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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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The structure-directing role of heterologous seeds in the synthesis of zeolite

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Green Energy & Environment 2024年第5期9卷 792-801页

作者： Haoyang Zhang binyu Wang Wenfu Yan State Key Laboratory of Inorganic Synthesis&Preparative Chemistry College of ChemistryJilin UniversityChangchun130012China

Zeolites have been widely used as catalysts,ion-exchangers,and adsorbents in chemical industries,detergent industry,steel industry,glass industry,ceramic industry,medical and healthﬁeld,and environmentalﬁeld,and recently applied in energy ***-assisted synthesis is a very effective approach in promoting the crystallization of *** some cases,the target zeolite cannot be formed in the absence of seed *** homologous seed-assisted synthesis,the structure of the seed zeolite is the same to that of the target zeolite,while the structure of the seed zeolite is different to that of the target zeolite in the heterologous seed-assisted *** this review,we brieﬂy summarized the heterologous seed-assisted syntheses of zeolites and analyzed the structure-directing effect of heterologous seeds and surveyed the“common composite building units(CBUs)hypothesis”and the“common secondary building units(SBUs)hypothesis”.However,both hypotheses cannot explain all observations on the heterologous seed-assisted ***,we proposed that the formation of the target zeolite does need nuclei with the structure of target zeolite and the formation of the nuclei of the target zeolite can be promoted by either the undissolved seed crystals with the same CBUs or SBUs to the target zeolite or by the facilitated appropriate distribution of the speciﬁc building units due to the presence of the heterologous seed that does not have any common CBUs and SBUs with the target zeolite.

关键词： Zeolite Heterologous seed Synthesis Structure-directing effect

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基于CiteSpace的我国病耻感研究热点及研究前沿

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职业与健康 2024年第13期40卷 1837-1842页

作者：钟思思王雪灵杨槟羽李智莹林梦盈陈爱云广州医科大学卫生管理学院广东广州511436

目的挖掘国内病耻感研究的主要内容、热点和前沿,为促进病耻感研究和发展提供参考。方法利用CiteSpace软件对中国知网数据库2000—2022年的1167篇病耻感研究文献进行可视化分析。结果自2015年起研究文献数量逐年增加,并在2021年突破1000... 详细信息

目的挖掘国内病耻感研究的主要内容、热点和前沿,为促进病耻感研究和发展提供参考。方法利用CiteSpace软件对中国知网数据库2000—2022年的1167篇病耻感研究文献进行可视化分析。结果自2015年起研究文献数量逐年增加,并在2021年突破1000篇;得到分别以周英、罗小年为核心的合作团队图谱;高发文量机构共13所;得到包括#0病耻感、#1影响因素、#2直肠癌等10个聚类;精神疾病和精神病突现强度最强。结论病耻感研究核心作者群未能共同协作,缺乏明显的跨机构合作网络。研究热点和重点在精神疾病方面,内容涵盖生活质量、影响因素、社会支持等,直肠癌、艾滋病、护理是目前研究前沿。

关键词：病耻感 CiteSpace 可视化分析

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Zeolites for the separation of ethylene,ethane,and ethyne

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Frontiers of Chemical Science and Engineering 2024年第9期18卷 137-146页

作者： binyu Wang Qiang Li Haoyang Zhang Jia-Nan Zhang Qinhe Pan Wenfu Yan State Key Laboratory of Inorganic Synthesis&Preparative Chemistry College of ChemistryJilin UniversityChangchun 130012China Key Laboratory of Advanced Energy Catalytic and Functional Materials Preparation College of Materials Science and EngineeringZhengzhou UniversityZhengzhou 450012China Key Laboratory of Advanced Materials of Tropical Island Resources(Ministry of Education) School of Chemistry and Chemical EngineeringHainan UniversityHaikou 570228China

The cost-effective separation of ethylene(C_(2)H_(4)),ethyne(C_(2)H_(2)),and ethane(C_(2)H_(6))poses a significant challenge in the contemporary chemical *** contrast to the energy-intensive high-pressure cryogenic distillation process,zeolite-based adsorptive separation offers a low-energy *** review provides a concise overview of recent advancements in the adsorptive separation of C_(2)H_(4),C_(2)H_(2),and C_(2)H_(6)using zeolites or zeolite-based *** commences with an examination of the industrial significance of these compounds and the associated separation ***,it systematically examines the utilization of various types of zeolites with diverse cationic species in such separation *** then it explores how different zeolitic structures impact adsorption and separation capabilities,considering principles such as cation-πinteraction,π-complexation,and steric separation concerning C_(2)H_(4),C_(2)H_(2),and C_(2)H_(6)***,it discusses methods to enhance the separation performance of zeolites and zeolite-based adsorbents,encompassing structural design,modifications,and ion exchange ***,it summarizes current research trends and future directions,highlighting the potential application value of zeolitic materials in the field of C_(2)H_(4),C_(2)H_(2),and C_(2)H_(6)separation and offering recommendations for further investigation.

关键词： zeolite ethylene ethane cation-πinteraction π-complexation

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疲劳裂纹叶片振动的非线性特性研究

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西北工业大学学报 1999年第2期17卷 198-204页

作者：杨海燕杨秉玉刘启州西北工业大学

以带疲劳裂纹悬臂梁为例研究疲劳裂纹对叶片固有频率及强迫振动响应的影响。应用传递矩阵法求解裂纹叶片振动响应，选用余弦函数模拟疲劳裂纹的开合过程，理论分析了裂纹叶片的非线性振动特性，并进行裂纹试件实验。理论分析及实验结果... 详细信息

以带疲劳裂纹悬臂梁为例研究疲劳裂纹对叶片固有频率及强迫振动响应的影响。应用传递矩阵法求解裂纹叶片振动响应，选用余弦函数模拟疲劳裂纹的开合过程，理论分析了裂纹叶片的非线性振动特性，并进行裂纹试件实验。理论分析及实验结果都表明疲劳裂纹不仅使悬臂梁的固有频率下降，而且引起强迫振动响应的非线性特征。最后，就叶片裂纹故障监测特征量的选取做了分析、讨论。

关键词：叶片疲劳裂纹振动特性非线性振动固有频率

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Emission and optical characteristics of brown carbon in size-segregated particles from three types of Chinese ships

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Journal of Environmental Sciences 2024年第8期142卷 248-258页

作者： Fengqin yang Fan Zhang Zeyu Liu Yingjun Chen Yan Zhang Can Wu Yali Lei Shijie Liu binyu Xiao Xinyi Wan Yubao Chen Yong Han Min Cui Cheng Huang Gehui Wang Key Lab of Geographic Information Science of the Ministry of Education School of Geographic SciencesEast China Normal UniversityShanghai 200241China Institute of Eco-Chongming 20 Cuiniao Rd.ChongmingShanghai 202150China State Environmental Protection Key Laboratory of Formation and Prevention of the Urban Air Pollution Complex Shanghai Academy of Environmental SciencesShanghai 200233China Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention(LAP3) Department of Environmental Science and EngineeringFudan UniversityShanghai 200438China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092China Department of Civil and Environmental Engineering and State Key Laboratory of Marine Pollution The Hong Kong Polytechnic UniversityKowloon 100872Hong KongChina College of Environmental Science and Engineering Yangzhou UniversityYangzhou 225009China

Brown carbon(BrC)is one of the important light absorption substances that have high light absorption ability under short wavelength ***,limit studies have focused on the BrC emission from *** this study,size-segregated particulate matters(PM)were collected from three different types of ships,light absorption characteristics and size distribution of methanol-soluble BrC and water-soluble BrC in PM from ship exhausts were *** showed that four-stroke low-power diesel fishing boat(4-LDF)had the highest mass concentrations of methanol-soluble organic carbon(MSOC)and water-soluble organic carbon(WSOC),followed by 2-stroke high-power heavy-fuel-oil vessel(2-HHV),and fourstroke high-power marine-diesel vessel(4-HMV).While 2-HHV had obviously higher light absorption coefficients of methanol-soluble BrC(Abs365,M)and water-soluble BrC(Abs365,W)in unit weight of PM than the other two types of *** tested ships presented comparable or higher absorption efficiency of BrC in water extracts(MAE365,W)compared with other BrC emission *** of BrC was concentrated in fine particles,and the particle size distributions of both Abs365,Mand Abs365,Wshowed bimodal patterns,peaking at0.43–0.65μm and 4.7–5.8μm,***,different particle size distributions were found for MAE365,Mbetween diesel and heavy fuel oil ***,different wavelength dependence in particles with different size were also *** exhaust could be confirmed as a non-ignorable BrC emission source,and complex influencing factor could affect the light absorption characteristics of ship *** size should also be considered when light absorption ability of BrC was evaluated.

关键词： Ship emission Brown carbon Light absorption Size distribution

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平行流交叉口左转非机动车钩形转弯优化设计

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哈尔滨工业大学学报 2023年第3期55卷 1-9页

作者：宋浪胡晓伟杨滨毓安实哈尔滨工业大学交通科学与工程学院哈尔滨150090 黑龙江省智能交通管理与技术重点实验室哈尔滨150090

为提升平行流交叉口的运行效率,消除左转非机动车和直行机动车冲突,将钩形转弯的概念引入到平行流交叉口设计中,给出非机动车过街控制策略,并结合机动车通行和行人过街,将其整合到一个统一的优化模型中。考虑信号相位相序、绿灯时长、... 详细信息

为提升平行流交叉口的运行效率,消除左转非机动车和直行机动车冲突,将钩形转弯的概念引入到平行流交叉口设计中,给出非机动车过街控制策略,并结合机动车通行和行人过街,将其整合到一个统一的优化模型中。考虑信号相位相序、绿灯时长、周期时长、左转非机动车待行区容量、非机动车清空时长、车道平衡等约束条件,以机动车通过量最大为优化目标,建立线性规划优化模型。研究结果表明:两步过街和优化设计解决了左转非机动车安全过街问题,是平行流交叉口非机动车过街设置的有效替代设计方案;在低高两种流量场景下,相对于常规设计,两步过街分别降低了35.02%、55.52%的机动车延误,优化设计分别降低了42.71%、65.60%的机动车延误;两步过街会造成左转非机动车延误大幅增加,不适用于左转非机动车流量较高的场景;常规设计机动车最大通过量受直行机动车流量和左转非机动车流量的影响最为严重,说明消除左转非机动车和直行机动车冲突,对提升交叉口通行能力作用显著,有助于推动绿色出行发展。

关键词：交通工程左转非机动车线性规划平行流交叉口钩形转弯行人过街

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荣昌猪唾液腺全长cDNA文库的构建及ESTs分析

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西北农林科技大学学报（自然科学版） 2017年第3期45卷 17-23页

作者：甘玲梅宏远杨滨宇西南大学荣昌校区动物医学系重庆荣昌402460

【目的】构建荣昌猪唾液腺全长cDNA文库,并进行部分表达序列标签(ESTs)的测序及分析,为荣昌猪种质资源的保存、开发和挖掘提供重要的分子信息。【方法】以14日龄荣昌猪仔猪为材料,取其唾液腺,采用SMART法构建唾液腺全长cDNA文库,并进行E... 详细信息

【目的】构建荣昌猪唾液腺全长cDNA文库,并进行部分表达序列标签(ESTs)的测序及分析,为荣昌猪种质资源的保存、开发和挖掘提供重要的分子信息。【方法】以14日龄荣昌猪仔猪为材料,取其唾液腺,采用SMART法构建唾液腺全长cDNA文库,并进行ESTs测序、注释及功能分析。【结果】初级文库滴度为5.88×106PFU/mL,重组率为99.67%,大部分插入片段长度为400~2 000bp。共获得144条有效ESTs序列,共计108条非重复序列,包括23个重叠群和85个单一序列,77(占71.29%)条序列为已知功能基因,31(占28.71%)条为未知功能序列,其中18条为新基因。GO分类和KEGG途径分析结果显示,荣昌猪唾液腺表达基因功能主要包括细胞成分、分子功能和生物学过程3个类群。在细胞成分类群中,细胞外的成分所占比例最高;在分子功能类群中,酶抑制剂活性所占比例最高;而在生物过程类群中,以转运和定位等过程最突出。表达的基因主要参与补足物和凝固级联、百日咳、加压素调控的水再吸收及味觉传导等代谢途径。【结论】成功构建了荣昌猪唾液腺全长cDNA文库,解析了荣昌猪唾液腺的表达特征。

关键词：荣昌猪唾液腺全长cDNA文库 LD-PCR SMART技术表达序列标签

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Identification of key genes and signaling pathways based on transcriptomic studies of aerobic and resistance training interventions in sarcopenia in SAMP8 mice

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Sports Medicine and Health Science 2024年第4期6卷 358-369页

作者： Lunyu Li Xiaotian Guan Ying Huang Bo Qu binyu Yao Haili Ding School of Sports Medicine and Health Chengdu Sport UniversityChengduChina Institute of Sports Medicine and Health Chengdu Sport UniversityChengduChina

We examined the effects of resistance and aerobic exercise on the gene expression and biometabolic processes of aging skeletal muscle in senescence-accelerated mouse/prone 8 mice,a model of sarcopenia,and compared them with senescence-accelerated mouse/resistant 1 mice acting as *** found that exercise improved muscle strength,endurance,fiber size,also modulated genes and pathways related to synaptic transmission,potassium transport,JAK-STAT signaling,and PI3K-Akt *** results suggested that BDNF,JAK2,RhoC,Myh6,Stat5a,Tnnc1,and other genes may mediate the beneficial effects of exercise on sarcopenia through these pathways.

关键词： Resistance training Aerobic training Sarcopenia Transcriptome

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yangtze River Delta Aerosol liquid water in PM_(2.5)and its roles in secondary aerosol formation at a regional site of yangtze River Delta

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Journal of Environmental Sciences 2024年第4期138卷 684-696页

作者： Ruifang Shi Fei Zhang Yemin Shen Jiasi Shen Bingye Xu binyu Kuang Zhengning Xu Lingling Jin Qian Tang Xudong Tian Zhibin Wang College of Environmental and Resource Sciences Zhejiang Provincial Key Laboratory of Organic Pollution Process and ControlZhejiang UniversityHangzhou 310058China ZJU-Hangzhou Global Scientific and Technological Innovation Center Zhejiang UniversityHangzhou 311215China Zhejiang Ecological and Environmental Monitoring Center Hangzhou 310012China

Aerosol liquid water content(ALWC)plays an important role in secondary aerosol *** this study,a whole year field campaign was conducted at Shanxi in north Zhejiang Province during *** estimated by ISORROPIA-Ⅱ was then investigated to explore its characteristics and relationship with secondary *** exhibited a highest value in spring(66.38μg/m^(3)),followed by winter(45.08μg/m^(3)),summer(41.64μg/m^(3)),and autumn(35.01μg/m^(3)),*** was supposed that the secondary inorganic aerosols(SIA)were facilitated under higher ALWC conditions(RH>80%),while the secondary organic species tended to form under lower ALWC *** RH(>80%)promoted the NO_(3)^(-)formation via gas-particle partitioning,while SO_(4)^(2-)was generated at a relative lower RH(>50%).The ALWC was more sensitive to NO_(3)^(-)(R=0.94)than SO_(4)^(2-)(R=0.90).Thus,the self-amplifying processes between the ALWC and SIA enhanced the particle mass *** sensitivity of ALWC and OX(NO_(2)+O_(3))to secondary organic carbon(SOC)varied in different seasons at Shanxi,more sensitive to aqueous-phase reactions(daytime R=0.84;nighttime R=0.54)than photochemical oxidation(daytime R=0.23;nighttime R=0.41)in wintertime with a high level of OX(daytime:130-140μg/m^(3);nighttime:100-140μg/m^(3)).The self-amplifying process of ALWC and SIA and the aqueous-phase formation of SOC will enhance aerosol formation,contributing to air pollution and reduction of visibility.

关键词： Aerosol liquid water content Nitrate Sulfate Secondary organic compounds Aqueous-phase reaction

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