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GenOrigin: A comprehensive protein-coding gene origination database on the evolutionary timescale of life

Journal of Genetics and Genomics 2021年第12期48卷 1122-1129页

作者： yi-bo tong Meng-Wei Shi Sheng Hu Qian Yu-Jie Chen Zhi-Hui Luo yi-Xuan Tu Yu-Li Xiong ying-Jie Geng Chunyan Chen Zhen-Xia Chen Hubei Hongshan Laboratory College of Biomedicine and HealthHuazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of Agricultural Bioinformatics College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Center for Ecological and Environmental Sciences Northwestern Polytechnical UniversityXi’an 710072China Interdisciplinary Sciences Institute Huazhong Agricultural UniversityWuhan 430070China Shenzhen Institute of Nutrition and Health Huazhong Agricultural UniversityShenzhen 518000China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here,we systematically date the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using a protein-family-based pipeline with Wagner parsimony algorithm. We also collect gene age estimate data from other studies and uniformly distribute the gene age estimates to time ranges in a million years for comparison across studies. All the data are cataloged into Gen Origin(http://***/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age, and gene ontology. In Gen Origin, the information such as gene age estimates,annotation, gene ontology, ortholog, and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, is provided to researchers for exploring gene functions.

关键词： Gene age Gene family Comparative analysis

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西乐葆和雷帕霉素联合作用对人乳腺癌MDA-MB-231细胞的抗肿瘤效应

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中华实验外科杂志 2008年第8期25卷 1021-1023页

作者：易彤波李海志武正炎南京医科大学第一附属医院乳腺内分泌外科中心 210029

目的观察西乐葆和雷帕霉素联合作用对于人乳腺癌MDA-MB-231细胞的抗肿瘤效应。方法不同浓度的西乐葆（20、40、60、80μmol／L）、雷帕霉素（1、10、100、1000nmol／L）单独及60μmol／L西乐葆和100nmol／L雷帕霉素两者联合作用对MDA-MB... 详细信息

目的观察西乐葆和雷帕霉素联合作用对于人乳腺癌MDA-MB-231细胞的抗肿瘤效应。方法不同浓度的西乐葆（20、40、60、80μmol／L）、雷帕霉素（1、10、100、1000nmol／L）单独及60μmol／L西乐葆和100nmol／L雷帕霉素两者联合作用对MDA-MB-231细胞生长的影响通过噻唑蓝（MTT）比色法检测。对细胞周期和凋亡的影响使用流式细胞仪进行分析。蛋白印迹实验检测HER2和HER3的表达情况及磷酸化Akt（473）水平。结果西乐葆、雷帕霉素对于MDA-MB-231细胞生长抑制具有浓度和时间依赖性。60μmol／L西乐葆和100nmol／L雷帕霉素联合应用细胞生长抑制率及凋亡率为[（88．0±8．0）％，（32．5±3．0）％]，与两者单独应用细胞生长抑制率及凋亡率[（52．0±5．0）％，（12．6±2．0）％；（54．0±6．0）％，（7．2±2．0）％]比较差异有统计学意义（P〈0．01）。联合应用对MDA-MB-231细胞抗肿瘤效应与降低细胞HER2和HER3的表达及磷酸化Akt（473）水平有关。结论西乐葆和雷帕霉素联合能增强对人乳腺癌DA-MB-231细胞的抗肿瘤效应，对于HER2、HER3阳性乳腺癌具有潜在的临床应用价值。

关键词：西乐葆雷帕霉素乳腺癌

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Application of the improved dung beetle optimizer,muti-head attention and hybrid deep learning algorithms to groundwater depth prediction in the Ningxia area,China

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Atmospheric and Oceanic Science Letters 2025年第1期18卷 18-23页

作者： Jiarui Cai bo Sun Huijun Wang yi Zheng Siyu Zhou Huixin Li Yanyan Huang Peishu Zong Collaborative Innovation Center on forecast and Evaluation of Meteorological Disasters/Key Laboratory of Meteorological Disaster Ministry of Education/Joint International Research Laboratory of Climate and Environment ChangeNanjing University of Information Science and TechnologyNanjingChina Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) ZhuhaiChina China Meteorological Administration Key Laboratory of Transportation MeteorologyNanjingChina Jiangsu Meteorological Observatory NanjingChina

Due to the lack of accurate data and complex parameterization,the prediction of groundwater depth is a chal-lenge for numerical *** learning can effectively solve this issue and has been proven useful in the prediction of groundwater depth in many *** this study,two new models are applied to the prediction of groundwater depth in the Ningxia area,*** two models combine the improved dung beetle optimizer(Dbo)algorithm with two deep learning models:The Multi-head Attention-Convolution Neural Network-Long Short Term Memory networks(MH-CNN-LSTM)and the Multi-head Attention-Convolution Neural Network-Gated Recurrent Unit(MH-CNN-GRU).The models with Dbo show better prediction performance,with larger R(correlation coefficient),RPD(residual prediction deviation),and lower RMSE(root-mean-square error).Com-pared with the models with the original Dbo,the R and RPD of models with the improved Dbo increase by over 1.5%,and the RMSE decreases by over 1.8%,indicating better prediction *** addition,compared with the multiple linear regression model,a traditional statistical model,deep learning models have better prediction performance.

关键词： Groundwater depth Multi-head attention Improved dung beetle optimizer CNN-LSTM CNN-GRU Ningxia

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悬浮培养联合化疗药物筛选乳腺癌干细胞

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中国癌症杂志 2008年第3期18卷 172-175页

作者：李海志易彤波武正炎南京医科大学第一附属医院普外科江苏南京210029

背景与目的:数量上的稀少和不断分化的能力阻碍了肿瘤干细胞的分离和纯化,现有的筛选方法只是富集了异质性的肿瘤干细胞群,无法取得更为原始的、接近源头的肿瘤干细胞。本文以肿瘤干细胞假说为理论依据,探讨悬浮培养联合化疗药物分离、... 详细信息

背景与目的:数量上的稀少和不断分化的能力阻碍了肿瘤干细胞的分离和纯化,现有的筛选方法只是富集了异质性的肿瘤干细胞群,无法取得更为原始的、接近源头的肿瘤干细胞。本文以肿瘤干细胞假说为理论依据,探讨悬浮培养联合化疗药物分离、培养、纯化及鉴定小鼠乳腺癌干细胞的可行性研究。方法:无血清悬浮培养小鼠乳腺癌TM40D细胞,流式细胞仪检测CD44+CD24-细胞含量。选取CD44+CD24-含量最多代数的细胞,加入不同血浆峰浓度(peak plasma concentrations,PPC)的联合化疗药物紫杉醇和表柔比星,作用24 h后继续无血清培养,Annexin-V FITC/PI流式细胞仪法检测细胞凋亡。将筛选得到的细胞以不同的数量接种到BALB/C小鼠皮下,观察致瘤能力。结果:无血清悬浮培养第10代的细胞中CD44+CD24-比例最高(77%)。接种0.35 PPC组100个细胞即可见肿瘤生成。结论:小鼠乳腺癌TM40D细胞中存在肿瘤干细胞,悬浮培养联合化疗药物筛选乳腺癌干细胞在方法上是可行的。

关键词：肿瘤干细胞悬浮培养化疗药物乳腺癌移植瘤

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Homologous CoS2 interface with directed electron transfer and strong chloridion repulsion for efficient seawater oxidation

引用

Science China Chemistry 2025年

作者： Yuan Tian Jiang-bo Chen Jie ying Ge Tian Yu-Xuan Xiao yi Lu Si-Ming Wu Wei Geng Ling Shen Xiao-Yu Yang State Key Laboratory of Advanced Technology for Materials Synthesis and Processing and School of Materials Science and Engineering and Shenzhen Research Institute & Laoshan Laboratory Wuhan University of Technology School of Chemical Engineering and Technology Sun Yat-Sen University National Energy Key Laboratory for New Hydrogen-Ammonia Energy Technologies Foshan Xianhu Laboratory

Seawater electrolysis is a highly promising method to produce high energy density hydrogen,especially in dry areas that have scarce freshwater ***,application of seawater electrolysis is confronted by two major problems associated with catalysts employed for the anodic oxygen evolution reaction （OER） including the competitive hypochlorite evolution reaction（HCER） and strong chloridion （Cl–） triggered *** studies aimed at overcoming these problems,a facile method has been developed to synthesize a homologous CoS2heterojunction as an OER *** to a difference in work functions at the interface and increased electron density,this material has directed electron transfer and strong chloridion repulsion properties,*** have shown that CoS2achieves low overpotentials of 289 and 322 mV at 10 mA cm-2current density in respective alkaline （1 M KOH） and alkaline simulated seawater ***,the outstanding stability of CoS2is reflected in a negligible decline in activity during promotion of the OER for 100 *** of density functional theory calculations reveal that the homologous CoS2heterojunction promotes directed electron transport for optimizing adsorption/desorption of reactive species and heightens the Cl-adsorption energy for strongly repulsing Cl-,phenomena that enhance OER performance in alkaline simulated seawater.

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circT P63-N suppresses the proliferation and metastasis of nasopharyngeal carcinoma via engaging with HSP90AB1 to modulate the YAP1/Hippo signaling pathway

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Science China Life Sciences 2025年

作者： Dan Wang Sicheng Zuo Junshang Ge Hongke Qu Jie Wu Na yi Lei Shi Yumin Wang Yongzhen Mo Chunmei Fan yi He Pan Chen Ming Zhou bo Xiang Wei Xiong Wenjia Guo Zhaoyang Zeng Can Guo NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine Central South University Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education Cancer Research Institute and School of Basic Medicine Sciences Central South University Furong Laboratory Cancer Research Institute Affiliated Cancer Hospital of Xinjiang Medical University Xinjiang Key Laboratory of Translational Biomedical Engineering

Circular RNAs(circRNAs) play pivotal roles in the development and progression of various diseases, including malignant tumors. However,the biological functions and the underlying mechanisms of many circRNAs remain elusive. In this study, we identified a novel circRNA,circTP63-N, generated through the splicing of exons 2–4 of the TP63 gene in nasopharyngeal carcinoma(NPC). circTP63-N was found to be downregulated in clinical samples of NPC. both in vitro and in vivo experiments unequivocally demonstrated that circTP63-N inhibits the proliferation and metastasis of NPC cells. Further investigations revealed that circTP63-N interacted with the HSP90AB1 protein, leading to the recruitment of LATS/YAP1 proteins. This, in turn, induced phosphorylation and ubiquitination-dependent degradation of YAP1, resulting in reduced nuclear translocation of YAP1 and inhibition of the transcriptional activation of downstream oncogenic genes, including INHBA, MMP3, and CCNE2. Our findings highlight the identification of circTP63-N, a novel circRNA encoded by an important tumor-relevant gene TP63 and elucidate its molecular mechanism as a tumor suppressor in NPC. These insights offer novel potential molecular markers and therapeutic targets for the clinical diagnosis and treatment of NPC.

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基于存储过程分页优化Web数据查询性能

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微计算机应用 2004年第4期25卷 475-479页

作者：李光耀易虎李波同济大学计算机应用上海200092

随着因特网的广泛应用 ,Web应用程序开发已成为主流 ,如何提高访问Web数据的性能 ,一直受到开发人员的重视。本文首先分析了访问Web数据的特点 ;然后提出了一种基于存储过程分页方法 ,分析了该方法的特点以及对提高访问Web数据性能的作... 详细信息

随着因特网的广泛应用 ,Web应用程序开发已成为主流 ,如何提高访问Web数据的性能 ,一直受到开发人员的重视。本文首先分析了访问Web数据的特点 ;然后提出了一种基于存储过程分页方法 ,分析了该方法的特点以及对提高访问Web数据性能的作用 ,并在 NET平台上使用该方法实现了对Web数据的访问 ;最后对三种不同的访问Web数据方案进行测试和比较 ,测试结果表明利用存储过程很好地改善了数据访问性能。

关键词：数据库应用程序 Web 数据查询存储过程优化

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吻合器治疗脱垂性内痔(附30例报告)

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临床医药实践 2003年第7期12卷 488-489页

作者：易彤波田小林戴凌广西桂林医学院附院广西桂林541001

目的 :探讨利用吻合器通过直肠下端黏膜及黏膜下层环形切除 ,肛垫悬吊治疗脱垂性内痔的可行性和安全性。方法 :采用该术式治疗 3 0例期、期环形脱垂内痔患者 ,分析经 PPH治疗的临床资料。结果 :平均手术时间 15m in,术后平均住院 4d... 详细信息

目的 :探讨利用吻合器通过直肠下端黏膜及黏膜下层环形切除 ,肛垫悬吊治疗脱垂性内痔的可行性和安全性。方法 :采用该术式治疗 3 0例期、期环形脱垂内痔患者 ,分析经 PPH治疗的临床资料。结果 :平均手术时间 15m in,术后平均住院 4d。 2 6例患者吻合后内痔立即完全回缩 ,4例手术后第 2天完全回缩。 3例术后第 1天～第 6天有便血 ,经保守治疗后好转。术后诉肛门部疼痛者 3例 ,尿潴留 5例。随访 10个月效果良好无复发。结论 :PPH治疗期、期环形脱垂性内痔是一种新技术 ,具有安全、显效、快捷、住院时间少、恢复快等优点。

关键词：吻合器治疗脱垂性内痔直肠下端黏膜

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Synthesis of chiral phosphine derivatives through a copper（I）-catalyzed desymmetric SNAr reaction

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Science China Chemistry 2025年

作者： Shuai Zhang Pei-Zhi Liu Yan-bo Li Qi Zhang Jun-Zhao Xiao yi-Fan Wang Tian-Yu Wei Jia-Wei Jiang Ye Wang Qian Peng Liang yin Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences State Key Laboratory of Elemento-Organic Chemistry and Tianjin Key Laboratory of Biosensing and Molecular Recognition College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Haihe Laboratory of Sustainable Chemical Transformations

Axially chiral phosphines are a class of extremely important ligands in asymmetric catalysis. Herein, an unprecedented copper（I）-catalyzed asymmetric SNAr reaction with HP（S）R2is uncovered, which delivers a series of axially chiral phosphine derivatives in high yields with excellent enantioselectivity. Furthermore, the diastereoselective reaction with the kinetic resolution of racemic HP（S）ArR proceeds smoothly, providing the products with moderate diastereoselectivity and excellent enantioselectivity. Control experiments indicate that HP（S）Ph2is much more active than HPPh2and HP（O）Ph2as the pronucleophile in the present reaction. It is found that the SNAr reaction （the first SNAr） proceeds in a desymmetric manner, providing the desired chiral products while a continued SNAr reaction （the second SNAr） slightly occurs in a kinetic resolution manner in the present catalytic system, which enhances the ee of the desired chiral products. DFTcalculations support a concerted reaction pathway rather than a step-wise mechanism. Finally, axially chiral olefin-phosphines produced by the present method work as suitable ligands in Pdcatalyzed asymmetric allylic substitution with C-, N-, and O-nucleophiles and Rh-catalyzed asymmetric addition of arylboronic acid to benzil.

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The detection, extraction and parameter estimation of extreme-mass-ratio inspirals with deep learning

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 86-96页

作者： Qianyun Yun Wen-Biao Han yi-Yang Guo He Wang Minghui Du Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Shanghai Astronomical Observatory Chinese Academy of Sciences School of Physics and Astronomy Shanghai Jiao Tong University School of Astronomy and Space Science University of Chinese Academy of Sciences Taiji Laboratory for Gravitational Wave Universe (Beijing/Hangzhou) University of Chinese Academy of Sciences Lanzhou Center for Theoretical Physics Key Laboratory of Theoretical Physics of Gansu Province Key Laboratory of Quantum Theory and Applications of MoE Lanzhou University Institute of Theoretical Physics & Research Center of Gravitation Lanzhou University International Centre for Theoretical Physics Asia-Pacific (ICTP-AP) University of Chinese Academy of Sciences (UCAS) Center for Gravitational Wave Experiment National Microgravity Laboratory Institute of Mechanics Chinese Academy of Sciences

One of the primary goals of space-borne gravitational wave detectors is to detect and analyze extreme-mass-ratio inspirals(EMRIs). This task is particularly challenging because EMRI signals are complex, lengthy, and faint. In this work, we introduce a2-layer convolutional neural network(CNN) approach to detect EMRI signals for space-borne detectors, achieving a true positive rate(TPR) of 96.9% at a 1% false positive rate(FPR) for signal-to-noise ratio(SNR) from 50 to 100. Especially, the key intrinsic parameters of EMRIs such as the mass, spin of the supermassive black hole(SMBH) and the initial eccentricity of the orbit can also be inferred directly by employing a neural network. The mass and spin of the SMBH can be determined at 99% and 92% respectively. This will greatly reduce the parameter spaces and computing cost for the following Bayesian parameter *** model also has a low dependency on the accuracy of the waveform model. This study underscores the potential of deep learning methods in EMRI data analysis, enabling the rapid detection of EMRI signals and efficient parameter estimation.

关键词： gravitational wave EMRIs deep-learing

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