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Gene regulatory network inference based on causal discovery integrating with graph neural network

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Quantitative Biology 2023年第4期11卷 434-450页

作者： Ke Feng hongyang jiang Chaoyi Yin Huiyan Sun School of Artificial Intelligence Jilin UniversityChangchunChina international Center of Future Science Jilin UniversityChangchunChina Engineering Research Center of Knowledge-Driven Human-Machine Intelligence Ministry of EducationChangchunChina

Gene regulatory network (GRN) inference from gene expression data is asignificant approach to understanding aspects of the biological system.Compared with generalized correlation-based methods, causality-inspiredones seem more rational to infer regulatory relationships. We proposeGRINCD, a novel GRN inference framework empowered by graph representationlearning and causal asymmetric learning, considering both linearand non-linear regulatory relationships. First, high-quality representation ofeach gene is generated using graph neural network. Then, we apply theadditive noise model to predict the causal regulation of each regulator-targetpair. Additionally, we design two channels and finally assemble them forrobust prediction. Through comprehensive comparisons of our frameworkwith state-of-the-art methods based on different principles on numerousdatasets of diverse types and scales, the experimental results show that ourframework achieves superior or comparable performance under variousevaluation metrics. Our work provides a new clue for constructing GRNs,and our proposed framework GRINCD also shows potential in identifyingkey factors affecting cancerdevelopment.

关键词： causal discovery ensemble learning gene regulatory network inference gene regulatory networks graph neural network key regulators of disease development

新型Na^(+)/H^(+)逆向转运蛋白UPF0118的Na^(+)结合鉴定

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东北农业大学学报 2024年第3期55卷 62-70页

作者：李红洋华贝杰姜巨全东北农业大学生命科学学院哈尔滨150030

UPF0118蛋白是一种新型Na^(+)(Li^(+))/H^(+)逆向转运蛋白,属于AI-2E超家族,目前已被划分至Na^(+)/H^(+)逆向转运蛋白亚家族,但无直接证据表明该蛋白可与Na+产生相互作用。为鉴定UPF0118蛋白是否具有Na^(+)结合功能,利用PCR技术扩增upf0... 详细信息

UPF0118蛋白是一种新型Na^(+)(Li^(+))/H^(+)逆向转运蛋白,属于AI-2E超家族,目前已被划分至Na^(+)/H^(+)逆向转运蛋白亚家族,但无直接证据表明该蛋白可与Na+产生相互作用。为鉴定UPF0118蛋白是否具有Na^(+)结合功能,利用PCR技术扩增upf0118基因编码序列,通过Eco RⅠ和PstⅠ酶切位点构建至原核表达载体p ETDuet-1,转化至E. coli BL21*(DE3),对诱导后大量表达的蛋白进行Ni^(2+)亲和层析和凝胶过滤层析,利用等温滴定量热技术对纯化蛋白进行滴定。结果表明,在pH 5.5条件下,Na^(+)滴入导致蛋白溶液产生明显放热现象。在pH 5.5条件下该蛋白具有Na^(+)结合功能,证明该蛋白Na+结合功能为其功能单元与分子机制的研究奠定基础。

关键词： UPF0118 Na^(+)/H^(+)逆向转运蛋白等温滴定量热法蛋白纯化

Effects of Probiotics on Gut Microbiota in Type 2 Diabetes Patients

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Journal of Advances in Medicine Science 2022年第1期5卷 1-6页

作者： Yan Zhang hongyang jiang Dianyuan Liu Shengxue Li Qing Wang Department of Endocrinology and Metabolism China-Japan Union Hospital of Jilin UniversityChangchunJilin130021China

Objective:To study the effect of probiotics on gut microbiota in Type 2 diabetes patients and its clinical application value.Methods:Select Type 2 diabetes patients to take orally probiotics for 24 weeks,collect stool samples of subjects at the baseline and end of the trial,identify and analyze gut microbiota of each sample by 16srRNA high-throughput sequencing,and compare the changes of blood glucose,blood lipid and insulin resistance before and after the intervention.Results:A total of 75 patients completed clinical observations.16srRNA high-throughput sequencing showed that the proportion of the subjects with increased Actinobacteria and Tenericutes at the end of the trial has increased(37.8% and 75.7% respectively).The genus level analysis showed that the number of subjects with increased intestinal probiotics and with decreased conditioned pathogens all increased.Cluster analysis before and after intervention showed that the gut microbiota of samples in the same group had a higher similarity.Compared with the subjects at the baseline status,at the end of the trial after the intervention,fasting blood glucose(FBG)of the subjects significantly decreased(P<0.05),the proportion of the subjects with triglyceride(TG)and cholesterol up to standard increased,and HOMA-IR was significantly improved(P<0.05).Conclusions:Probiotics can regulate the gut microbiota of Type 2 diabetes patients,promote fasting blood glucose(FBG)to reach the standard and improve insulin resistance,and help improve lipid metabolism.

关键词： Probiotics Type 2 diabetes Insulin resistance Gut microbiota

Chinese Society of Cardiology guidelines on the diagnosis and treatment of adult fulminant myocarditis

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Science China(Life Sciences) 2024年第5期67卷 913-939页

作者： Chinese Society of Cardiology,Chinese Medical Association,Writing Group jiangang jiang hongyang Shu Dao Wen Wang Rutai Hui Chenze Li Xiao Ran Hong Wang Jing Zhang Shaoping Nie Guanglin Cui Dingcheng Xiang Qun Shao Shengyong Xu Discussion experts:Ning Zhou Yuming Li Wei Gao Yuguo Chen Yuan Bian Guoping Wang Liming Xia Yan Wang Chunxia Zhao Zhiren Zhang Yuhua Zhao Jianan Wang Shaoliang Chen Hong jiang Jing Chen Xianjin Du Mao Chen Yinxian Sun Sheng Li Hu Ding Xueping Ma Hesong Zeng Li Lin Shenghua Zhou Likun Ma Ling Tao Juan Chen Yiwu Zhou Xiaomei Guo 不详 Tongji Hospital Tongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China Fuwai Hospital National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100037China Zhongnan Hospital of Wuhan University Wuhan 430062China Fuwai Huazhong Cardiovascular Hospital Zhengzhou 450003China Beijing Anzhen Hospital Capital Medical UniversityBeijing 100029China Guangzhou General Hospital of Guangzhou Military Command Guangzhou 510010China Harbin Medical University Cancer Hospital Harbin 150081China Union Hospital Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China Taida Hospital Tianjin 300457China Peking University Third Hospital Beijing 100191China Qilu Hospital of Shandong University Jinan 250012China Kanghua Hospital DongguanGuangzhou 523080China Second Affiliated Hospital Zhejiang University School of Medicine Hangzhou 310003China Nanjing First Hospital Nanjing Medical UniversityNanjing 210006China Renmin Hospital of Wuhan University Wuhan 430060Wuhan West China Hospital Sichuan UniversityChengdu 610044China First Hospital of China Medical University Shenyang 110002China General Hospital of Ningxia Medical University Yinchuan 750003China The Second Xiangya Hospital Central South UniversityChangsha 410012China The First Affiliated Hospital of USTC University of Science and Technology of ChinaHefei 230002China The First Affiliated Hospital of Air Force Medical University Xi’an 710032China Central Hospital of Wuhan City Wuhan 430014China Tongji Medical College Huazhong University of Science and TechnologyWuhan 430030China

Fulminant myocarditis is an acute diffuse inflammatory disease of myocardium.It is characterized by acute onset,rapid progress and high risk of death.Its pathogenesis involves excessive immune activation of the innate immune system and formation of inflammatory storm.According to China’s practical experience,the adoption of the“life support-based comprehensive treatment regimen”(with mechanical circulation support and immunomodulation therapy as the core)can significantly improve the survival rate and long-term prognosis.Special emphasis is placed on very early identification,very early diagnosis,very early prediction and very early treatment.

关键词： fulminant myocarditis guidelines life support-based comprehensive treatment regimen diagnosis treatment cytokine storm overactivation of immunity

Evolution of microstructure and texture of AZ80 magnesium alloy under hot torsion with constant decreasing temperature rate

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Journal of Magnesium and Alloys 2024年第4期12卷 1619-1637页

作者： Yongbiao Yang Jinxuan Guo Cuiying Wang Wenxuan jiang Zhimin Zhang Qiang Wang Xing Zhang College of Materials Science and Engineering North University of ChinaLane 3Xueyuan RoadTaiyuanShanxi 030051China North hongyang mechanical and electronic limited company of Henan Province China

Hot torsion tests for AZ80 magnesium alloy were carried out in the temperature range of 380℃-260℃,with a constant decreasing temperature rate of 10℃/s in order to weaken the basal texture and refine the grains.The results indicated that the average grain sizes were refined forming gradient structure with increasing specimen radial position from center(12.2-5.4μm),and that the initial basal texture intensity of the extruded magnesium alloy was weakened from 46.2 to 8.3.Furthermore,the extension twins(ETs)could be disintegrated from the twins forming separated twins with smaller sizes.Interestingly,ETs with the same twin variant intersecting with each other could be coalesced forming grains with similar orientation,while ETs with different twin variants were separated by twins boundaries contributing to grain refinement.Moreover,in addition to the conventional continuous dynamic recrystallized(CDRX)grains with 30˚orientation rotated around C-axis of the parent grains,CDRXed grains with 30˚rotation around a-axis and random rotation axis were also discerned.Besides,the CDRX evolution induced twins were also elaborated,exhibiting the complex competition between CDRX and twining.Hot torsion deformation with constant decreasing temperatures rate is an effective way of grain refinement and texture modification.

关键词： Texture Microstructure Hot torsion Decreasing temperature AZ80

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尾矿库环境事故因素分析及建议

环境工程技术学报 2024年第3期14卷 1026-1033页

作者：袁华山张明慧陶霞王宏洋赵鑫张国宁江梅北京市密云区生态环境局环境基准与风险评估国家重点实验室中国环境科学研究院湖南省水处理过程与装备工程技术研究中心中机国际工程设计研究院有限责任公司生态环境部机动车排污监控中心中国环境科学研究院生态环境部环境标准研究所中国环境科学研究院

基于我国尾矿库环境风险特征,分析近年来尾矿库环境事故原因,并针对环境事故发生后的应急处理及环境次生灾害应急处理展开讨论。针对我国尾矿资源存量大、类型多,资源综合利用率较低以及矿山企业生产管理水平不高的实际问题,提出建议:... 详细信息

基于我国尾矿库环境风险特征,分析近年来尾矿库环境事故原因,并针对环境事故发生后的应急处理及环境次生灾害应急处理展开讨论。针对我国尾矿资源存量大、类型多,资源综合利用率较低以及矿山企业生产管理水平不高的实际问题,提出建议:一是要实现尾矿资源的综合利用,达到减量减排的目的;二是要对尾矿库采取系统性的污染治理,特别是针对因不可抗拒因素而引起的环境污染问题;三是要加强安全管理,减少溃坝等安全风险,从源头降低安全事故次生环境污染风险。

关键词：尾矿库尾矿环境风险应急处置

Chinese Society of Cardiology guidelines on the diagnosis and treatment of adult fulminant myocarditis

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Science China Life Sciences 2024年

作者： jiangang jiang hongyang Shu Dao Wen Wang Rutai Hui Chenze Li Xiao Ran Hong Wang Jing Zhang Shaoping Nie Guanglin Cui Dingcheng Xiang Qun Shao Shengyong Xu Ning Zhou Yuming Li Wei Gao Yuguo Chen Yuan Bian Guoping Wang Liming Xia Yan Wang Chunxia Zhao Zhiren Zhang Yuhua Zhao Jianan Wang Shaoliang Chen Hong jiang Jing Chen Xianjin Du Mao Chen Yinxian Sun Sheng Li Hu Ding Xueping Ma Hesong Zeng Li Lin Shenghua Zhou Likun Ma Ling Tao Juan Chen Yiwu Zhou Xiaomei Guo Peking University Third Hospital Qilu Hospital of Shandong University The First Affiliated Hospital of Air Force Medical University Zhongnan Hospital of Wuhan University First Hospital of China Medical University General Hospital of Ningxia Medical University The First Affiliated Hospital of USTC University of Science and Technology of China Fuwai Hospital National Center for Cardiovascular Diseases Chinese Academy of Medical Sciences and Peking Union Medical College Beijing Anzhen Hospital Capital Medical University Chinese Medical Association Harbin Medical University Cancer Hospital Union Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Renmin Hospital of Wuhan University Central Hospital of Wuhan City Taida Hospital Guangzhou General Hospital of Guangzhou Military Command West China Hospital Sichuan University Nanjing First Hospital Nanjing Medical University Chinese Society of Cardiology Kanghua Hospital Dongguan Fuwai Huazhong Cardiovascular Hospital Tongji Hospital Tongji Medical College Huazhong University of Science and Technology The Second Xiangya Hospital Central South University Second Affiliated Hospital Zhejiang University School of Medicine

Fulminant myocarditis is an acute diffuse inflammatory disease of myocardium. It is characterized by acute onset, rapid progress and high risk of death. Its pathogenesis involves excessive immune activation of the innate immune system and formation of inflammatory storm.According to China’s practical experience, the adoption of the “life support-based comprehensive treatment regimen”(with mechanical circulation support and immunomodulation therapy as the core) can significantly improve the survival rate and long-term prognosis. Special emphasis is placed on very early identification,very early diagnosis,very early prediction and very early treatment.

关键词：

肺移植术后膈肌移动度与自主呼吸试验期间呼吸功能参数的相关性

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临床超声医学杂志 2024年第4期26卷 306-309页

作者：王宋姜淑云张佳悦董妍田静许红阳南京医科大学无锡医学中心、南京医科大学附属无锡人民医院重症医学科江苏省无锡市214000

目的应用超声测量肺移植术后患者膈肌移动度(DE),分析其与自主呼吸试验(SBT)期间呼吸功能参数的相关性。方法选取于我院心肺诊疗中心行肺移植术患者114例,根据肺移植术后通过SBT的初次撤机结果分为撤机成功组92例和撤机失败组22例,均于... 详细信息

目的应用超声测量肺移植术后患者膈肌移动度(DE),分析其与自主呼吸试验(SBT)期间呼吸功能参数的相关性。方法选取于我院心肺诊疗中心行肺移植术患者114例,根据肺移植术后通过SBT的初次撤机结果分为撤机成功组92例和撤机失败组22例,均于SBT期间监测呼吸功能参数,包括血氧分压(PaO_(2))、潮气量(VT)、浅快呼吸指数(RSBI)及呼吸机支持时间;应用超声测量DE,比较两组上述参数的差异。采用Pearson相关分析法分析DE与呼吸功能参数的相关性。结果撤机成功组DE、PaO_(2)、VT均高于撤机失败组,RSBI低于撤机失败组,呼吸机支持时间短于撤机失败组,差异均有统计学意义(均P<0.05)。相关性分析显示,DE与PaO_(2)、VT、RSBI及呼吸机支持时间均存在相关性(r=0.478、0.734、-0.593、-0.567,均P<0.05)。结论肺移植术后超声所测DE与SBT期间呼吸功能参数均相关,可用于肺移植术后呼吸功能的评估以指导撤机时机的选择。

关键词：超声检查膈肌肺移植术呼吸监测

自我威胁启动下不同类型高自尊大学生对攻击性词语的注意偏向

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中国心理卫生杂志 2024年第5期38卷 452-457页

作者：段彩彬周会姜宇朱红阳王彤黄馨慧蹇东伟沈阳农业大学学生处沈阳110866 辽宁师范大学心理学院辽宁大连116029 辽宁金融职业学院教务处沈阳110122

目的:考察自我威胁启动下,不同类型高自尊大学生对攻击性词语的注意偏向特点。方法:选取650名大学生,通过外显自尊量表(SES)选出高自尊被试。然后,通过内隐自尊测验(IAT)筛选出不同类型高自尊(脆弱型、安全型)组各43人。每组分别参加不... 详细信息

目的:考察自我威胁启动下,不同类型高自尊大学生对攻击性词语的注意偏向特点。方法:选取650名大学生,通过外显自尊量表(SES)选出高自尊被试。然后,通过内隐自尊测验(IAT)筛选出不同类型高自尊(脆弱型、安全型)组各43人。每组分别参加不同难易程度的瑞文标准推理测验(SPM)完成自我威胁启动,然后完成空间线索实验。当线索无效时,根据两组对攻击性词语的反应时与中性词语的反应时差值(RTI)的变异程度,获得注意偏向特点。结果:在高自我威胁启动下,脆弱型高自尊组RTI值高于安全型高自尊组(P0.05)。结论:相较于安全型高自尊,脆弱型高自尊更易受自我威胁的影响,其在高自我威胁启动下,注意偏向表现为注意固着。

关键词：脆弱型高自尊安全型高自尊自我威胁启动注意偏向