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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 1.,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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Tomato CYP94C1.inactivates bioactive JA-lle to attenuate jasmonate-mediated defense during fruit ripening

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Molecular Plant 2024年第4期17卷 509-512页

作者： Tianxia Yang Lei Deng Qinyang Wang Chuanlong Sun Muhammad Ali Fangming Wu Huawei Zhaj Qian Xu Peiyong xin Shujing Cheng Jinfang Chu Tingting Huang Chang-{1. Li Chuanyou Li Key Laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China College of Life Sciences Shandong Agricultural UniversityTai'an 271018China Taishan Academy of Tomato Innovation Tai'an 271018China CAS Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China College of Horticulture Science and Engineering Shandong Agricultural UniversityTaian 271018China Institute of Vegetable Qingdao Academy of Agricultural SciencesQingdao 266100China Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China) Ministry of AgricultureBeijing Vegetable Research CenterBeijing Academy of Agriculture and Forestry SciencesBejing 100097China Frontiers Science Center for Molecular Design Breeding(MOE) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Dear Editor,Fruit rot caused by necrotrophic pathogens results in substantial reductions in fruit yield and revenues worldwide(Petrasch et al.,201.).A widespread phenomenon in fleshy fruit species is the susceptibility of ripe fruits to necrotrophs(Silva et al.,2021.,which facilitates seed dispersal(Forlani et al.,201.)but causes severe post-harvest losses in *** most of the nutritional and sensory qualities of fruits are elaborated at the ripening stage(Liu et al.,201.),balancing fruit ripening and pathogen resistance to maintain fruit quality has proven to be challenging.A deeper understanding of the mechanisms underlying the increased susceptibility of fruits to necrotrophs during ripening could lead to new strategies for producing necrotrophy-resistant fruits without compromising ripening-relatedquality.

关键词： susceptibility maintain fruit

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Accurate prediction of biliary atresia with an integrated model using MMP-7 levels and bile acids

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World Journal of Pediatrics 2024年第8期20卷 822-833页

作者： Yi-Jiang Han Shu-Qi Hu Jin-Hang Zhu Xiao Cai Deng-Ming Lai bao-Hai Chen Kun Zhu Qiao Tong {1.-Rui Zhou Jia-Le Deng Jin-Fa Tou Zhuo Fang Li-Zhong Du Department of Neonatal Surgery Children’s HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhouChina Department of Data and Analytics WuXi Diagnostics Innovation Research InstituteShanghaiChina Department of Information Center Children’s HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhouChina Department of Pathology Children’s HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhouChina Department of Neonatology Children’s HospitalZhejiang University School of MedicineNational Clinical Research Center for Child HealthHangzhouChina

Background Biliary atresia(BA)is a rare fatal liver disease in children,and the aim of this study was to develop a method to diagnose BA *** We determined serum levels of matrix metalloproteinase-7(MMP-7),the results of 1. liver tests,and the levels of 20 bile acids,and integrated computational models were constructed to diagnose *** Our findings demonstrated that MMP-7 expression levels,as well as the results of four liver tests and levels of ten bile acids,were significantly different between 86 BA and 59 non-BA patients(P1.000)than liver test *** AUC was 0.983(95%CI 0.962,1.000)for MMP-7 levels combined with liver test results and bile acid *** addition,we found that MMP-7 levels were highly correlated with gamma-glutamyl transferase levels and the liver fibrosis *** The innovative integrated models based on a large number of indicators provide a noninvasive and cost-effective approach for accurately diagnosing BA in children.

关键词： Bile aid.Biliary atresia Diagnosis Liver fibrosis Liver test MMP-7

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清代陕甘地区新建厅城的特征及其在清代城市史上的地位

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北方民族大学学报（哲学社会科学版） 2024年第1期 138-147页

作者：魏欣宝南京大学历史学院江苏南京210023

从陕甘地区新建厅制城市的历史进程来看,清朝在内地的边缘地带置厅筑城一般是地域开发的结果,在边疆地区置厅筑城则是多民族交往交流交融的产物。从城池选址的大位置角度来看,清代的交通路线与政区地理格局是影响厅城选址的重要因素。... 详细信息

从陕甘地区新建厅制城市的历史进程来看,清朝在内地的边缘地带置厅筑城一般是地域开发的结果,在边疆地区置厅筑城则是多民族交往交流交融的产物。从城池选址的大位置角度来看,清代的交通路线与政区地理格局是影响厅城选址的重要因素。就小位置而言,因地方长官着重考虑政治、军事因素,城址大多面临诸多地理条件的不足,但得益于清代对上述地域开发的深入,大量的厅城城址沿用至今。对于清代的城市发展而言,厅城作为清代特有的建置城市类型,在城市体系构建和整体城市发展中具有重要的地位,并成为多民族交往交流交融的枢纽。

关键词：清代陕甘厅制城市城市变迁城市选址城市地位

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考虑输出约束和输入饱和的弹仓自适应控制

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兵工学报 2024年第3期45卷 789-797页

作者：鲍丹卫俞凯金鑫侯保林南京理工大学机械工程学院江苏南京210094

针对存在参数不确定性和外部扰动的某链式回转弹仓的位置跟踪控制问题,提出一种自适应控制方案。该方案基于神经模糊系统(Neuro-Fuzzy System,NFS)、非线性扰动观测器(Nonlinear Disturbance Observer,NDO)及障碍Lyapunov函数(Barrier L... 详细信息

针对存在参数不确定性和外部扰动的某链式回转弹仓的位置跟踪控制问题,提出一种自适应控制方案。该方案基于神经模糊系统(Neuro-Fuzzy System,NFS)、非线性扰动观测器(Nonlinear Disturbance Observer,NDO)及障碍Lyapunov函数(Barrier Lyapunov Function,BLF),在实现高精度控制的同时满足输出约束和输入饱和的工程条件。通过BLF的设计,保证弹仓的位移跟踪误差约束在给定范围内。结合神经网络的函数逼近能力和模糊逻辑系统的推理能力,用于估计系统中的不确定性,减小对模型的依赖;两者结合的NFS作为NDO的一部分,进一步补偿估计误差和外部扰动,提高控制性能。此外,控制器设计考虑了运动过程中的执行器输入饱和问题。仿真结果表明,所设计的控制器在3种典型工况以及系统参数变化情况下均可实现弹仓的高精度位置跟踪控制,满足系统的约束条件。

关键词：链式回转弹仓自适应控制神经模糊系统输出约束输入饱和

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老年骨质疏松性椎体压缩性骨折及再骨折的诊疗

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中国中西医结合杂志 2024年第5期44卷 517-520页

作者：刘保新广州医科大学附属中医医院骨伤科广州510015

骨质疏松症(osteoporosis,OP)是以骨量减少,骨超微结构退化为特征,致骨脆性增加,易于骨折的一种老年骨骼疾病。近年来,我国逐步步入老年社会,OP患者逐年增多,骨质疏松性骨折(osteoporotic fracture,OF)的发病率也呈现出上升的趋势^([1.... 详细信息

骨质疏松症(osteoporosis,OP)是以骨量减少,骨超微结构退化为特征,致骨脆性增加,易于骨折的一种老年骨骼疾病。近年来,我国逐步步入老年社会,OP患者逐年增多,骨质疏松性骨折(osteoporotic fracture,OF)的发病率也呈现出上升的趋势^([1.2])。OP的三大并发症为疼痛、脊柱变形和骨折。其中,骨折危害最大,即脆性骨折。OF多发生于脊柱、桡骨远端、肱骨近端与髋部等部位。其中,50%以上OF发生于脊柱,好发于胸腰椎^([3,4])。

关键词：骨质疏松性骨折骨量减少桡骨远端再骨折肱骨近端老年骨质疏松性椎体压缩性骨折脆性骨折骨骼疾病

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Chinese herbal medicine Ginkgo biloba *** for ischemic stroke:An overview of systematic reviews and meta-analyses

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Journal of Integrative Medicine 2024年第2期22卷 163-179页

作者： Tian-tian Meng Ya-ping You Min Li Jian-bo Guo xin-bin Song Jing-yi Ding Xiao-long Xie An-qi Li Shang-jin Li Xiang-jun Yin Peng Wang Zhe Wang {1.-liang Wang Qing-yong He Department of Cardiology Guang'anmen HospitalChina Academy of Chinese Medical SciencesBeijing 100032China Department of Rehabilitation Dongfang HospitalBeijing University of Chinese MedicineBeijing 100071China School of Chemistry and Chemical Engineering Shanghai Jiao Tong UniversityShanghai 200240China School of Chinese Medicine the University of Hong KongHong KongChina Graduate School Henan University of Chinese MedicineZhengzhou 450008Henan ProvinceChina Department of Acupuncture and Moxibustion Dongzhimen HospitalBeijing University of Chinese MedicineBeijing 100010China Department of Cardiology Guang’anmen HospitalChina Academy of Chinese Medical SciencesZhengzhou 450008Henan ProvinceChina School of Integrated Traditional Chinese and Western Medicine Southwest Medical UniversityHangzhou 310053Zhejiang ProvinceChina School of Basic Medical Sciences Zhejiang Chinese Medical UniversityHangzhu 310053Zhejang ProvinceChina Department of Neurology the First Affiliated Hospital of Henan University of Chinese MedicineZhengzhou 450003Henan ProvinceChina

Background:Ginkgo biloba ***(GBLPs)are a class of Chinese herbal medicine used in the adjuvant treatment of ischemic stroke(IS).Recently,several systematic reviews(SRs)and meta-analyses(MAs)of GBLPs for IS have been ***:This overview aims to assess the quality of related SRs and *** strategy:Pub Med,Embase,Cochrane Library,Web of Science,Chinese Biological Medicine,China National Knowledge Infrastructure,Wanfang,and Chinese Science and Technology Journals databases were searched from their inception to December 31.*** criteria:SRs and MAs of randomized controlled trials(RCTs)that explored the efficacy of GBLPs for patients with IS were *** extraction and analysis:Two independent reviewers extracted data and assessed the methodological quality,risk of bias(ROB),reporting quality,and credibility of evidence of the included SRs and MAs using A Measurement Tool to Assess Systematic Reviews 2(AMSTAR 2),Risk of Bias in Systematic Reviews(ROBIS),the Preferred Reporting Items for Systematic Reviews and Meta-analyses(PRISMA),and the Grading of Recommendations Assessment,Development and Evaluation(GRADE),***,descriptive analysis and data synthesis were ***:Twenty-nine SRs/MAs involving 1.9 outcomes were included in this *** overall methodological quality of all SRs/MAs was critically low based on AMSTAR 2,and 28 had a high ROB based on the *** to the PRISMA statement,the reporting items of the included SRs/MAs are relatively *** results based on GRADE showed that of the 1.9 outcomes,8 were rated as moderate quality,24 as low quality,and 87 as very low *** on the data synthesis,GBLPs used in conjunction with conventional treatment were superior to conventional treatment alone for decreasing neurological function ***:GBLPs can be considered a beneficial supplemental therapy for ***,because of the low quality of the existing eviden

关键词： statement synthesis alone

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Jianpi Gushen Huayu decoction ameliorated diabetic nephropathy through modulating metabolites in kidney,and inhibiting TLR4/NF-κB/NLRP3 and JNK/P38 pathways

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World Journal of Diabetes 2024年第3期15卷 502-518页

作者： Zi-Ang Ma Li-xin Wang Hui Zhang Han-Zhou Li Li Dong Qing-Hai Wang Yuan-Song Wang {1.-ChaoPan Shu-Fang Zhang Huan-Tian Cui Shu-Quan Lv Graduate School Hebei University of Chinese MedicineShijiazhuang 050000Hebei ProvinceChina Department of Endocrinology Cangzhou Hospital of Integrated Traditional Chinese Medicine and Western Medicine of Hebei Province Affiliated to Hebei University of Chinese MedicineCangzhou 061000Hebei ProvinceChina School of Integrative Medicine Tianjin University of Traditional Chinese MedicineTianjin 300000China The First School of Clinical Medicine Yunnan University of Traditional Chinese MedicineKunming 065000Yunnan ProvinceChina Department of Endocrinology Hebei Cangzhou Hospital of Integrative MedicineCangzhou 061000Hebei ProvinceChina

BACKGROUND Jianpi Gushen Huayu Decoction(JPGS)has been used to clinically treat diabetic nephropathy(DN)for many ***,the protective mechanism of JPGS in treating DN remains *** To evaluate the therapeutic effects and the possible mechanism of JPGS on *** We first evaluated the therapeutic potential of JPGS on a DN mouse *** then investigated the effect of JPGS on the renal metabolite levels of DN mice using non-targeted ***,we examined the effects of JPGS on c-Jun N-terminal kinase(JNK)/P38-mediated apoptosis and the inflammatory responses mediated by toll-like receptor 4(TLR4)/nuclear factor-kappa B(NF-κB)/NOD-like receptor family pyrin domain containing 3(NLRP3).RESULTS The ameliorative effects of JPGS on DN mice included the alleviation of renal injury and the control of inflammation and oxidative *** metabolomic analysis revealed that JPGS altered the metabolites of the kidneys in DN mice.A total of 51.differential metabolites were *** analysis results indicated that nine pathways significantly changed between the control and model groups,while six pathways significantly altered between the model and JPGS *** related to cysteine and methionine metabolism;alanine,tryptophan metabolism;aspartate and glutamate metabolism;and riboflavin metabolism were identified as the key pathways through which JPGS affects *** experimental validation showed that JPGS treatment reduced the expression of TLR4/NF-κB/NLRP3 pathways and JNK/P38 pathway-mediated apoptosis related *** JPGS could markedly treat mice with streptozotocin(STZ)-induced DN,which is possibly related to the regulation of several metabolic pathways found in ***,JPGS could improve kidney inflammatory responses and ameliorate kidney injuries in DN mice via the TLR4/NF-κB/NLRP3 pathway and inhibit JNK/P38 pathwaymediated apoptosis in DN mice.

关键词： Diabetic nephropathy Jianpi Gushen Huayu Decoction Oxidative stress Inflammation Untargeted metabolomics Toll-like receptor 4/nuclear factor-kappa B/NOD-like receptor family pyrin domain containing 3 pathway c-Jun N-terminal kinase/P38-mediated apoptosis

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黄河内蒙段开河期细菌群落结构特征研究

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中国环境科学 2024年第3期44卷 1487-1496页

作者：史玉娇李文宝郭鑫内蒙古农业大学水资源利用与保护自治区重点实验室内蒙古呼和浩特010018 黄河流域内蒙段水资源与水环境综合治理协同创新中心内蒙古呼和浩特010018

为探索黄河内蒙段开河初期水-土介质中细菌群落组成情况及生态网络结构,于2021.4月中旬进行取样,共获得黄河水样6个和土样4个.利用1.S rRNA基因高通量测序方法对水、土样品进行测定,并从菌门及菌属水平对二者的细菌群落组成进行了分析... 详细信息

为探索黄河内蒙段开河初期水-土介质中细菌群落组成情况及生态网络结构,于2021.4月中旬进行取样,共获得黄河水样6个和土样4个.利用1.S rRNA基因高通量测序方法对水、土样品进行测定,并从菌门及菌属水平对二者的细菌群落组成进行了分析.结果显示:河漫滩土样细菌群落结构的分布较水样更为分散,且土样中细菌群落丰富度、均匀度及多样性均高于水体,二者多样性存在显著的组间差异;在菌门水平上,变形菌门、放线菌门和酸杆菌门等是构成水-土样品的优势细菌门类,其中变形菌门在河水中相对丰度均值约为36.57%,在土样中则下降到25.39%,而酸杆菌门主要存在土样中,相对丰度约为1..1.%;在菌属水平上, hgcI_clade(6.1.%~1..75%)、CL500-29_marine_group(2.97%~5.05%)和Acinetobacter(0.74%~1..24%)是水体中的优势菌属,而norank_f__norank_o__norank_c__KD4-96(1.95%~4.91.)、 norank_f__norank_o__Vicinamibacterales(2.35%~4.67%)和norank_f__Gemmatimonadaceae (2.20%~4.73%)是土样中的优势菌属;不同菌属对水-土细菌群落结构的响应并不一致,其中分别归属于酸杆菌门和芽单胞菌门的norank_f__norank_o__Vicinamibacterales及norank_f__Gemmatimonadaceae等是联系水-土细菌群落的主要菌属,而归属于放线菌门的hgcI_clade和CL500-29_marine_group等是造成水、土优势菌门存在差异的主要菌属;虽然土样较水样拥有更大的生态网络结构,且Delftia、Candidatus_Methylopumilus、Arthrobacter和Rb41.是维持黄河内蒙段水、土介质生态网络结构的关键菌属,但相较于土样网络结构,水体网络结构中不同模块关键菌门及菌属间的生态功能较为一致.

关键词：细菌群落水土介质网络结构开河期黄河内蒙段

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Measurement of the neutron-induced total cross sections of ^(nat)Pb from 0.3 eV to 20 MeV on the Back-n at CSNS

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Nuclear Science and Techniques 2024年第2期35卷 85-93页

作者： Jie-Ming Xue Song Feng Yong-Hao Chen Han Yi Min Xiao Pin-Jing Cheng xin-Xiang Li Rong Liu Yi-Wei Yang Zi-Jie Han Da-Jun Zhao Hao-Qiang Wang {1.-Qian Li Ji-Rong Zhao Lei-Xun Tang Wen Luo Bo Zheng School of Nuclear Science and Technology University of South ChinaHengyang 421001China Institute of High Energy Physics Chinese Academy of Sciences(CAS)Beijing 100049China Spallation Neutron Source Science Center Dongguan 523803China Institute of Nuclear Physics and Chemistry China Academy of Engineering PhysicsMianyang 621900China

The neutron-induced total cross sections of natural lead have been measured in a wide energy range(0.3 eV-20 MeV)on the back-streaming white neutron beamline(Back-n)at the China Spallation Neutron *** energy was determined by the neutron total cross-section spectrometer using the time-of-flight technique.A fast multi-cell fission chamber was used as the neutron detector,and a 1.-mm-thick high-purity natural lead sample was employed for the neutron transmission *** on-beam background was determined using Co,In,Ag,and Cd *** excitation function of ^(nat)Pb(n,tot)reaction below 20 MeV was calculated using the TALYS-1.96 nuclear-reaction modeling *** present results were compared with previous results,the evaluated data available in the five major evaluated nuclear data libraries(i.e.,ENDF/B-VIII.0,JEFF-3.3,JENDL-5,CENDL-3.2,and BROND-3.1.,and the theoretical calculation *** agreement was found between the new results and those of previous experiments and with the theoretical curves in the corresponding *** measurement obtained the neutron total cross section of natural lead with good accuracy over a wide energy range and added experimental data in the resonance energy *** provides more reliable experimental data for nuclear engineering design and nuclear data evaluation of lead.

关键词： Neutron-induced total cross section Natural lead Time-of-flight TALYS-1.96 CSNS Back-n white neutron beamline

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