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

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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

Storage time affects the level and diagnostic efficacy of plasma biomarkers for neurodegenerative diseases

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Neural Regeneration Research 2025年第8期20卷 2373-2381页

作者： Lifang Zhao Mingkai Zhang Qimeng Li Xuemin Wang jie Lu ying Han Yanning Cai Department of Clinical Biobank Xuanwu HospitalCapital Medical UniversityBeijingChina Beijing Geriatric Medical Research Center BeijingChina Department of Neurology Xuanwu HospitalCapital Medical UniversityBeijingChina Department of Radiology and Nuclear Medicine Xuanwu HospitalCapital Medical UniversityBeijingChina Beijing Key Laboratory of Magnetic Resonance Imaging and Brain Informatics BeijingChina Key Laboratory of Neurodegenerative diseases Ministry of EducationBeijingChina School of Biomedical Engineering Hainan UniversityHaikouHainan ProvinceChina Center of Alzheimer’s Disease Beijing Institute for Brain DisordersBeijingChina National Clinical Research Center for Geriatric Diseases BeijingChina Institute of Biomedical Engineering Shenzhen Bay LaboratoryGaoke Innovation CenterShenzhenGuangdong ProvinceChina Department of Neurobiology Xuanwu HospitalCapital Medical UniversityBeijingChina

Several promising plasma biomarker proteins,such as amyloid-β(Aβ),tau,neurofilament light chain,and glial fibrillary acidic protein,are widely used for the diagnosis of neurodegenerative ***,little is known about the long-term stability of these biomarker proteins in plasma samples stored at-80°*** aimed to explore how storage time would affect the diagnostic accuracy of these biomarkers using a large *** samples from 229 cognitively unimpaired individuals,encompassing healthy controls and those experiencing subjective cognitive decline,as well as 99 patients with cognitive impairment,comprising those with mild cognitive impairment and dementia,were acquired from the Sino Longitudinal Study on Cognitive Decline *** samples were stored at-80°C for up to 6 years before being used in this *** results showed that plasma levels of Aβ42,Aβ40,neurofilament light chain,and glial fibrillary acidic protein were not significantly correlated with sample storage ***,the level of total tau showed a negative correlation with sample storage ***,in individuals without cognitive impairment,plasma levels of total protein and tau phosphorylated protein threonine 181(p-tau181)also showed a negative correlation with sample storage *** was not observed in individuals with cognitive ***,we speculate that the diagnostic accuracy of plasma p-tau181 and the p-tau181 to total tau ratio may be influenced by sample storage ***,caution is advised when using these plasma biomarkers for the identification of neurodegenerative diseases,such as Alzheimer's ***,in cohort studies,it is important to consider the impact of storage time on the overall results.

关键词： Alzheimer’s disease amyloid-β diagnostic ability glial fibrillary acidic protein neurodegeneration neurofilament light chain plasma biomarkers single molecule array storage time tau

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

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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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AI预测天然染料在丝绸上的最佳染色工艺与色牢度研究

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丝绸 2025年第1期62卷 40-48页

作者：刘莹陈杰南宁师范大学美术与设计学院南宁530001 武汉大学物理科学与技术学院武汉430000

随着环境问题的日益严峻,为了提高实验效率、节约成本,推动可持续发展战略在染料与纺织品领域的应用,文章首先对天然染料染色的数据进行了收集与预处理,然后采用Xgboost集成学习算法构建AI模型并进行了模型训练与验证,评估了模型的有效... 详细信息

随着环境问题的日益严峻,为了提高实验效率、节约成本,推动可持续发展战略在染料与纺织品领域的应用,文章首先对天然染料染色的数据进行了收集与预处理,然后采用Xgboost集成学习算法构建AI模型并进行了模型训练与验证,评估了模型的有效性和预测精度。该模型实现了天然染料在丝绸上染色工艺与效果的高效模拟与预测,从而显著缩短了实验时间并降低了资源损耗。这一方法提高了研究效率和经济效益。研究表明,该模型在预测反应最佳酸碱度(pH值)、水洗色牢度(CFW)和摩擦色牢度(CFR)方面具有较高的准确率,在验证集中三者的预测准确率高达94.12%、93.75%、100%,在真实的测试集上分别拥有87.50%、94.12%、82.35%的准确率,同时具备有效性与可迁移性。集成学习的方法通过极小的部署成本和极短的耗时为天然染料染色性能的探索给出了极具价值的指导,也为AI机器学习与纺织染色的学科的交叉应用拓展了可能性。

关键词： AI预测 Xgboost 天然染料丝绸色牢度

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Unraveling the mechanism of action of Shangxia Liangji formula for treating insomnia:a metabolomics and network pharmacology approach

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Traditional Medicine Research 2025年第2期10卷 16-29页

作者： Xia-jie Quan Hao Liang Yong-Hong Tang Li Jiang Xiong-ying Ji Feng-ying Zhang Ping Zhang Bo Ouyang Department of Information The Affiliated Nanhua HospitalHengyang Medical SchoolUniversity of South ChinaHengyang 421002China Department of Neurology The Affiliated Nanhua HospitalHengyang Medical SchoolUniversity of South ChinaHengyang 421002China Department of Gastroscopy The Affiliated Nanhua HospitalHengyang Medical SchoolUniversity of South ChinaHengyang 421002China Department of Traditional Chinese Medicine The Affiliated Nanhua HospitalHengyang Medical SchoolUniversity of South ChinaHengyang 421002China

Background:Insomnia is a prevalent clinical condition and Shangxia Liangji formula(SXLJF)is a well-established method of ***,the specific mechanism of action of SXLJF remains ***:The mouse model of insomnia was established by intraperitoneal injection of ***-two mice were randomly divided into a negative control group,model group,SXLJF group(18.72 g/kg/day),and positive control group(diazepam,2 mg/kg)and treated with the corresponding drugs for 7 consecutive *** open field test and pentobarbital-induced sleeping test were ***-MS-based untargeted metabolomics and network pharmacology were applied to explore the potential targets of SXLJF for treating ***,key targets were validated using ***:Behavioral tests demonstrated that SXLJF reduced the total distance,average velocity,central distance,and sleep latency,and prolonged sleep *** and network pharmacology revealed potential targets,signaling pathways,metabolic pathways,and metabolites associated with the anti-insomnia effects of ***,tyrosine hydroxylase(TH)and tyrosine metabolism emerged as crucial metabolic pathways and targets,***-qPCR results supported the role of TH in the mechanism of SXLJF in treating ***:In conclusion,TH and tyrosine metabolism may represent significant targets and pathways for SXLJF in treating insomnia.

关键词： Shangxia Liangji formula insomnia metabolomics network pharmacology tyrosine hydroxylase tyrosine metabolism

Metastable seed-crystals: epitaxial growth of branched-array organic heterostructure nanowires

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Science China Chemistry 2025年

作者： Jin Feng Zhen-Yu geng Ting-Yao Song ying-Xin Ma Chuan-Zeng Wang Wei Zhang Hong-Tao Lin Jin Zhou Shu-Ping Zhuo Shu-Hai Chen Xue-Dong Wang School of Chemistry and Chemical Engineering Shandong University of Technology Institute of Functional Nano & Soft Materials (FUNSOM) Jiangsu Key Laboratory for Carbon-Based Functional Materials & DevicesSoochow University College of Chemistry and Chemical Engineering Hunan Normal University

Tunable light–matter interactions are exhibited by organic low-dimensional crystals, making these crystals a promising platform for organic photonics. However, the precise synthesis of organic low-dimensional crystals remains challenging due to the stochastic nature of molecular nucleation processes. Herein, the directed nucleation process is driven by the introduction of metastable seed-crystals as the trunk, which ultimately leads to branched-array organic heterostructures. The successful formation of organic heterostructures with high-density branched arrays is attributed to the highest attachment energy (Eatt（023）=-104.25 kcal mol-1) of the exposed （023） crystal plane during the seed-crystal growth route. Significantly, these as-prepared heterostructures inherently have an ultralow lattice mismatch ratio η of 0.7%between trunk and branch, which contributes to the multi-channel photon transportation. Therefore, this work provides valuable insights into a versatile synthetic strategy for accessing low-dimensional heterostructures for integrated optoelectronics.

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Partial-TMR: A New Method for Protecting Register Files Against Soft Error Based on Lifetime Analysis

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Journal of Computer Science & Technology 2021年第5期36卷 1089-1101页

作者： Xian-geng Liang ying-Ke Gao geng-Xin Hua Beijing Institute of Control Engineering China Academy of Space TechnologyBeijing 100090China

High-energy particles in the space can easily cause soft error in register file(RF).As a critical structure in a processor,RF often stores data for long periods of time and is read frequently,resulting in a higher probability of spreading corrupted data to other parts of the *** triple modular redundancy(TMR)is a common and effective fault tolerance method that enables multi-bit error *** full TMR for all the registers could cause excessive area and power ***,some registers in RF have less impact on processor ***,there is no need to design TMR for *** paper designs an efficient strategy which can rate the registers in RF based on their *** on the proposed strategy,a new RF fault tolerance method named Partial-TMR formulates in this paper,which selectively protects more vulnerable registers against multi-bit error,and improves fault tolerance *** integer RF,Partial-TMR improves its soft error correction capability by 24.5%relative to the baseline system and 3%relative to ParShield,while for floating-point RF,the improvement comes to 5.17%and 0.58%*** soft error correction capability of Partial-TMR is slightly lower than that of full TMR by 1%to 3%,but Partial-TMR significantly cuts the area and power *** with full TMR,Partial-TMR decreases the area and power overheads by 71.6%and 64.9%,*** also has little impact on the ***-TMR is a more cost-effective fault tolerance method compared with ParShield and full TMR.

关键词： register file soft error lifetime analysis selective protection triple modular redundancy(TMR)

Finite-time sliding mode attitude control for a reentry vehicle with blended aerodynamic surfaces and a reaction control system

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Chinese Journal of Aeronautics 2014年第4期27卷 964-976页

作者： geng jie Sheng Yongzhi Liu Xiangdong Key Laboratory for Intelligent Control&Decision of Complex Systems Beijing Institute of Technology School of Automation Beijing Institute of Technology

This paper proposes a finite-time robust flight controller, targeting for a reentry vehicle with blended aerodynamic surfaces and a reaction control system（RCS）. Firstly, a novel finite-time attitude controller is pointed out with the introduction of a nonsingular finite-time sliding mode manifold. The attitude tracking errors are mathematically proved to converge to zero within finite time which can be estimated. In order to improve the performance, a second-order finite-time sliding mode controller is further developed to effectively alleviate chattering without any deterioration of robustness and accuracy. Moreover, an optimization control allocation algorithm, using linear programming and a pulse-width pulse-frequency（PWPF） modulator, is designed to allocate torque commands for all the aerodynamic surface deflections and on–off switching-states of RCS *** are provided for the reentry vehicle considering uncertain parameters and external disturbances for practical purposes, and the results demonstrate the effectiveness and robustness of the attitude control system.

关键词： Chattering alleviation Control allocation Finite-time convergence Flight control systems Second-order sliding mode Singularity elimination Sliding mode control

Scheme of optimal fault detection for linear discrete time-varying systems with delayed state

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Journal of Systems Engineering and Electronics 2017年第5期28卷 979-985页

作者： Maiying Zhong jie Chen Yue geng School of Instrumentation Science and Opto-electronics Engineering Beihang University College of Electrical Engineering and Automation Shandong University of Science and Technology

This paper deals with the problem of the optimal fault detection (FD) for linear discrete time-varying (LDTV) systems with delayed state and l(2)-norm bounded unknown input. The novelty lies in the designing of an evaluation function for the robust FD. The basic idea is to directly construct an evaluation function by using a weighted l(2)-norm of the measurement output, which achieves an optimal trade-off between the sensitivity to fault and the robustness to l(2)-norm bounded unknown input. To avoid complex computation, a feasible solution is obtained via the recursive computation by applying the orthogonal projection. It is shown that such an evaluation function provides a unified scheme for both the cases of unknown input being l(2)-norm bounded and jointly normal distribution, while a threshold may be chosen based on a priori knowledge of unknown input. A numerical example is given to demonstrate the effectiveness of the proposed method.

关键词： fault detection evaluation function linear discrete time-varying system time-delay