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Development of a High-throughput Sequencing Platform for Detection of Viral Encephalitis Pathogens Based on Amplicon Sequencing

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Biomedical and Environmental Sciences 2024年第3期37卷 294-302页

作者： ZHANG Ya Li SU Wen Zhe WANG Rui chen LI Yan ZHANG Jun Feng LIU sheng Hui HU Dan He xu Chong Xiao YIN Jia Yu YIN Qi Kai HE ying LI Fan FU {4. Hong NIE Kai LIANG Guo Dong TAO Yong xu Song Tao MA Chao Feng WANG Huan Yu Shaanxi university of Chinese Medicine Xianyang 712000ShaanxiChina National key laboratory of Intelligent Tracking and Forecasting for Infectious Diseases National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China Guangzhou Center for Disease Control and Prevention Guangzhou 510000GuangdongChina Shandong Center for Disease Control and Prevention Jinan 250000ShandongChina Department of Ophthalmology Beijing Chaoyang HospitalCapital Medical UniversityBeijing 100020China Xi'an Center for Disease Control and Prevention Xi’an 710054ShaanxiChina

Objective Viral encephalitis is an infectious disease severely affecting human *** is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other *** laboratory diagnosis of viral encephalitis is a worldwide ***,high-throughput sequencing technology has provided new tools for diagnosing central nervous system ***,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon *** We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant *** detection ability of the primers was verified by software simulation and the detection of known positive *** sequencing was used to validate the samples,and consistency was compared with Sanger *** The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted *** sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger *** Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral *** is also a useful tool for the high-volume screening of clinical samples.

关键词： Viral encephalitis Amplicon sequencing High-throughput sequencing Multipathogen detection

Overexpression of TRPV1 activates autophagy in human lens epithelial cells under hyperosmotic stress through Ca^(2+)-dependent AMPK/mTOR pathway

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International Journal of Ophthalmology(English edition) 2024年第3期17卷 420-434页

作者： Liu-Hui Huang Jiao Lyu sheng chen Ting-Yi Liang Yu-Qing Rao Ping Fei Jing Li Hai-ying Jin Pei-Quan Zhao Department of Ophthalmology Shanghai Xinhua Hospital Affiliated with Shanghai Jiao Tong University School of MedicineShanghai 200092China Department of Ophthalmology Shanghai Tenth People’s Hospital Affiliated with Shanghai Tongji University School of MedicineShanghai 200072China Centre for Eye Research Australia Royal Victorian Eye and Ear HospitalEast MelbourneVictoria 3002Australia Ophthalmology Department of SurgeryUniversity of MelbourneEast MelbourneVictoria 3002Australia Shenzhen Eye Hospital Shenzhen Key Laboratory of OphthalmologyAffiliated Shenzhen Eye Hospital of Jinan UniversityShenzhen 518040Guangdong ProvinceChina Department of Ophthalmology Shanghai East HospitalSchool of MedicineTongji UniversityShanghai 200120China

●AIM:To explore whether autophagy functions as a cellular adaptation mechanism in lens epithelial cells(LECs)under hyperosmotic stress.●METHODS:LECs were treated with hyperosmotic stress at the concentration of 270,300,4.0,500,or 600 mOsm for 6,12,18,24. in *** chain reaction(PCR)was employed for the mRNA expression of autophagyrelated genes,while Western blotting detected the targeted protein *** transfection of stub-RFP-sens-GFPLC3 autophagy-related double fluorescence lentivirus was conducted to detect the level of autophagy *** electron microscopy was used to detect the existence of *** interfering RNA of autophagy-related gene(ATG)7,transient receptor potential vanilloid(TRPV)1 overexpression plasmid,related agonists and inhibitors were employed to their influence on autophagy related *** cytometry was employed to test the apoptosis and intracellular Ca^(2+)*** membrane potential was measured by JC-1 *** cell counting kit-8 assay was used to calculate the cellular *** wound healing assay was used to evaluate the wound closure *** 6.0 software was utilized to evaluate the data.●RESULTS:The hyperosmotic stress activated autophagy in a pressure-and time-dependent manner in *** 1 protein expression and conversion of LC3B II to LC3B I increased,whereas sequestosome-1(SQSTM1)protein expression *** Ca^(2+)influx was stimulated caused by hyperosmotic stress,levels of mammalian target of rapamycin(mTOR)phosphorylation decreased,and the level of AMP-activated protein kinase(AMPK)phosphorylation increased in the early *** on this evidence,autophagy activation through the Ca^(2+)-dependent AMPK/mTOR pathway might represent an adaptation process in LECs under hyperosmotic *** stress decreased cellular viability and accelerated apoptosis in LECs and cellular migration *** of autophagy by ATG7 knockdown had sim

关键词： cataract posterior capsular opacification lens epithelial cell hyperosmotic stress autophagy apoptosis transient receptor potential vanilloid 1

Code Component Composition Reuse Is a New Programming Paradigm

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wuhan university Journal of Natural Sciences 2001年第Z1期6卷 292-297页

作者： ying shi 1,yuan sheng qiong 1,{4. gang 1,He Ke Qing 2 1.State key laboratory of software Engineering, wuhan university, wuhan 430072, china 2.School of Computer Science and Technology, wuhan university, wuhan 430072, china State key laboratory of software Engineering Wuhan University Wuhan China School of Computer Science and Technology Wuhan University Wuhan China

After describing the characteristics of programming paradigm, this paper introduces the approach of code component composition reuse in detail, proposes and discusses viewpoint that code component composition reuse is a kind of new programming paradigm. This paper also specifies the characteristics of this new programming paradigm in detail, and points out some issues that must be resolved for using this new programming paradigm.

关键词： programming paradigm code component code component composition reuse

Optimal Policies for Quantum Markov Decision Processes

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International Journal of Automation and computing 2021年第3期18卷 410-421页

作者： Ming-sheng ying yuan Feng sheng-{4. ying Centre for Quantum software and Information University of Technology SydneyNSW 2007Australia State key laboratory of Computer Science Institute of SoftwareChinese Academy of SciencesBeijing 100190China Department of Computer Science and Technology Tsinghua UniversityBeijing 100084China

Markov decision process(MDP)offers a general framework for modelling sequential decision making where outcomes are *** particular,it serves as a mathematical framework for reinforcement *** paper introduces an extension of MDP,namely quantum MDP(q MDP),that can serve as a mathematical model of decision making about quantum *** develop dynamic programming algorithms for policy evaluation and finding optimal policies for q MDPs in the case of *** results obtained in this paper provide some useful mathematical tools for reinforcement learning techniques applied to the quantum world.

关键词： Quantum Markov decision processes quantum machine learning reinforcement learning dynamic programming decision making

关于社区花园设计的中西方研究综述——基于CiteSpace软件的可视化分析

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湖北科技学院学报 2024年第5期44卷 106-116页

作者：刘瑛伍旭坤郭圣能张妍崔盈盈皖江工学院艺术设计学院安徽马鞍山243001 马鞍山景观生态修复研究重点实验室安徽马鞍山243001 安徽工业大学艺术与设计学院安徽马鞍山243002

在倡导城市更新的新政下,在全球气候变化日趋紧张的今天,社区花园这一概念在理论实践中日益深入人心。基于CiteSpace软件可视化系统重点分析了国内外文献的重要研究,包括关键词、研究方法和主要发现,对社区花园的研究进行了综述。通过分... 详细信息

在倡导城市更新的新政下,在全球气候变化日趋紧张的今天,社区花园这一概念在理论实践中日益深入人心。基于CiteSpace软件可视化系统重点分析了国内外文献的重要研究,包括关键词、研究方法和主要发现,对社区花园的研究进行了综述。通过分析,主要研究了当前社区花园领域的知识结构、研究热点和研究趋势,为应用于社区花园研究理论及其设计实践提供参考,启发针对不同场地、人群、情境、需求的社区花园设计思路。研究表明了社区花园对于改善生物多样性和生态环境治理的重要性,综合考虑对于健康的促进及幸福感的增加,同时公众参与共治共建也促进了社区的认同感和可持续发展。

关键词：社区花园气候变化可持续设计微更新 CiteSpace 公众参与

蒙药材砂引草HPLC指纹图谱及6个成分含量测定研究

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药物分析杂志 2024年第5期44卷 816-826页

作者：郝俊生包红英斯日古冷孟和任娅婷红艳辛颖通辽市市场检验检测中心通辽028000 蒙药研发国家地方联合工程研究中心通辽028000 内蒙古民族大学蒙医药学院通辽028000 扎赉特旗市场监督管理局兴安盟137600

目的:建立不同产地蒙药材砂引草Tournefortia sibirica Linnaeus的HPLC指纹图谱并测定其6个成分(咖啡酸、异槲皮苷、槲皮苷、迷迭香酸、紫草酸和丹酚酸B)的含量,为砂引草质量控制提供依据。方法:采用Agilent Eclipse Plus C_(18)色谱柱(... 详细信息

目的:建立不同产地蒙药材砂引草Tournefortia sibirica Linnaeus的HPLC指纹图谱并测定其6个成分(咖啡酸、异槲皮苷、槲皮苷、迷迭香酸、紫草酸和丹酚酸B)的含量,为砂引草质量控制提供依据。方法:采用Agilent Eclipse Plus C_(18)色谱柱(250 mm×4.6 mm,5μm),以0.2%磷酸溶液(A)-乙腈(B)为流动相,进行梯度洗脱(0~60 min,9%B→38%B),检测波长330 nm。对不同产地砂引草进行分析,采用国家药典委员会“中药色谱指纹图谱相似度评价系统软件”(2012版),建立砂引草指纹图谱,同时测定6个成分含量。结果:HPLC指纹图谱共标定了不同产地砂引草中11个共有峰,指认了咖啡酸、异槲皮苷、槲皮苷、迷迭香酸、紫草酸和丹酚酸B 6个成分,17批砂引草药材与对照指纹图谱之间的相似度在0.931~0.996。经方法学考察,咖啡酸、异槲皮苷、槲皮苷、迷迭香酸、紫草酸和丹酚酸6个成分精密度试验RSD依次为1.9%、1.0%、1.4.、0.19%、1.1%和0.32%;重复性试验RSD依次为3.5%、2.3%、3.3%、0.14.、1.1%和0.19%;稳定性试验RSD依次为0.80%、1.1%、1.7%、0.52%、0.54.和0.78%。咖啡酸、异槲皮苷、槲皮苷、迷迭香酸、紫草酸和丹酚酸B在0.0033~0.0295、0.0119~0.1073、0.014.~0.1328、0.0928~0.8352、0.0689~0.1058、0.0688~0.6199μg·mL^(-1)浓度范围内线性关系良好(均为r=1.000);平均回收率在93.9%~102.3%,按干燥品计含量在0.004.~0.013%、0.030%~0.259%、0.032%~0.256%、0.256%~1.24.%、0.018%~0.072%和0.062%~0.4.9%。结论:建立的砂引草HPLC指纹图谱及6个成分含量测定方法稳定、可靠、重复性好,可为砂引草质量控制及开发研究提供参考。

关键词：蒙药材砂引草指纹图谱聚类分析主成分分析含量测定咖啡酸异槲皮苷槲皮苷迷迭香酸紫草酸丹酚酸B

全身低载高频振动参数交互作用下松质骨力学行为的模拟研究

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医疗卫生装备 2024年第7期45卷 17-23页

作者：李明志刘海英李胜刚张春秋天津理工大学天津市先进机电系统设计与智能控制重点实验室天津300384 天津理工大学机电工程国家级实验教学示范中心天津300384

目的:研究在全身低载高频振动(low-magnitude high-frequency vibration,LMHFV)参数交互作用下松质骨的力学行为,以为临床治疗废用性骨质疏松提供理论指导。方法:选取股骨中段松质骨通过Mimics软件进行三维重建,并将其导入Comsol软件中... 详细信息

目的:研究在全身低载高频振动(low-magnitude high-frequency vibration,LMHFV)参数交互作用下松质骨的力学行为,以为临床治疗废用性骨质疏松提供理论指导。方法:选取股骨中段松质骨通过Mimics软件进行三维重建,并将其导入Comsol软件中建立三维流固耦合有限元模型。设定12种振动方案(振动加速度幅值a为0.015×g、0.02×g、0.03×g,振动频率f为30、4.、60、100 Hz)进行模拟研究,分析LMHFV参数交互作用下松质骨的流体力学微环境、应力及变形位移的分布规律。结果:骨小梁表面骨髓流速及其变形位移随a增加而增大,随f增加而减小。在振动方案(0.015×g/0.02×g/0.03×g,30 Hz)下,骨小梁产生的变形位移平均值较高。在LMHFV参数范围(0.02×g~0.03×g,30~35 Hz)内,骨小梁的von Mises应力值较高。结论:全身LMHFV可显著改善松质骨的受力及流体力学环境,临床上可通过合理调控LMHFV参数来提高力介导的成骨细胞生物活性,进而促进骨生成。

关键词： LMHFV 力学行为松质骨有限元模型骨质疏松

BENCHIP： Benchmarking Intelligence Processors

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Journal of Computer Science & Technology 2018年第1期33卷 1-23页

作者： Jin-Hua Tao Zi-Dong Du Qi Guo Hui-ying Lan Lei Zhang sheng-yuan Zhou Ling-Jie xu Cong Liu Hai-Feng Liu Shah Tang Allen Rush Willian {4. Shao-Li Liu Yun-Ji {4. Tian-shi {4. State key laboratory of Computer Architecture Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China School of Computer and Control Engineering University of Chinese Academy of Sciences Beijing 100049 China Intelligent Processor Research Center Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China Cambricon Ltd. Beijing 100190 China A libaba Infrastructure Service A libaba Group Hangzhou 311121 China Iflytek Co. Ltd. Hefei 230088 China Beijing Jingdong Century Trading Co. Ltd. Beijing 100176 China RDA Microdectronics Inc. Shanghai 201203 China Advanced Micro Devices Inc. Sunnyvale CA 94085 U.S.A.

The increasing attention on deep learning has tremendously spurred the design of intelligence processing hardware. The variety of emerging intelligence processors requires standard benchmarks for fair comparison and system optimization （in both software and hardware）. However, existing benchmarks are unsuitable for benchmarking intelligence processors due to their non-diversity and nonrepresentativeness. Also, the lack of a standard benchmarking methodology further exacerbates this problem. In this paper, we propose BENCHIP, a benchmark suite and benchmarking methodology for intelligence processors. The benchmark suite in BENCHIP consists of two sets of benchmarks： microbenchmarks and macrobenchmarks. The microbenchmarks consist of single-layer networks, They are mainly designed for bottleneck analysis and system optimization. The macrobenchmarks contain state-of-the-art industrial networks, so as to offer a realistic comparison of different platforms. We also propose a standard benchmarking methodology built upon an industrial software stack and evaluation metrics that comprehensively reflect various characteristics of the evaluated intelligence processors, BENCHIP is utilized for evaluating various hardware platforms, including CPUs, GPUs, and accelerators. BENCHIP will be open-sourced soon.

关键词： deep learning intelligence processor benchmark

Transfer synthetic over-sampling for class-imbalance learning with limited minority class data

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Frontiers of Computer Science 2019年第5期13卷 996-1009页

作者： xu-ying LIU sheng-Tao WANG Min-Ling ZHANG School of Computer Science and Engineering Southeast University Nanjing 210096 China key laboratory of Computer Network and Information Integration (Southeast university) Ministry of Education Nanjing 210096 China Collaborative Innovation Center for Wireless Communications Technology Nanjing 210096 China

The problem of limited minority class data is encountered in manyclass imbalanced applications, but has received little attention. Synthetic over-sampling, as popular class-imbalance learning methods, could introduce much noise when minority class has limited data since the synthetic samples are not i.i.d. samples of minority class. Mos t sophisticated synthetic sampling methods tackle this problem by denoising or generating samples more consistent with ground-truth data distribution. But their assumptions about true noise or ground-truth data distribution may not hold. To adapt synthetic sampling to the problem of limited minority class data, the proposed Traso framework treats synthetic minority class samples as an additional data source, and exploits transfer learning to transfer knowledge from them to minority class. As an implementation, TrasoBoost method firstly generates synthetic samples to balance class sizes. Then in each boosting iteration, the weights of synthetic samples and original data decrease and increase respectively when being misclassified, and remain unchanged otherwise. The misclassified synthetic samples are potential noise, and thus have smaller influence in the following iterations. Besides, the weights of minority class instances have greater change than those of majority class instances to be more influential. And only original data are used to estimate error rate to be immune from noise. Finally, since the synthetic samples are highly related to minority class, all of the weak learners are aggregated for prediction. Experimental results show TrasoBoost outperforms many popular class-imbalance learning methods.

关键词： machine learning data mining class imbalance over sampling boosting transfer learning