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Metabolite acetyl-L-carnitine participates in Bifidobacterium animalis F1-7 to ameliorate atherosclerotic inflammation by downregulating theTLR4/NF-κB pathway

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Food Science and Human Wellness 2024年第2期13卷 813-822页

作者： Xi Liang Zhe Zhang Xiaoying Tian Qingyu Cui haiyan Lu Maozhen Zhao Tongjie Liu Huaxi Yi Pimin gong Lanwei Zhang Department of Nutrition and Food Hygiene School of public healthQingdao UniversityQingdao 266071China College of Food Science and Engineering Ocean University of ChinaQingdao 266003China

This study aimed to explore the effect of Bifidobacterium animalis F1-7 on the improvement of atherosclerotic inflammation.Arteriosclerosis model ApoE^(-/-)mice were orally administered with B.animalis F1-7 for 12 weeks.The probiotic intervention reduced the plaque areas in aorta and the accumulation of macrophages,and downregulated the expression of toll-like receptor 4(TLR4)/nuclear factorκB(NF-κB)pathway to reduce the levels of inflammatory factors.The widely-targeted metabolomics analysis showed that acetyl-L-carnitine(ALC)in the intestine of atherosclerotic mice was significantly increased after B.animalis F1-7 intervention.Correlation analysis proved that ALC was associated with atherosclerotic inflammatory response.By using oxidized low density lipoprotein induced macrophage foam cells,we further verified that ALC could reduce lipid accumulation and inflammatory response in foam cells by downregulating the TLR4/NF-κB pathway.Finally,our results revealed that B.animalis F1-7 upregulated the metabolite ALC to downregulate the inflammatory responses,leading to the reduction of plaque accumulation of atherosclerosis.

关键词： Bifidobacterium animalis F1-7 Atherosclerosis Inflammation Metabonomics Acetyl-L-carnitine

Virome diversity of ticks feeding on domestic mammals in China

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Virologica Sinica 2023年第2期38卷 208-221页

作者： Zijun Yang Hao Wang Shixing Yang Xiaochun Wang Quan Shen Likai Ji Jian Zeng Wen Zhang haiyan gong Tongling Shan Shanghai Veterinary Research Institute Chinese Academy of Agricultural SciencesShanghai200241China Department of Microbiology School of MedicineJiangsu UniversityZhenjiang212013China Department of Clinical Laboratory Huai'an HospitalXuzhou Medical UniversityHuai'an223002China Center of Clinical Laboratory The First Affiliated Hospital of Soochow UniversitySuzhou215006China

Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses.From 2017 to 2018,640 ticks were collected in eight different provinces in central and western China.Six species were detected,including H.longicornis,De.everestianus,Rh.microplus,Rh.turanicus,Rh.sanguineous,and Hy.asiaticum.Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform,resulting in 13.44 G(5.88×10^(7))of 250-bp-end reads,in which 2,437,941 are viral reads.We found 27 nearly complete genome sequences,including 16 genome sequences encoding entire protein-coding regions(lack of 30 or 50 end non-coding regions)and complete viral genomes,distributed in the arboviral family(Chuviridae,Rhabdoviridae,Nairoviridae,Phenuiviridae,Flaviviridae,Iflaviridae)as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans.In addition,13 virus sequences found in Chuviridae,Nairoviridae,Flaviviridae,Iflaviridae,Hepeviridae,Parvoviridae,and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera.Besides,an epidemiological survey shows a high prevalence(9.38%and 15.63%)of two viruses(Ovine Copiparvovirus and Bovine parvovirus 2)in the tick cohort.

关键词： Central and western China Viral metagenomes Tick-borne virus Phylogenetic analysis Domestic mammals Tick virome

Computational methods for identifying enhancer-promoter interactions

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Quantitative Biology 2023年第2期11卷 122-142页

作者： haiyan gong Zhengyuan Chen Yuxin Tang Minghong Li Sichen Zhang Xiaotong Zhang Yang Chen School of Computer and Communication Engineering BeijingAdvanced Innovation Center for Materials Genome EngineeringUniversity of Science and Technology BeijingBeijing 100083China State Key Laboratory of Medical Molecular Biology Department of Biochemistry and Molecular BiologyInstitute of Basic Medical SciencesSchool of Basic MedicineChinese Academy of Medical SciencesPeking Union Medical CollegeBeijing 100005China Shunde Innovation School University of Science and Technology BeijingFoshan 528399China

Background:As parts of the cis-regulatory mechanism of the human genome,interactions between distal enhancers and proximal promoters play a crucial role.Enhancers,promoters,and enhancer-promoter interactions(EPIs)can be detected using many sequencing technologies and computation models.However,a systematic review that summarizes these EPI identification methods and that can help researchers apply and optimize them is still needed.Results:In this review,we first emphasize the role of EPIs in regulating gene expression and describe a generic framework for predicting enhancer-promoter interaction.Next,we review prediction methods for enhancers,promoters,loops,and enhancer-promoter interactions using different data features that have emerged since 2010,and we summarize the websites available for obtaining enhancers,promoters,and enhancer-promoter interaction datasets.Finally,we review the application of the methods for identifying EPIs in diseases such as cancer.Conclusions:The advance of computer technology has allowed traditional machine learning,and deep learning methods to be used to predict enhancer,promoter,and EPIs from genetic,genomic,and epigenomic features.In the past decade,models based on deep learning,especially transfer learning,have been proposed for directly predicting enhancer-promoter interactions from DNA sequences,and these models can reduce the parameter training time required of bioinformatics researchers.We believe this review can provide detailed research frameworks for researchers who are beginning to study enhancers,promoters,and their interactions.

关键词： enhancer promoter enhancer-promoter interaction machine learning deep learning

Epidemiology of toxoplasmosis: role of the tick Haemaphysalis longicornis

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Infectious Diseases of Poverty 2016年第1期5卷 120-125页

作者： Yongzhi Zhou Houshuang Zhang Jie Cao haiyan gong Jinlin Zhou Key Laboratory of Animal Parasitology of Ministry of Agriculture Shanghai Veterinary Research InstituteChinese Academy of Agricultural SciencesShanghai 200241China Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses Yangzhou 225009China

Background:Toxoplasma gondii infection is mainly caused by ingestion of water or food that is contaminated with oocysts excreted by cats,or by eating raw meat containing T.gondii tissue cysts.However,oral transmission does not explain the common occurrence of toxoplasmosis in a variety of hosts,such as herbivorous animals,birds,and wild rodents.Little information exists on the maintenance of T.gondii parasites in nature and routes of transmission to domestic and wild animal hosts.Therefore,this study evaluated the role of Haemaphysalis longicornis ticks in the epidemiology of toxoplasmosis.Methods:The real-time polymerase chain reaction(qPCR)technique was used to detect the presence of T.gondii DNA in ticks collected from the field.To observe the amount of dynamic changes of T.gondii in the tick’s body and its infectivity,microinjection of green fluorescence parasites was performed.Under laboratory conditions,we evaluated if H.longicornis ticks were infected with T.gondii and their potential to transmit the infection to other hosts using traditional parasitological methods coupled with molecular detection techniques.Results:The infection rates of T.gondii parasites among field-collected adult and nymph H.longicornis ticks were 11.26%and 5.95%,respectively.T.gondii can survive and remain infective in a tick’s body for at least 15 days.We found that blood feeding of infected ticks did not transmit T.gondii to hosts,however,ingestion of infected ticks may be a transmission route between ticks and other common hosts.Conclusion:The T.gondii infection in ticks could serve as a reservoir for toxoplasmosis transmission.

关键词： Tick Haemaphysalis longicornis Toxoplasma gondii Transmission Epidemiology

Isolation and characterization of mpox virus from the first mpox case in Shenzhen,China

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Virologica Sinica 2024年第2期39卷 335-337页

作者： Lin Cheng Liuqing Yang Miao Wang Yabo Peng haiyan Wang Xiaoxiang Yang Juanjuan Zhao Mingxia Zhang Fuxiang Wang Zheng Zhang Institute for Hepatology National Clinical Research Center for Infectious DiseaseShenzhen Third People's HospitalShenzhen518112China Department of Infectious Diseases Shenzhen Third People's HospitalShenzhen 518112China The Second Affiliated Hospital School of MedicineSouthern University of Science and TechnologyShenzhen 518112China

Dear Editor,Unlike previous outbreaks of the mpox(previously known as monkeypox),which were localized in Africa and resulted in small numbers of infections due to limited human-to-human transmission,the current outbreak beginning in May 2022,has spread rapidly primarily through human-to-human transmission in non-endemic countries(gong et al.,2022).As of 27 Sep 2023,115 countries and regions have reported cases of mpox to the World Health Organization(WHO),bringing the total number of confirmed cases to 90,618 including 125 deaths.Although the number of new cases has decreased in most WHO regions in the second half of 2022,the curves reveal a long outbreak tail in different subregions of the Americas.More worrying,106 mpox cases were reported in the mainland of China in June 2023.

关键词： mainland bringing

基于密度聚类的染色质拓扑相关结构域识别方法

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生物医学工程学杂志 2024年第3期41卷 552-559页

作者：龚海燕张司臣张晓彤北京科技大学新材料技术研究院北京100083 北京科技大学计算机与通信工程学院北京100083 北京科技大学顺德创新学院广东佛山528399

高通量染色质构象捕获(Hi-C)技术的快速发展为染色质结构分析提供了丰富的基因组位点间交互作用数据,但目前基于Hi-C数据的已有拓扑相关结构域(TAD)识别方法存在准确率低、参数敏感等问题。在此背景下,本文设计并实现了一种基于空间密... 详细信息

高通量染色质构象捕获(Hi-C)技术的快速发展为染色质结构分析提供了丰富的基因组位点间交互作用数据,但目前基于Hi-C数据的已有拓扑相关结构域(TAD)识别方法存在准确率低、参数敏感等问题。在此背景下,本文设计并实现了一种基于空间密度聚类的TAD识别方法。该方法首先对原始Hi-C数据进行预处理,得到归一化后的Hi-C接触矩阵数据;然后计算位点之间的距离矩阵,基于位点的核心距离和可达距离生成可达性图,并提取聚类簇;最后基于聚类结果和TAD提取边界。该方法能够识别出内聚性更高的TAD结构,且TAD边界处富集了更多的ChIP-seq因子。实验结果表明,本文方法在TAD识别中更准确,更具有现实意义。

关键词：高通量染色质构象捕获拓扑相关结构域染色质结构密度聚类生物信息学分析

GH4169合金DP工艺中的热变形行为及应变补偿本构模型

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兵器材料科学与工程 2024年第3期47卷 1-7页

作者：贡宣洋张海燕赵忠宁波工程学院机械与汽车工程学院浙江宁波315336

针对GH4169合金的Delta工艺(delta process,DP),以δ时效处理后的GH4169(delta processed GH4169,DP-GH4169)合金为研究对象,用Gleeble-3800热/力模拟试验机在温度为954~996℃和应变率为0.005~0.1 s^(-1)下对DP-GH4169合金进行等温恒应变率压缩试验,分析其热变形行为。基于Arrhenius模型和考虑应变对材料参数的影响,建立DP-GH4169合金的应变补偿本构模型。结果表明:DP-GH4169合金热变形中的主要软化机制为动态再结晶和片层状δ相球化;当应变率高于0.01 s^(-1)时,合金发生了不连续屈服行为;当应变大于0.8后,由于加工硬化作用大于软化作用,流动应力和变形激活能随应变增大而增大;建立的应变补偿本构模型具有较好的预测精度,线性相关系数R和平均相对误差分别为0.9915和4.2498%,能用于表征DP-GH4169合金热变形时的流动应力。

关键词： DP工艺 GH4169合金热变形本构模型

除冰盐冻融作用下混凝土界面粘结强度与界面过渡区细观力学性能的关系

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材料导报 2024年第5期38卷 165-171页

作者：朱本清余红发巩旭吴成友麻海燕青海大学土木工程学院西宁810000 南京航空航天大学机场与土木工程系南京211106 青海省建筑节能材料与工程安全重点实验室西宁810000

界面过渡区(Interfacial transition zone, ITZ)是混凝土内部结构的薄弱环节,也是外界侵蚀性离子向内扩散渗透的通道。通过除冰盐快速冻融实验研究了在除冰盐冻融环境下混凝土界面宏观和细观力学性能的变化规律。结果表明,混凝土粗骨料... 详细信息

界面过渡区(Interfacial transition zone, ITZ)是混凝土内部结构的薄弱环节,也是外界侵蚀性离子向内扩散渗透的通道。通过除冰盐快速冻融实验研究了在除冰盐冻融环境下混凝土界面宏观和细观力学性能的变化规律。结果表明,混凝土粗骨料与砂浆的界面粘结强度和ITZ显微硬度在盐冻过程中均呈现出典型的两段式线性变化,即随着盐冻循环次数增加而增强的初始强化阶段和随着盐冻循环次数增加而降低的后期劣化阶段;初始界面粘结强度或ITZ显微硬度随着水胶比的增大而减小,初始强化速率减慢,后期劣化速率加快,且低水胶比的混凝土有着较好的抗盐冻性能;盐冻过程中混凝土粗骨料和砂浆的界面粘结强度与ITZ显微硬度之间具有较明显的相关性。此研究结果为盐冻环境下混凝土细观力学分析提供了基础数据。

关键词：混凝土除冰盐单面冻融界面过渡区力学性能显微硬度

Comparison of Viromes in Ticks from Different Domestic Animals in China

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Virologica Sinica 2020年第4期35卷 398-406页

作者： Tingting Zhao haiyan gong Xiaojuan Shen Wen Zhang Tongling Shan Xiangqian Yu Seong Jin Wang Li Cui Shanghai Key Laboratory of Veterinary Biotechnology School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Veterinary Research Institute Chinese Academy of Agricultural SciencesShanghai 200241China Shanghai Pudong New District Center for Animal Diseases Control and Prevention Shanghai 201299China School of Medicine Jiangsu UniversityZhenjiang 2012013China

Ticks are involved in the transmission of various arboviruses and some tick-borne viruses pose significant threats to the health of humans or livestock.This study aimed to investigate the geographical distribution of tick species and tickassociated viruses in central and eastern China.Total 573 ticks from domestic animals including dogs,sheep and cattle were collected in 2017.Two genera of ticks were identified including Rhipicephalus and Haemaphysalis.Sequencing was performed on Miseq Illumina platform to characterize the tick viromes from the four different sampling locations.Following trimming,13,640 reads were obtained and annotated to 19 virus families.From these sequences,above 37.74%of the viral reads were related to the RNA viruses.Virome comparison study revealed that the tick viral diversity was considerably different in the two identified tick genera.The viral diversity of R.microplus was significantly different from that of other Rhipicephalus species.On the other hand,substantial overlap in viral species was observed between the same genera.In addition,we found no evidence that the natural host played a major role in shaping virus diversity based on the comparison of their viromes.Rather,the geographic location seems to significantly influence the viral families.Phylogenetic study indicated that the novel negative-sense RNA viruses identified in this study was closely related to Bole tick virus 1 and 3 viruses.In conclusion,the present study provides a baseline for comparing viruses detected in ticks,according to species,natural hosts,and geographic locations.

关键词： Ticks Viral metagenomics Virome