村,按三要素的完备性分为4类8型。3)传统村落难以村村同等、同样、同步振兴,仅1.09%的村落三要素俱全,46.88%的村落三要素俱缺;只有约5%的村落有优势主导产业,近70%的村落人口空心化,超过2/3的村落缺乏区位优势。但有要素优势的村落分布更均衡,有利于形成以点带面的振兴格局。4)传统村落根据资源转化要素类型的不同,可相应采取转化示范、人口集聚、产业提升、区位改善、人口驱动、产业带动、区位拉动、资源保护等路径分类推进乡村振兴,并分4个梯队有序实现乡村振兴。

关键词：传统村落分类资源转化乡村振兴中国

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基于扎根理论的互联网营销师胜任力模型构建——以直播人员为例

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科技创新与生产力 2024年第1期45卷 26-28,31页

作者：彭晓琼刘庆南宁理工学院广西南宁530031 广西国际商务职业技术学院广西南宁530007

运用扎根理论的研究方法,对电子商务方向的专家学者、电商企业管理层和一线主播进行访谈并收集资料。采用开放式、主轴和选择性编码等方式进行质性分析,将互联网营销师的人才胜任力素质指标归纳为知识素养、个人形象、自我展示、团队素... 详细信息

运用扎根理论的研究方法,对电子商务方向的专家学者、电商企业管理层和一线主播进行访谈并收集资料。采用开放式、主轴和选择性编码等方式进行质性分析,将互联网营销师的人才胜任力素质指标归纳为知识素养、个人形象、自我展示、团队素养、执行能力5个要素,构建互联网营销师的胜任力模型,为后续互联网营销师胜任力模型的实证研究提供基础和依据。

关键词：扎根理论互联网营销师主播胜任力模型

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网络化聚吡咯/聚氨酯复合材料的抗静电性能研究

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中国塑料 2024年第2期38卷 33-38页

作者：段书谦刘姝雅刘江慧成晓琼蒙丹张先群陈肖付海贵州师范大学材料与建筑工程学院贵阳550025 贵州省教育厅轻质材料工程研究中心贵阳550025

导电剂填充树脂制备高分子抗静电复合材料时,其添加量直接决定着复合材料的导电率,但导电剂的微观形态深刻影响着导电通道的效能。利用软模板制备不同网络结构特征的聚吡咯(PPy)材料,将其与聚氨酯(PU)通过溶液共混制备PPy/PU复合材料,考... 详细信息

导电剂填充树脂制备高分子抗静电复合材料时,其添加量直接决定着复合材料的导电率,但导电剂的微观形态深刻影响着导电通道的效能。利用软模板制备不同网络结构特征的聚吡咯(PPy)材料,将其与聚氨酯(PU)通过溶液共混制备PPy/PU复合材料,考察PPy的结构差异对复合材料电导率的影响。利用线径在20~35 nm和30~50 nm范围的网络化PPy材料,分析了其添加量为1%~3%(质量分数,下同)时所制备的PPy/PU复合材料的电导率,对比PPy颗粒制得复合材料电导率均达到了10^(-7) S/m数量级。复合材料在100%~500%形变下,导电率均出现降低,但网络化PPy/PU复合材料仅下降1个数量级,其中1%添加量的网络化PPy/PU复合材料与3%PPy颗粒制备PU复合材料的导电率相当。结果表明,网络化导电剂在复合材料形变条件下,其原生网络维持了复合材料中导电通道的完整性,使得材料在形变下依然保持较高的电导率。

关键词：网络化聚吡咯抗静电复合材料形变条件导电性能

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Simulation and prediction of multi-scenario evolution of ecological space based on FLUS model: A case study of the Yangtze River Economic Belt, China

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Journal of Geographical Sciences 2023年第2期33卷 373-391页

作者： liu xiaoqiong WANG Xu CHEN Kunlun LI Dan School of Environmental Studies China University of GeosciencesWuhan 430074China China Institute of Mountaineering and Outdoor Sports Wuhan 430074China School of Geography and Information Engineering China University of GeosciencesWuhan 430074China School of Physical Education China University of GeosciencesWuhan 430074China Institute of Geography and Tourism Guangdong University of Finance&EconomicsGuangzhou 510320China

Building the Yangtze River Economic Belt(YREB)is one of China’s three national development policies in the new era.The ecological environment of the Yangtze River Economic Belt must be protected not only for regional economic development but also for regional ecological security and ecological progress in this region.This paper takes the ecological space of the Yangtze River Economic Belt as the research object,based on land use data in 2010 and 2015,and uses the FLUS model to simulate and predict the ecological space of the research area in 2035.The variation of the research area’s ecological space area and its four sub-zones has remarkable stability under diverse situations.Both the production space priority scenarios(S1)and living space priority scenarios(S2)saw a fall in ecological space area,with the former experiencing the highest reduction(a total reduction of 25,212 km^(2)).Under the ecological space priority scenarios(S3)and comprehensive space optimization scenario(S4),the ecological space area increased,and the ecological space area expanded even more under the former scenario(a total growth of 23,648 km^(2)).In Yunnan-Guizhou,the ecological space is relatively stable,with minimal signs of change.In Sichuan-Chongqing,the Sichuan Basin,Zoige Grassland,and Longmen Mountains were significant regions of area changes in ecological space.In the middle reaches of the Yangtze River,the ecological space changes mainly occur in the Wuyi Mountains,Mufu Mountains,and Dabie Mountains,as well as the surrounding waters of Dongting Lake.The Yangtze River Delta’s changes were mainly observed in the eastern Dabie Mountains and Jianghuai Hills.

关键词： ecological space multi-scenario simulation prediction FLUS model Yangtze River Economic Belt extensive protection of the Yangtze River

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Arsenic trioxide inhibits the activity of SphK1 by decreasing the level of phosphatidylserine and phosphatidic acid in the human gastric cancer cell line MGC-803

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BIOCELL 2022年第3期46卷 737-743页

作者： PEI liu ZHE CHEN xiaoqiong MA Key Laboratory of Digestive Pathophysiology of Zhejiang Province Institute of Cancer ResearchFirst Affiliated HospitalZhejiang Chinese Medical UniversityHangzhou310006China

Sphingosine kinase 1(SphK1)is an important synthetase during the synthesis of sphingosine-1-phosphate(S1P)from sphingosine(Sph).Previous studies demonstrated that arsenic trioxide(As_(2)O_(3))could reduce the level of S1P in human gastric cancer cell line MGC-803,indicating that As_(2)O_(3) may inhibit the activity of SphK1.In this study,the effect of As_(2)O_(3) on the SphK1 activation pathway was investigated.Western blot and quantitative real-time PCR analysis were used to evaluate the changes in protein and mRNA levels.The multi-dimensional mass spectrometry-based shotgun lipidomics method(MDMS-SL)was used for the quantitative detection of phosphatidylserine(PS)and phosphatidic acid(PA).The results revealed that As_(2)O_(3) did not affect the protein and mRNA expression of SphK1 in the MGC-803 cells.However,As_(2)O_(3) increased the levels of p-ERK1/2 and CIB1 in the SphK1 activation pathway and decreased the levels of PS and PA in the MGC-803 cells.The outcomes suggested that As_(2)O_(3) may enhance the activity of SphK1 by increasing the levels of p-ERK1/2 and CIB1 and decrease the activity of SphK1 by decreasing the levels of PS and PA.It was suggested that the inhibition effect is stronger and resulting in an overall decrease in the activity of SphK1.

关键词： As_(2)O_(3) SphK1 PS PA

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