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Hierarchical learning of gastric cancer molecular subtypes by integrating multi-modal DNA-level omics data and clinical stratification

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Quantitative Biology 2024年第2期12卷 182-196页

作者： Binyu yang Siying Liu Jiemin Xie Xi Tang Pan Guan Yifan Zhu Xuemei Liu yunhui Xiong Zuli yang Weiyao Li Yonghua Wang Wen Chen Qingjiao Li Li C.Xia Department of Statistics and Financial Mathematics School of MathematicsSouth China University of TechnologyGuangzhouChina School of Physics and Optoelectronics South China University of TechnologyGuangzhouChina Department of Pathology The Sixth Affiliated HospitalSun Yat-sen UniversityGuangzhouChina School of Food Science and Engineering South China University of TechnologyGuangzhouChina Department of Laboratory Medicine the Eighth Affiliated HospitalSun Yat-sen UniversityShenzhenChina

Molecular subtyping of gastric cancer(GC)aims to comprehend its genetic ***,the efficacy of current subtyping methods is hampered by their mixed use of molecular features,a lack of strategy optimization,and the limited availability of public GC *** is a pressing need for a precise and easily adoptable subtyping approach for early DNA-based screening and *** on TCGA subtypes,we developed a novel DNA-based hierarchical classifier for gastric cancer molecular subtyping(HCG),which employs gene mutations,copy number aberrations,and methylation patterns as *** incorporating the closely related esophageal adenocarcinomas dataset,we expanded the TCGA GC dataset for the training and testing of HCG(n=453).The optimization of HCG was achieved through three hierarchical strategies using Lasso-Logistic regression,evaluated by their overall the area under receiver operating characteristic curve(auROC),accuracy,F1 score,the area under precision-recall curve(auPRC)and their capability for clinical stratification using multivariate survival ***-specific DNA alteration biomarkers were discerned through difference tests based on HCG defined *** HCG classifier demonstrated superior performance in terms of overall auROC(0.95),accuracy(0.88),F1 score(0.87)and auPRC(0.86),significantly improving the clinical stratification of patients(overall p-value=0.032).Difference tests identified 25 subtype-specific DNA alterations,including a high mutation rate in the SYNE1,ITGB4,and COL22A1 genes for the MSI subtype,and hypermethylation of ALS2CL,KIAA0406,and RPRD1B genes for the EBV *** is an accurate and robust classifier for DNA-based GC molecular subtyping with highly predictive clinical stratification *** training and test datasets,along with the analysis programs of HCG,are accessible on the GitHub website(***/LabxSCUT).

关键词： DNA alterations gastric cancer hierarchical classification molecular subtyping multi-omics

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A competitive microcystin-LR immunosensor based on Au NPs@metal-organic framework(MIL-101)

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Chinese Chemical Letters 2019年第3期30卷 664-667页

作者： Kunlei Zhang Kun Dai Ruyan Bai Yuchan Ma Yan Deng Delei Li Xi Zhang Rong Hu yunhui yang College of Chemistry and Chemical Engineering Yunnan Normal University

An electrochemical immunosensor was developed for ultrasensitive detection of microcystin-LR in water. MIL-101, a porous metal-organic frameworks(MOFs) material based on trivalent chromium skeleton were synthesized by hydrothermal synthesis method, and loaded with Au nanoparticles(Au NPs) to prepare Au NPs@MIL-101 composite materials which were used as a marker to label anti microcystin-LR(Anti-MC-LR). The composite materials have strong catalytic properties to the oxidation of ascorbic acid. Anti-MC-LR was immobilized on glassy carbon electrode surface using electrodeposition graphene oxide(GO) as an immobilization matrix to construct a competitive microcystin-LR immunosensor. The electrochemical immunosensor display linear relationship in the range of 0.05 ng/mL-75 μg/mL with linear correlation coefficient of 0.9951 and detection limit of 0.02 ng/mL(S/N = 3). This sensor was used to detect microcystin-LR in the water sample. The recovery was 102.43%,which is satisfied. The good testing results indicate the sensor has a great prospect in practical application.

关键词： Microcystin-LR Metal-organic frameworks MIL-101 Competitive Electrochemical immunosensor

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Human umbilical cord mesenchymal stem cells attenuate diabetic nephropathy through the IGF1R-CHK2-p53 signalling axis in male rats with type 2 diabetes mellitus

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第7期25卷 568-580页

作者： Hao ZHANG Xinshu WANG Bo HU Peicheng LI Yierfan ABUDUAINI Hongmei ZHAO Ayinaer JIEENSIHAN Xishuang CHEN Shiyu WANG Nuojin GUO Jian YUAN yunhui LI Lei LI Yuntong yang Zhongmin LIU Zhaosheng TANG Hua WANG Department of Endocrinology Shanghai East HospitalSchool of MedicineTongji UniversityShanghai 200120China Research Center for Translational Medicine Shanghai East HospitalSchool of MedicineTongji UniversityShanghai 200120China Department of Cardiology Shanghai East HospitalSchool of MedicineTongji UniversityShanghai 200120China Department of Biochemistry and Molecular Biology School of MedicineTongji UniversityShanghai 200331China Shanghai Institute of Stem Cell Research and Clinical Translation Shanghai East HospitalShanghai 200120China Ji’an Hospital Shanghai East HospitalJi’an 343000China

diabetes mellitus(DM)is a disease syndrome characterized by chronic hyperglycaemia.A long-term high-glucose environment leads to reactive oxygen species(ROS)production and nuclear DNA *** umbilical cord mesenchymal stem cell(HUcMSC)infusion induces significant antidiabetic effects in type 2 diabetes mellitus(T2DM)***-like growth factor 1(IGF1)receptor(IGF1R)is important in promoting glucose metabolism in diabetes;however,the mechanism by which HUcMSC can treat diabetes through IGF1R and DNA damage repair remains *** this study,a DM rat model was induced with high-fat diet feeding and streptozotocin(STZ)administration and rats were infused four times with *** glucose,interleukin-6(IL-6),IL-10,glomerular basement membrane,and renal function were *** that interacted with IGF1R were determined through coimmunoprecipitation *** expression of IGF1R,phosphorylated checkpoint kinase 2(p-CHK2),and phosphorylated protein 53(p-p53)was examined using immunohistochemistry(IHC)and western blot ***-linked immunosorbent assay(ELISA)was used to determine the serum levels of 8-hydroxydeoxyguanosine(8-OHdG).Flow cytometry experiments were used to detect the surface markers of *** identification of the morphology and phenotype of HUcMSC was performed by way of oil red“O”staining and Alizarin red *** rats exhibited abnormal blood glucose and IL-6/10 levels and renal function changes in the glomerular basement membrane,increased the expression of IGF1 and ***1R interacted with CHK2,and the expression of p-CHK2 was significantly decreased in IGF1R-knockdown *** cisplatin was used to induce DNA damage,the expression of p-CHK2 was higher than that in the IGF1R-knockdown group without cisplatin *** infusion ameliorated abnormalities and preserved kidney structure and function in DM *** expression of IGF1,IGF1R,p-CHK2,and p-p53,and the level of 8-OHdG in the DM group increased sign

关键词： Insulin-like growth factor 1 receptor(IGF1R) Checkpoint kinase 2(CHK2) Protein 53(p53) Diabetes mellitus Human umbilical cord mesenchymal stem cell(HUcMSC) DNA damage repair

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基于相关滤波的高速图像旋转运动估计算法

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激光与光电子学进展 2023年第10期60卷 259-264页

作者：杨赟辉朱鸿泰程虎刘丹中科芯集成电路有限公司江苏无锡214072

针对载体姿态变化引起的相机旋转运动,提出一种基于相关滤波的高速图像旋转运动估计算法(GPCF)。在灰度投影法的基础上,该算法采用相关滤波代替互相关运算进行角度估计。通过构建循环移位矩阵,扩充负样本数量,有效提高旋转运动估计的精... 详细信息

针对载体姿态变化引起的相机旋转运动,提出一种基于相关滤波的高速图像旋转运动估计算法(GPCF)。在灰度投影法的基础上,该算法采用相关滤波代替互相关运算进行角度估计。通过构建循环移位矩阵,扩充负样本数量,有效提高旋转运动估计的精度和鲁棒性。构建噪信比公式,以定量分析噪声对旋转运动估计算法的影响程度。理论分析和实验结果均表明,GPCF能够实时估计图像序列旋转角度,且精度和稳定性相比灰度投影法具有较大提升。

关键词：图像处理旋转运动估计灰度投影法互相关相关滤波

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基于Cu^(2+)诱导信号放大策略的电化学适体传感器检测赭曲霉毒素A

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分析试验室 2023年第5期42卷 595-600页

作者：牛鹏博李德蕾胡蓉杨通杨云慧云南师范大学化学化工学院昆明650500

构建了一种基于Cu^(2+)诱导信号放大策略的新型电化学适体传感器,并用于赭曲霉毒素A(OTA)的检测。带有poly(T)的OTA核酸适体与电极表面捕获DNA探针杂交,在Cu^(2+)和抗坏血酸存在下,poly(T)的末端作为模板可原位生长铜纳米团簇(CuNCs)。... 详细信息

构建了一种基于Cu^(2+)诱导信号放大策略的新型电化学适体传感器,并用于赭曲霉毒素A(OTA)的检测。带有poly(T)的OTA核酸适体与电极表面捕获DNA探针杂交,在Cu^(2+)和抗坏血酸存在下,poly(T)的末端作为模板可原位生长铜纳米团簇(CuNCs)。在没有目标OTA的情况下,将连接CuNCs的金电极浸入酸性环境中以释放Cu^(2+)。在-1.6 V电位下富集Cu^(2+)后,通过差分脉冲伏安(DPV)信号记录溶出铜的最强电流值。随着OTA的加入,OTA适配体与目标OTA紧密结合,金电极上的CuNCs减少,导致DPV电流响应降低。该方法线性范围为0.1~50.0 ng/mL,检出限为41.2 pg/mL。Cu^(2+)诱导的电化学适体传感器可应用于咖啡溶液样品中目标物OTA的分析。

关键词：赭曲霉毒素A 电化学适体传感器铜纳米团簇铜离子信号放大

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Health Risk Assessment of Employees Exposed to Chlorination By-products of Recreational Water in Large Amusement Parks in Shanghai

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Biomedical and Environmental Sciences 2024年第8期37卷 865-875页

作者： Weizhao Cao Yiming Zheng Wenxuan Zhao Lisha Shi yunhui Zhang Lijun Zhang Jian Chen Key Lab of Health Technology Assessment National Health Commission of the People’s Republic of China(Fudan University)Shanghai 200032China Key Laboratory of Public Health Safety Ministry of EducationSchool of Public HealthFudan UniversityShanghai 200032China Division of Public Health Service and Safety Assessment Shanghai Municipal Center for Disease Control and PreventionShanghai 200336China Shanghai Institute of Preventive Medicine Shanghai 200336China

Objective Chlorination is often used to disinfect recreational water in large amusement parks;however,the health hazards of chlorination disinfection by-products(DBPs)to occupational populations are *** study aimed to assess the exposure status of chlorinated DBPs in recreational water and the health risks to employees of large amusement *** Exposure parameters of employees of three large amusement parks in Shanghai were investigated using a *** typical chlorinated DBPs in recreational water and spray samples were quantified by gas chromatography,and the health risks to amusement park employees exposed to chlorinated DBPs were evaluated according to the WHO's risk assessment *** Trichloroacetic acid,dibromochloromethane,bromodichloromethane,and dichloroacetic acid were detected predominantly in recreational *** carcinogenic and non-carcinogenic risks of the five DBPs did not exceed the risk *** addition,the carcinogenic and non-carcinogenic risks of mixed exposure to DBPs were within the acceptable risk *** Typical DBPs were widely detected in recreational water collected from three large amusement parks in Shanghai;however,the health risks of DBPs and their mixtures were within acceptable limits.

关键词： Risk assessment Water Environmental health Occupational exposure Chlorinated disinfection by-product

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婚礼上的“悲”:滇东北次方言苗族叙事芦笙史歌“阿作”田野调查与研究

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中国非物质文化遗产 2023年第3期 53-58页

作者：杨云惠云南昭通学院艺术学院

“阿作”是滇东北次方言苗族用于缅怀先辈迁徙的芦笙叙事史歌,内容反映苗族先祖蚩尤部落在与黄帝、炎帝部落的战争中失利,先逃出的年轻人返回城内寻找失散族人,最后安全撤离的场景。现已衍化为滇东北次方言苗族婚礼上最隆重的仪式,且在... 详细信息

“阿作”是滇东北次方言苗族用于缅怀先辈迁徙的芦笙叙事史歌,内容反映苗族先祖蚩尤部落在与黄帝、炎帝部落的战争中失利,先逃出的年轻人返回城内寻找失散族人,最后安全撤离的场景。现已衍化为滇东北次方言苗族婚礼上最隆重的仪式,且在男方家“正酒”当晚,表演形式为芦笙和古歌同时进行。该仪式沿袭历史事件中队伍的组合,有特定的人员结构顺序,酒、芦笙、古歌缺一不可。通过吹唱“悲”的历史教育子孙后代,传承族群文化。由于滇东北次方言苗族芦笙发音管是参照苗语声调而制,芦笙曲调与苗语发音有切合之处,故而苗族先辈在逃亡和寻找族人的过程中,通过芦笙传递信息。仪式过程中,芦笙手根据历史事件发生的地点及时间先后,严格按顺序吹奏,所吹曲调实际是通过芦笙讲述当年的逃亡过程,并配以不同的脚步动作,代表事件发生的不同场景,同时,歌师配合芦笙唱相应的古歌,因此,“阿作”仪式也被人们称之为“苗族‘阿作’芦笙舞”。

关键词：阿作婚礼滇东北次方言苗族迁徙芦笙古歌

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Initial COVID-19 severity influenced by SARS-CoV-2-specific T cells imprints T-cell memory and inversely affects reinfection

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Signal Transduction and Targeted Therapy 2024年第6期9卷 2791-2803页

作者： Gang yang Jinpeng Cao Jian Qin Xinyue Mei Shidong Deng Yingjiao Xia Jun Zhao Junxiang Wang Tao Luan Daxiang Chen Peiyu Huang Cheng Chen Xi Sun Qi Luo Jie Su yunhui Zhang Nanshan Zhong Zhongfang Wang The Affiliated Hospital of Kunming University of Science and Technology.Department of Respiratory and Critical Care Medicine The First People’s Hospital of Yunnan provinceKunmingYunnanChina Guangzhou National Laboratory BiolandGuangzhouGuangdongChina State Key Laboratory of Respiratory Disease&National Clinical Research Center for Respiratory Disease Guangzhou Institute of Respiratory Healththe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhou Medical UniversityGuangzhouChina

The immunoprotective components control COVID-19 disease severity,as well as long-term adaptive immunity maintenance and subsequent reinfection risk discrepancies across initial COVID-19 severity,remain ***,we longitudinally analyzed SARS-CoV-2-specific immune effectors during the acute infection and convalescent phases of 165 patients with COVID-19 categorized by *** found that early and robust SARS-CoV-2-specific CD4^(+)and CD8^(+)T cell responses ameliorate disease progression and shortened hospital stay,while delayed and attenuated virus-specific CD8^(+)T cell responses are prominent severe COVID-19 *** antiviral antibody generation rather than titer level associates with severe ***,initial COVID-19 severity imprints the long-term maintenance of SARS-CoV-2-specific adaptive immunity,demonstrating that severe convalescents exhibited more sustained virus-specific antibodies and memory T cell responses compared to mild/moderate ***,initial COVID-19 severity inversely correlates with SARS-CoV-2 reinfection ***,our study unravels the complicated interaction between temporal characteristics of virus-specific T cell responses and COVID-19 severity to guide future SARS-CoV-2 wave management.

关键词： severity immunity infection

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Observation of accurately designed bound states in the continuum in momentum space

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Photonics Research 2024年第4期12卷 638-647页

作者： JIAJU WU JINGGUANG CHEN XIN QI ZHIWEI GUO JIAJUN WANG FENG WU YONG SUN yunhui LI HAITAO JIANG LEI SHI JIAN ZI HONG CHEN MOE Key Laboratory of Advanced Micro-Structured Materials School of Physics Science and EngineeringTongji UniversityShanghai 200092China State Key Laboratory of Surface Physics Key Laboratory of Micro-and Nano-Photonic Structures(Ministry of Education)and Department of PhysicsFudan UniversityShanghai 200433China School of Optoelectronic Engineering Guangdong Polytechnic Normal UniversityGuangzhou 510665China

Bound states in the continuum(BICs)in artificial photonic structures have received considerable attention since they offer unique methods for the extreme field localization and enhancement of light-matter ***,the symmetry-protected BICs are located at high symmetric points,while the positions of accidental BICs achieved by tuning the parameters will appear at some points in momentum *** to now,to accurately design the position of the accidental BIC in momentum space is still a ***,we theoretically and experimentally demonstrate an accurately designed accidental BIC in a two-coupled-oscillator system consisting of bilayer gratings,where the optical response of each grating can be described by a single resonator *** changing the interlayer distance between the gratings to tune the propagation phase shift related to wave vectors,the position of the accidental BIC can be arbitrarily controlled in momentum ***,we present a general method and rigorous numerical analyses for extracting the polarization vector fields to observe the topological properties of BICs from the polarization-resolved transmission ***,an application of the highly efficient second harmonic generation assisted by quasi-BIC is *** work provides a straightforward strategy for manipulating BICs and studying their topological properties in momentum space.

关键词： polarization tuning resonator

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可转债与控制权私利下公司投资决策

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系统工程学报 2022年第2期37卷 194-206页

作者：宋丹丹杨运慧唐小林湖南大学金融与统计学院湖南长沙410079

探究可转债和控制权私利对公司投资决策和代理成本的影响.通过建立实物期权模型,基于均衡定价原理,分析计算了投资期权价值、最优投资策略以及控股股东的代理成本.研究结果表明,相比普通债,可转债能显著地提高控股股东的投资期权价值,... 详细信息

探究可转债和控制权私利对公司投资决策和代理成本的影响.通过建立实物期权模型,基于均衡定价原理,分析计算了投资期权价值、最优投资策略以及控股股东的代理成本.研究结果表明,相比普通债,可转债能显著地提高控股股东的投资期权价值,但同时降低公司价值.控股股东倾向于利用可转债为公司融资,但从社会福利角度公司更倾向于利用普通债融资.同时,可转债不仅有效地抑制了控股股东的过度投资行为,而且显著地缓解了控股股东与中小投资者之间的代理冲突.

关键词：控制权私利可转债最优投资决策代理冲突

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