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An executable framework for modeling and validating cooperative capability requirements in emergency response system

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Journal of Systems Engineering and Electronics 2021年第4期32卷 889-906页

作者： CHAI Lei WANG Zhixue HE Ming HE Hongyue YU Minggang Institute of Command Control Engineering Army Engineering University of PLANanjing 210007China

As the scale of current systems become larger and larger and their complexity is increasing gradually,research on executable models in the design phase becomes significantly important as it is helpful to simulate the execution process and capture defects of a system in advance.Meanwhile,the capability of a system becomes so important that stakeholders tend to emphasize their capability requirements when developing a system.To deal with the lack of official specifications and the fundamental theory basis for capability requirement,we propose a cooperative capability requirements(CCR)meta-model as a theory basis for researchers to refer to in this research domain,in which we provide detailed definition of the CCR concepts,associations and rules.Moreover,we also propose an executable framework,which may enable modelers to simulate the execution process of a system in advance and do well in filling the inconsistency and semantic gaps between stakeholders’requirements and their models.The primary working mechanism of the framework is to transform the alf activity meta-model into the communicating sequential process(CSP)process meta-model based on some mapping rules,after which the internal communication mechanism between process nodes is designed to smooth the execution of behaviors in a CSP system.Moreover,a validation method is utilized to check the correctness and consistency of the models,and a self-fixing mechanism is used to fix the errors and warnings captured during the validation process automatically.Finally,a validation report is generated and fed back to the modelers for system optimization.

关键词： executable model capability requirement consistency validation alf epsilon

A new alf from Litopenaeus vannamei and its SNPs related to WSSV resistance

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Chinese Journal of Oceanology and Limnology 2014年第6期32卷 1232-1247页

作者：刘敬文于洋李富花张晓军相建海 Key Laboratory of Experimental Marine Biology Institute of OceanologyChinese Academy of Sciences University of Chinese Academy of Sciences National & Local Joint Engineering Laboratory of Ecological Mariculture Institute of OceanologyChinese Academy of Sciences

Anti-lipopolysaccharide factors(alfs) are basic components of the crustacean immune system that defend against a range of pathogens.The cDNA sequence of a new alf,designated nLvalf2,with an open reading frame encoding 132 amino acids was cloned.Its deduced amino acid sequence contained the conserved functional domain of alfs,the LPS binding domain(LBD).Its genomic sequence consisted of three exons and four introns.nLvalf2 was mainly expressed in the Oka organ and gills of shrimps.The transcriptional level of nLvalf2 increased significantly after white spot syndrome virus(WSSV) infection,suggesting its important roles in protecting shrimps from WSSV.Single nucleotide polymorphisms(SNPs)were found in the genomic sequence of nLvalf2,of which 38 were analyzed for associations with the susceptibility/resistance of shrimps to WSSV.The loci g.2422 A>G,g.2466 T>C,and g.2529 G>A were significantly associated with the resistance to WSSV(P<0.05).These SNP loci could be developed as markers for selection of WSSV-resistant varieties of Litopenaeus vannamei.

关键词：单核苷酸多态性凡纳滨对虾 WSSV alf cDNA序列白斑综合症病毒氨基酸序列基因组序列

合浦绒螯蟹四种抗菌肽基因克隆及在弧菌胁迫下的表达

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合浦绒螯蟹四种抗菌肽基因克隆及在弧菌胁迫下的表达

作者：任天娇北部湾大学

学位级别：硕士

合浦绒螯蟹(Eriocheir hepuensis)俗称毛蟹,属绒螯蟹属,和中华绒螯蟹为不同的地理亚种。合浦绒螯蟹经济价值较高,易受到各种环境因子胁迫,但关于合浦绒螯蟹应对这些因子胁迫的免疫调控研究相比于中华绒螯蟹较少。因此,本研究对抗菌肽两... 详细信息

合浦绒螯蟹(Eriocheir hepuensis)俗称毛蟹,属绒螯蟹属,和中华绒螯蟹为不同的地理亚种。合浦绒螯蟹经济价值较高,易受到各种环境因子胁迫,但关于合浦绒螯蟹应对这些因子胁迫的免疫调控研究相比于中华绒螯蟹较少。因此,本研究对抗菌肽两个家族中的四个基因进行克隆与表达研究。主要研究结果如下:1)alf2基因克隆及在弧菌胁迫下的表达合浦绒螯蟹alf2(Ehalf2)基因CDS长为363 bp,编码了120个氨基酸。序列分析发现,Ehalf2具有alf家族典型的结构域,即含有两个保守半胱氨酸的LPS结合域(LBD)。在溶藻弧菌胁迫下,在心脏中不同时间段Ehalf2的表达量多数高于肝胰腺和鳃。在肝胰腺中,Ehalf2基因在48 h时表达量最高;在鳃中,Ehalf2基因在6 h时表达量最高;在心脏中,Ehalf2基因在12 h时表达量最高。在副溶血弧菌胁迫下,在肝胰腺中不同时间段Ehalf2的表达量多数高于心脏和鳃。在肝胰腺和鳃中,Ehalf2基因都在12 h时表达量最高;在心脏中,Ehalf2基因在6 h时表达量达到最高值。2)alf3基因克隆及在弧菌胁迫下的表达合浦绒螯蟹alf3(Ehalf3)基因CDS长为372 bp,编码了123个氨基酸。序列分析发现,Ehalf3具有含两个保守半胱氨酸的LPS结合域(LBD)。在溶藻弧菌胁迫下,在肝胰腺和心脏中不同时间段Ehalf3的表达量多数差异不显著。在肝胰腺中,Ehalf3基因在3 h时表达量最高;在鳃中,Ehalf3基因在9 h时表达量最高;在心脏中,Ehalf3基因都在12 h时表达量最高。在副溶血弧菌胁迫后,在肝胰腺中不同时间段Ehalf3的表达量都多数高于鳃。在肝胰腺中,Ehalf3基因在48 h时表达量最高;在鳃中,Ehalf3基因在12 h时表达量最高;在心脏中,Ehalf3基因在6 h时表达量达到最高值。3)Crustin1基因克隆及在弧菌胁迫下的表达合浦绒螯蟹Crustin1(EhCru1)基因CDS长为315 bp,编码了104个氨基酸。序列分析发现,EhCru1拥有一个信号肽、一个Cys-rich区和一个含8个保守半胱氨酸的WAP结构域。根据分类原则,EhCru1属于Ⅰ型Crustin。在溶藻弧菌胁迫下,在心脏中不同时间段EhCru1的表达量多数高于肝胰腺。在肝胰腺、鳃和心脏中,EhCru1基因都在48 h时表达量达到最高值。在副溶血弧菌胁迫下,在肝胰腺中不同时间段EhCru1的表达量多数高于鳃和心脏。在肝胰腺和鳃中,EhCru1基因都在12 h时表达量最高;在心脏中,EhCru1基因都在6 h时表达量达到最高值。4)Crustin2基因克隆及在弧菌胁迫下的表达合浦绒螯蟹Crustin2(EhCru2)基因CDS长为339 bp,编码了112个氨基酸。序列分析发现,EhCru2拥有一个信号肽、一个Cys-rich区和一个含9个保守半胱氨酸的WAP结构域。根据分类原则,EhCru2属于Ⅰ型Crustin。在溶藻弧菌胁迫下,在心脏中不同时间段EhCru2的表达量都高于肝胰腺。在肝胰腺和心脏中,EhCru2都在48 h时表达量达到最高值;在鳃中,EhCru2基因在3 h时表达量最高。在副溶血弧菌胁迫后,在肝胰腺中不同时间段EhCru2的表达量都高于鳃和心脏。在肝胰腺和鳃中,EhCru2基因都在12 h时表达量最高;在心脏中,EhCru2基因都在6 h时表达量达到最高值。综上,本研究克隆了合浦绒螯蟹抗菌肽中的抗脂多糖因子Ehalf2和Ehalf3基因以及Crustin基因家族中的EhCru1和EhCru2基因,通过荧光定量PCR分析了它们在不同组织和受到不同细菌胁迫后的表达变化情况,发现合浦绒螯蟹在溶藻弧菌或副溶血弧菌胁迫下,Ehalf2、Ehalf3基因和EhCru1、EhCru2基因的表达都显著上调,说明本实验中的四种抗菌肽基因都可能参与了合浦绒螯蟹的细菌免疫应答反应。但对于它们具体的功能及作用机制还有待于应用RNAi和过表达等技术更深一步地研究。

关键词：合浦绒螯蟹 alf Crustin 基因克隆基因表达弧菌

Aberrant methylation of the TDMR of the GTF2AIL promoter does not affect fertilisation rates via TESE in patients with hypospermatogenesis

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Asian Journal of Andrology 2013年第5期15卷 634-639页

作者： Kazuhiro Sugimoto Eitetsu Koh Masashi Iijima Masaki Taya Yuji Maeda Mikio Namiki Departments of Integrative Cancer Therapy and Urology Andrology Unit Kanazawa University Graduate School of Medical Science Takara Kanazawa 920-8641 Japan

Increasing evidence shows a relationship between epigenetic regulation and male infertility. The GTF2A1L gene promoter contains the DNA methylation site of a tissue-specific differentially methylated region （TDMR）. Eighty-six patients with non-obstructive azoospermia were assessed for the DNA methylation state of CpG islands in the GTF2AIL promoter using testicular genomic DNA. Based on histological criteria, 26 of the 86 patients had normal spermatogenesis （controls）, 17 had hypospermatogenesis and 26 had a Sertoli cell-only phenotype or tubular sclerosis. GTF2AIL TDMR methylation was significantly lower in testes DNA from control samples than from hypospermatogenic samples （P=0.029）. Patients with hypospermatogenesis were divided into two subgroups： high DNA methylation （HM, n=5） and low DNA methylation （LM, n= 12）. The GTF2AIL TDMR methylation rate differed significantly between the HM and LM groups （P=0.0019）, and GTF2A 1L expression was significantly higher among the LM than in the HM patients （P=0.023）. High TDMR methylation was correlated with low GTF2AIL gene expression levels. Both groups demonstrated relatively good outcomes with respect to sperm retrieval, fertilisation, pregnancy and childbirth rates. We observed that aberrant GTF2AIL gene expression was not correlated with fertilisation rates. The testicular sperm extraction （TESE） technique may be used to overcome male infertility due to aberrant TDMR methvlation.

关键词： alf azoospermia CpG island hypospermatogenesis MALDI-TOF MS testicular sperm extraction （TESE）

利用生物信息学筛查APAP诱发alf患者外周血中的关键基因

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河南大学学报（自然科学版） 2022年第2期52卷 179-191页

作者：邹巧玲黄卫锋袁秋林关涛三峡大学人民医院湖北宜昌443002 三峡大学医学院湖北宜昌443002

从GEO数据库(https://www.***.nlm.***.gov/)下载数据集GSE80751,该数据集包含22例人体血液样本(对照组5例,ALI组5例,alf组12例),以|Log FC|>1.5,P<0.05分别筛选出急性肝损伤(acute liver injury,ALI)组与对照组、急性肝衰竭(acute liv... 详细信息

从GEO数据库(https://www.***.nlm.***.gov/)下载数据集GSE80751,该数据集包含22例人体血液样本(对照组5例,ALI组5例,alf组12例),以|Log FC|>1.5,Palf)组与对照组的差异表达基因,并分别对其进行功能富集分析和信号通路富集分析,筛选对乙酰氨基酚(acetaminophen,APAP)诱发alf过程中的关键基因及重要通路.其次构建差异表达基因在蛋白层面的生物网络,并将网络数据导入Cytoscape实现可视化,利用Cytoscape中的插件寻找与疾病发生密切相关的功能模块及核心基因.以ALI组数据为对照,重点分析了alf组数据,结果筛选出alf组满足阈值要求的差异表达基因共266个,包括上调基因239个,下调基因27个,其中alf组中特异性上调基因120个,特异性下调基因15个,且基因NAMPT在ALI组表达上调,在alf组表达下调.alf组差异表达基因的GO分析结果显示,上调基因主要参与细胞分化和细胞周期调控等过程,下调基因主要参与免疫反应和细胞因子介导的炎症反应等过程.KEGG通路分析结果显示,上调基因主要富集于细胞周期调控、系统性红斑狼疮、补体和凝血级联等通路,下调基因没有富集到明显通路.对比分析ALI组和alf组所获取的疾病相关功能模块,发现p53信号通路与alf的发生具有相关性.利用cytoHubba插件中的网络拓扑算法MCC在alf组差异表达基因中共筛选出25个显著差异表达基因,且都表达上调,进一步验证其在发生alf的肝组织细胞中的差异表达情况,发现NCAPG、DLGAP5、TOP2A、ASPM、NUSAP1和MKI67在alf组血液细胞和肝细胞中都显著差异表达.本文分析结果表明,细胞周期调控,免疫、炎症反应,细胞增殖与衰老等生物过程和p53信号通路可能与alf的发展过程相关,基因NCAPG、DLGAP5、TOP2A、ASPM、NUSAP1、MKI67和NAMPT可能是研究APAP诱发alf发生的新靶点和潜在血液标志物.

关键词：生物信息学 APAP alf 差异表达基因关键基因

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基于足尺alf车辙试验的车辙等效轴载换算

长安大学学报（自然科学版） 2013年第1期33卷 11-15页

作者：纪小平郑南翔牛思胜侯月琴长安大学特殊地区公路工程教育部重点实验室陕西西安710064 甘肃路桥公路投资有限公司甘肃兰州730030

为了确定沥青路面的车辙等效轴载换算系数,对3种路面结构进行了足尺alf(Acceler-ated Load Facility)加速加载车辙试验,并进行理论分析。根据车辙等效原则建立了轴载换算系数的方法;以3种路面结构在3种工况下的车辙数据为基础,得出车辙... 详细信息

为了确定沥青路面的车辙等效轴载换算系数,对3种路面结构进行了足尺alf(Acceler-ated Load Facility)加速加载车辙试验,并进行理论分析。根据车辙等效原则建立了轴载换算系数的方法;以3种路面结构在3种工况下的车辙数据为基础,得出车辙深度与轴载作用次数的关系,进而求解不同结构的车辙等效系数和车辙等效轴载换算系数。研究结果表明:3种路面结构的车辙等效轴载换算系数分别为4.56、4.90和2.71;改性沥青混合料比基质沥青混合料具有更小的轴载换算系数,说明其具有更低的轴载敏感性;推荐改性沥青混合料的车辙等效轴载换算系数为2.7,基质沥青混合料的为4.9。

关键词：道路工程沥青路面 alf 车辙等效轴载换算

BioLiverⅠ型生物人工肝支持系统治疗两种急性肝衰竭犬的实验研究

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