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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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Rottlerin plays an antiviral role at early and late steps of Zika virus infection

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Virologica Sinica 2022年第5期37卷 685-694页

作者： Shili Zhou Quanshi Lin Changbai Huang xiaotong luo Xu Tian Chao Liu Ping Zhang Key Laboratory of Tropical Diseases Control(Sun Yat-sen University) Ministry of EducationGuangzhou510080China Medical Research Center Guangdong Second Provincial General HospitalGuangzhou510317China Department of Immunology Zhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China Department of Microbiology Zhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China

Infection of Zika virus(ZIKV)may cause microcephaly and other neurological disorders,while no vaccines and drugs are *** study revealed that rottlerin confers a broad antiviral activity against several enveloped viruses,including ZIKV,vesicular stomatitis virus,and herpes simplex virus,but not against two naked viruses(enterovirus 71 and encephalomyocarditis virus).Rottlerin does not have a direct virucidal effect on the virions,and its antiviral effect is independent of its regulation on PKCδor *** pretreatment and post-treatment of rottlerin effectively reduce the viral replication of *** pretreatment of rottlerin disturbs the endocytosis of enveloped viruses,while the post-treatment of rottlerin acts at a late stage through disturbing the maturation of ***,administration of rottlerin in neonatal mice significantly decreased the ZIKV replication in vivo,and alleviated the neurological symptoms caused by *** work suggests that rottlerin exerts an antiviral activity at two distinct steps of viral infection,and can be potentially developed as a prophylactic and therapeutic agent.

关键词： Zika virus(ZIKV) Rottlerin Enveloped virus Replication

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VirusMap:A visualization database for the influenza A virus

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Journal of Genetics and Genomics 2017年第5期44卷 281-284页

作者： Yubin Xie xiaotong luo Zhihao He Yueyuan Zheng Zhixiang Zuo Qi Zhao Yanyan Miao Jian Ren Sun Yat-sen University Cancer Center State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat-sen UniversityGuangzhou 510060China State Key Laboratory of Biocontrol School of Life SciencesSun Yat-sen UniversityGuangzhou 510275China Collaborative Innovation Center of High Performance Computing National University of Defense TechnologyChangsha 410073China

Influenza A virus,a highly virulent pathogen that has caused several pandemic events over the course of human history,still remains a major threat to human health at *** most serious influenza pandemic in recorded history was the 1918 Spanish flu outbreak,which killed about 20-100 million people worldwide（Murray et al.,2006）.Also,

关键词： visualization threat Spanish killed Murray Influenza outbreak pathogen phylogenetic geographical

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DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 294-306页

作者： Yubin Xie xiaotong luo Yupeng Li Li Chen Wenbin Ma Junjiu Huang Jun Cui Yong Zhao Yu Xue Zhixiang Zuo Jian Ren State Key Laboratory of Oncology in South China Cancer Center Collaborative Innovation Center for Cancer Medicine School of Life Sciences Sun Yat-sen University Department of Bioinformatics & Systems Biology MOE Key Laboratory of Molecular Biophysics College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering Huazhong University of Science and Technology

Protein nitration and nitrosylation are essential post-translational modifications （PTMs）involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are linked to numerous chronic ***, the identification of substrates that undergo such modifications in a site-specific manner is an important research topic in the community and will provide candidates for targeted therapy. In this study, we aimed to develop a computational tool for predicting nitration and nitrosylation sites in proteins. We first constructed four types of encoding features, including positional amino acid distributions, sequence contextual dependencies, physicochemical properties, and position-specific scoring features, to represent the modified residues. Based on these encoding features, we established a predictor called DeepNitro using deep learning methods for predicting protein nitration and nitrosylation. Using n-fold cross-validation, our evaluation shows great AUC values for DeepNitro, 0.65for tyrosine nitration, 0.80 for tryptophan nitration, and 0.70 for cysteine nitrosylation, respectively,demonstrating the robustness and reliability of our tool. Also, when tested in the independent dataset, DeepNitro is substantially superior to other similar tools with a 7%à42%improvement in the prediction performance. Taken together, the application of deep learning method and novel encoding schemes, especially the position-specific scoring feature, greatly improves the accuracy of nitration and nitrosylation site prediction and may facilitate the prediction of other PTM sites. DeepNitro is implemented in JAVA and PHP and is freely available for academic research at http：//***.

关键词： Protein nitration and nitro-sylation Deep learning Web service Functional site prediction Feature extraction

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Radial shock wave therapy in the treatment of chronic constriction injury model in rats： a preliminary study

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Chinese Medical Journal 2014年第5期127卷 830-834页

作者： Fu Miao Cheng Hao Li Duoyi Yu xiaotong Ji Nan luo Fang Department of Anesthesiology and Pain Management Beijing Tiantan Hospital Capital Medical University Beijing 100050 China

Background Pain physicians pay close attention to neuropathic pain （NP）,since there is currently no ideal *** shock wave therapy （RSWT） is a noninvasive treatment to chronic pain of soft tissue *** far,there is no information on the use of RSWT for the treatment of *** we observe the effects of RSWT on a NP model induced by chronic constriction injury （CCI） in *** Four different energy densities （1.0,1.5,2.0 and 2.5 bar） RSWT administered as a single session or repeated sessions in rats with NP induced by CCI of the sciatic *** analgesic effect was assessed by measuring mechanical withdrawal threshold （MWT） and thermal withdrawal latency （TWL）.The safety was assessed through calculating sciatic functional index （SFI）.Results MWT and TWL increased after a single session of RSWT from day 1 to day 5 but retumed to baseline levels by day *** repeated sessions of RSWT,both the MWT and TWL were significantly higher than NP group （P ＜ 0.01）for at least 4 *** addition,no significant changes of SFI were observed in any groups after repeated sessions of RSWT and no increased pain or other side effects in any *** A single session of RSWT is rapidly effective in the treatment of CCI,but the efficacy maintained in a short ***,repeated sessions of RSWT have prolonged efficacy.

关键词： radial shock wave therapy extracorporeal shock wave treatment neuropathic pain chronic constriction injury model

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大学生在校情绪状态与心理韧性的相关性分析

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校园心理 2024年第4期22卷 304-309页

作者：区致刘颖赵公懿罗晓彤黄惠娥黄青霞邱云卿李常红广东第二师范学院教师教育学院广东广州510303 广东第二师范学院教育学院广东广州510303

目的为了解当前各类高等院校学生的日常情绪状态、心理韧性和学业情绪现状及各变量间的相关性。方法本研究采用贝克抑郁量表、心理弹性量表和大学生一般学业情绪问卷,随机向广东省部分高校的728名学生进行问卷调查。采用独立样本t检验... 详细信息

目的为了解当前各类高等院校学生的日常情绪状态、心理韧性和学业情绪现状及各变量间的相关性。方法本研究采用贝克抑郁量表、心理弹性量表和大学生一般学业情绪问卷,随机向广东省部分高校的728名学生进行问卷调查。采用独立样本t检验、单因素方差分析和Pearson相关分析进行统计分析。结果女生的抑郁量表得分高于男生(t=-2.248,P=0.237),差异无统计学意义。普通院校学生的抑郁量表得分高于重点院校和高职专科学生(F=4.228,P=0.015)。高年级学生抑郁量表得分更高(t=-2.522,P=0.854),差异无统计学意义。抑郁情绪得分与消极学业情绪呈正相关(P<0.05),心理韧性水平与学生的抑郁量表得分和消极学业情绪存在负相关(P<0.05)。结论大学生日常消极情绪影响学业情绪,心理韧性对大学生心理健康及学业情绪具有保护作用。高校在开展大学生管理工作时需要注意大学生的情绪状态,加强大学生心理韧性的培养以不断提高学生的心理健康水平。

关键词：韧性,心理大学生心理健康学业情绪

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Microbiome and metabolome dysbiosis analysis in impaired glucose tolerance for the prediction of progression to diabetes mellitus

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Journal of Genetics and Genomics 2024年第1期51卷 75-86页

作者： Boxun Zhang Xuan Zhang Zhen luo Jixiang Ren xiaotong Yu Haiyan Zhao Yitian Wang Wenhui Zhang Weiwei Tian Xiuxiu Wei Qiyou Ding Haoyu Yang Zishan Jin Xiaolin Tong Jun Wang Linhua Zhao Institute of Metabolic Diseases Guang'anmen HospitalChina Academy of Chinese Medical SciencesBeijing 100053China Faculty of Biological Science and Technology Baotou Teacher's CollegeBaotouInner Mongolia 014030China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Infinitus(China)Company Ltd GuangzhouGuangdong 510405China Affiliated Hospital of Changchun University of Chinese Medicine ChangchunJilin 130021China Department of Endocrinology Guang'anmen HospitalChina Academy of Chinese Medical SciencesBeijing 100053China Xinjiekou Community Health Service Center in Xicheng District Beijing 100035China Department of Spleen and Stomach Shenzhen Traditional Chinese Medicine HospitalShenzhenGuangdong 518033China University of Chinese Academy of Sciences Beijing 100049China Beijing University of Chinese Medicine Beijing 100105China Northeast Asia Institute of Traditional Chinese Medicine Changchun University of Chinese MedicineChangchunJilin 130117China

Gut microbiota and circulating metabolite dysbiosis predate important pathological changes in glucose metabolic disorders;however,comprehensive studies on impaired glucose tolerance(IGT),a diabetes mellitus(DM)precursor,are ***,we perform metagenomic sequencing and metabolomics on 47 pairs of individuals with IGT and newly diagnosed DM and 46 controls with normal glucose tolerance(NGT);patients with IGT are followed up after 4 years for progression to *** of baseline data reveals significant differences in gut microbiota and serum metabolites among the IGT,DM,and NGT *** addition,13 types of gut microbiota and 17 types of circulating metabolites showed significant differences at baseline before IGT progressed to DM,including higher levels of Eggerthella unclassified,Coprobacillus unclassified,Clostridium ramosum,L-valine,L-norleucine,and L-isoleucine,and lower levels of Eubacterium eligens,Bacteroides faecis,Lachnospiraceae bacterium 3_1_46FAA,Alistipes senegalensis,Megaspaera elsdenii,Clostridium perfringens,α-linolenic acid,10E,12Z-octadecadienoic acid,and dodecanoic acid.A random forest model based on differential intestinal microbiota and circulating metabolites can predict the progression from IGT to DM(AUC=0.87).These results suggest that microbiome and metabolome dysbiosis occur in individuals with IGT and have important predictive values and potential for intervention in preventing IGT from progressing to DM.

关键词： Impaired glucose tolerance Diabetes mellitus Gut microbiota Metabolomics

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陆地热泉钙华研究进展与展望

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沉积学报 2019年第6期37卷 1162-1180页

作者：文华国罗连超罗晓彤游雅贤杜磊油气藏地质及开发工程国家重点实验室(成都理工大学) 成都610059 成都理工大学沉积地质研究院成都610059

陆地热泉钙华是沉淀于富Ca2+和HCO-3热泉(普遍T≥30℃)的陆地碳酸盐沉积物/岩。热泉钙华独特的形成环境、岩石矿物学特征、地球化学特征和流体性质对古环境、古气候、早期生命起源、新构造运动、陆相热水沉积学、地热资源等方面研究具... 详细信息

陆地热泉钙华是沉淀于富Ca2+和HCO-3热泉(普遍T≥30℃)的陆地碳酸盐沉积物/岩。热泉钙华独特的形成环境、岩石矿物学特征、地球化学特征和流体性质对古环境、古气候、早期生命起源、新构造运动、陆相热水沉积学、地热资源等方面研究具有重要指示意义。尽管相关学者对陆地热泉钙华开展了相关研究,但由于热泉钙华沉积成岩过程中受复杂外界条件控制,其时空分布、沉积特征、矿物组成、地球化学特征、微生物作用、流体来源、成岩作用、古气候记录等系列科学问题有待深入研究。在国内外大量文献的基础上,结合研究团队对云南腾冲火山地热区热泉钙华的认识,综述了目前国内外学者对陆地热泉钙华的研究进展,总结了热泉钙华研究意义,提出了当前热泉钙华研究存在的问题及下步研究方向,为更加全面地认识陆地热泉钙华沉积及未来研究提供启示。

关键词：热泉钙华沉积特征岩石矿物学地球化学微生物早期成岩作用

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PIF4 interacts with ABI4 to serve as a transcriptional activator complex to promote seed dormancy by enhancing ABA biosynthesis and signaling

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Journal of Integrative Plant Biology 2024年第5期66卷 909-927页

作者： Xiaofeng luo Yujia Dai Baoshan Xian Jiahui Xu Ranran Zhang Muhammad Saad Rehmani Chuan Zheng Xiaoting Zhao Kaitao Mao xiaotong Ren Shaowei Wei Lei Wang Juan He Weiming Tan Junbo Du Weiguo Liu Shu Yuan Kai Shu Shaanxi Key Laboratory of Qinling Ecological Intelligent Monitoring and Protection School of Ecology and EnvironmentNorthwestern Polytechnical UniversityXi'an 710129China Research&Development Institute of Northwestern Polytechnical University in ShenzhenShenzhen 518057China College of Agronomy and Biotechnology China Agricultural UniversityBeijing 100193China Institute of Ecological Agriculture Sichuan Agricultural UniversityChengdu 611130China College of Resources Sichuan Agricultural UniversityChengdu 611130China

Transcriptional regulation plays a key role in the control of seed dormancy,and many transcription factors(TFs)have been ***,the mechanisms underlying the interactions between different TFs within a transcriptional complex regulating seed dormancy remain largely ***,we showed that TF PHYTOCHROME-INTERACTING FACTOR4(PIF4)physically interacted with the abscisic acid(ABA)signaling responsive TF ABSCISIC ACID INSENSITIVE4(ABI4)to act as a transcriptional complex to promote ABA biosynthesis and signaling,finally deepening primary seed *** pif4 and abi4 single mutants exhibited a decreased primary seed dormancy phenotype,with a synergistic effect in the pif4/abi4 double ***4 binds to ABI4 to form a heterodimer,and ABI4 stabilizes PIF4 at the protein level,whereas PIF4 does not affect the protein stabilization of ***,both TFs independently and synergistically promoted the expression of ABI4 and NCED6,a key gene for ABA *** genetic evidence is also consistent with the phenotypic,physiological and biochemical analysis ***,this study revealed a transcriptional regulatory cascade in which the PIF4–ABI4 transcriptional activator complex synergistically enhanced seed dormancy by facilitating ABA biosynthesis and signaling.

关键词： ABA ABI4 PIF4 seed dormancy and germination transcriptional complex

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低碳城市创新能力的驱动机制研究——基于fsQCA范式分析视角

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科学学与科学技术管理 2024年第5期45卷 92-104页

作者：罗公利王晓彤山东科技大学经济管理学院山东青岛266590

创新是经济绿色低碳发展的重要驱动因素。基于创新生态系统理论,以我国68个低碳试点城市为样本,运用模糊集定性比较分析方法探究创新能力提升的驱动机制。研究发现:(1)不存在导致城市高创新能力和非高创新能力的单一必要条件。(2)技术... 详细信息

创新是经济绿色低碳发展的重要驱动因素。基于创新生态系统理论,以我国68个低碳试点城市为样本,运用模糊集定性比较分析方法探究创新能力提升的驱动机制。研究发现:(1)不存在导致城市高创新能力和非高创新能力的单一必要条件。(2)技术创新主体、创新资源和创新基础设施对实现城市高创新能力具有重要意义。实现低碳城市高创新能力的驱动路径有5条,分别为“企业—智力—设施驱动型”、“主体—智力—设施均衡驱动型”、“资金—设施—主体均衡驱动型”、“资源—环境均衡驱动型”和“资源—设施—主体驱动型”。而导致低碳城市非高创新能力的路径有5条,其中非高知识创新主体和非高创新资源是导致非高创新能力的重要原因。(3)城市高创新能力和非高创新能力的前因条件呈现出非对称性特征,各城市应根据自身特点选择适合的路径提高城市创新能力。

关键词：创新生态系统创新能力驱动机制组态效应模糊集定性比较分析

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