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Dear-DIA^(XMBD): Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics

Research 2024年第1期6卷 707-720页

作者： qingzu he Chuan-Qi Zhong Xiang Li Huan Guo Yiming Li Mingxuan Gao Rongshan Yu Xianming Liu Fangfei Zhang Donghui Guo Fangfu Ye Tiannan Guo Jianwei Shuai Jiahuai Han Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials ResearchXiamen UniversityXiamen 361005China Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)and Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang 325001China School of Life Sciences Xiamen UniversityXiamen 361102China State Key Laboratory of Cellular Stress Biology Innovation Center for Cell Signaling NetworkXiamen 361102China Department of Computer Science Xiamen UniversityXiamen 361005China National Institute for Data Science in health and Medicine School of MedicineXiamen UniversityXiamen 361102China Bruker(Beijing)Scientific Technology Co.Ltd. BeijingChina Westlake Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake University18 Shilongshan RoadHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced Study18 Shilongshan RoadHangzhou 310024China Westlake Omics Ltd. Yunmeng Road 1HangzhouChina Department of Electronic Engineering Xiamen UniversityXiamen 361005China

Data-independent acquisition(DIA)technology for protein identification from mass spectrometry and related algorithms is developing rapidly.The spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising direction.In this paper,we proposed an untargeted analysis method,Dear-DIA^(XMBD),for direct analysis of DIA data.Dear-DIA^(XMBD) first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms,then uses the k-means clustering algorithm to aggregate fragments with similar representations into the same classes,and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides and between fragments and peptides.We show that Dear-DIA^(XMBD) performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms.

关键词： Deep Auto Independent

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RIP1-dependent linear and nonlinear recruitments of caspase-8 and RIP3 respectively to necrosome specify distinct cell death outcomes

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Protein & Cell 2021年第11期12卷 858-876页

作者： Xiang Li Chuan-Qi Zhong Rui Wu Xiaozheng Xu Zhang-Hua Yang Shaowei Cai Xiurong Wu Xin Chen Zhiyong Yin qingzu he Dianjie Li Fei Xu Yihua Yan Hong Qi Changchuan Xie Jianwei Shuai Jiahuai Han State Key Laboratory of Cellular Stress Biology School of Life SciencesInnovation Center for Cell Signaling NetworkXiamen UniversityXiamen 361102China Department of Physics Xiamen UniversityXiamen 361005China National Institute for Data Science in health and Medicine Xiamen 361102China Complex Systems Research Center Shanxi UniversityTaiyuan 030006ChinaState Key Laboratory of Cellular Stress BiologySchool of Life SciencesInnovation Center for Cell Signaling NetworkXiamen UniversityXiamen 361102China

There remains a significant gap in our quantitative understanding of crosstalk between apoptosis and necroptosis pathways.By employing the SWATH-MS technique,we quantified absolute amounts of up to thousands of proteins in dynamic assembling/de-assembling of TNF signaling complexes.Combining SWATH-MS-based network modeling and experimental validation,we found that when RIP1 level is below~1000 molecules/cell(mpc),the cell solely undergoes TRADD-dependent apoptosis.When RIP1 is above~1000 mpc,pro-caspase-8 and RIP3 are recruited to necrosome respectively with linear and nonlinear dependence on RIP1 amount,which well explains the co-occurrence of apoptosis and necroptosis and the paradoxical obser-vations that RIP1 is required for necroptosis but its increase down-regulates necroptosis.Higher amount of RIP1(>~46,000 mpc)suppresses apoptosis,leading to necroptosis alone.The relation between RIP1 level and occurrence of necroptosis or total cell death is biphasic.Our study provides a resource for encoding the com-plexity of TNF signaling and a quantitative picture how distinct dynamic interplay among proteins function as basis sets in signaling complexes,enabling RIP1 to play diverse roles in governing cell fate decisions.

关键词： necrosome protein complexes quantification RIP1 SWATH-MS network modeling

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A 3D-printed microhemispherical shell resonator with electrostatic tuning for a Coriolis vibratory gyroscope

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Microsystems & Nanoengineering 2024年第2期10卷 25-35页

作者： Baoyin Hou Ye Zhu Chaofan he Weidong Wang Zhi Ding Wen he Yong he Lufeng Che College of Information Science and Electronic Engineering Zhejiang UniversityHangzhou310027China Center for Microelectronics Shaoxing InstituteZhejiang UniversityShaoxing312035China State Key Laboratory of Fluid Power and Mechatronic Systems Zhejiang UniversityHangzhou310058China School of Mechanical Engineering Zhejiang UniversityHangzhou310058China

The emergence of microhemispherical resonant gyroscopes,which integrate the advantages of exceptional stability and long lifetime with miniaturization,has afforded new possibilities for the development of whole-angle gyroscopes.However,existing methods used for manufacturing microhemispherical resonant gyroscopes based on MEMS technology face the primary drawback of intricate and costly processing.here,we report the design,fabrication,and characterization of the first 3D-printable microhemispherical shell resonator for a Coriolis vibrating gyroscope.We remarkably achieve fabrication in just two steps bypassing the dozen or so steps required in traditional micromachining.By utilizing the intricate shaping capability and ultrahigh precision offered by projection microstereolithography,we fabricate 3D high-aspect-ratio resonant structures and controllable capacitive air gaps,both of which are extremely difficult to obtain via MEMS technology.In addition,the resonance frequency of the fabricated resonators can be tuned by electrostatic forces,and the fabricated resonators exhibit a higher quality factor in air than do typical MEMS microhemispherical resonators.This work demonstrates the feasibility of rapidly batch-manufacturing microhemispherical shell resonators,paving the way for the development of microhemispherical resonator gyroscopes for portable inertial navigation.Moreover,this particular design concept could be further applied to increase uptake of resonator tools in the MEMS community.

关键词： resonator tuning electrostatic

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Chemotherapy induces breast cancer stem cell enrichment through repression of glutathione S-transferase Mu

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Genes & Diseases 2024年第2期11卷 528-531页

作者： Jing he Yiran Yu Yilin he Jie he Guangyu Ji Haiquan Lu The Second Hospital and Advanced Medical Research Institute Cheeloo College of MedicineShandong UniversityJinanShandong 250012China Department of Nursing The First Affiliated Hospital of Shandong First Medical UniversityJinanShandong 250014China School of Medicine Xinjiang Medical UniversityUrumqiXinjiang 830054China School of Medicine Binzhou Medical UniversityYantaiShandong 264003China Oncology Department Jinan Zhangqiu District People's HospitalJinanShandong 250200China Key Laboratory for Experimental Teratology of the Ministry of Education Cheeloo College of MedicineShandong UniversityJinanShandong 250012China Center for Reproductive Medicine Shandong UniversityJinanShandong 250012China

Triple-negative breast cancer(TNBC)has aggressive characteristics as exemplified by the high risk of recurrence,metastasis,and patient mortality.1 Cytotoxic chemotherapy may reduce tumor burden initially,but leave behind chemo-resistant breast cancer stem cells(BCSCs)that lead to tumor recurrence and metastasis.2 Chemotherapy induces BCsC enrichment through the activation of glutathione biosynthesis pathways,which increases intracellular glutathione levels and specifies the BCSC phenotype through complicated downstream signaling pathways.3 Glutathione S-transferases(GSTs),a superfamily(which contains seven cytosolic classes:Alpha,Kappa,Mu,Omega,Pi,Theta,and Zeta,and one microsomal class MGSTs)of phase Il enzymes that catalyze the conjugation of glutathione with electrophilic compounds,play a critical role in detoxification and chemotherapy resistance of cancer cells.However,the role of GSTs in the regulation of BCSCs is largely elusive.

关键词： chemotherapy breast metastasis

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Coupled Numerical Simulation of Electromagnetic and Flow Fields in a Magnetohydrodynamic Induction Pump

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Fluid Dynamics & Materials Processing 2024年第4期20卷 889-899页

作者： he Wang Ying he College of Transportation Ludong UniversityYantai264025China College of Intelligent Manufacturing City College of HuizhouHuizhou516025China

Magnetohydrodynamic(MHD)induction pumps are contactless pumps able to withstand harsh environments.The rate of fluid flow through the pump directly affects the efficiency and stability of the device.To explore the influence of induction pump settings on the related delivery speed,in this study,a numerical model for coupled electromagnetic and flow field effects is introduced and used to simulate liquid metal lithium flow in the induction pump.The effects of current intensity,frequency,coil turns and coil winding size on the velocity of the working fluid are analyzed.It is shown that the first three parameters have a significant impact,while changes in the coil turns have a negligible influence.The maximum increase in working fluid velocity within the pump for the parameter combination investigated in this paper is approximately 618%.As the frequency is increased from 20 to 60 Hz,the maximum increase in the mean flow rate of the working fluid is approximately 241%.These research findings are intended to support the design and optimization of these devices.

关键词： Magnetic fluid multi-physical field coupling induction pump numerical simulation liquid metal conveying

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Honeycomb-like biochar framework coupled with Fe_(3)O_(4)/FeS nanoparticles as efficient heterogeneous Fenton catalyst for phenol degradation

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Journal of Environmental Sciences 2024年第2期136卷 390-399页

作者： Aihua Cheng Yi he Xiaohe Liu Chi he Department of Environmental Engineering College of Geology and EnvironmentXi’an University of Science and TechnologyXi’an 710054China State Key Laboratory of Multiphase Flow in Power Engineering School of Energy and Power EngineeringXi’an Jiaotong UniversityXi’an 710049China National Engineering Laboratory for VOCs Pollution Control Material and Technology University of Chinese Academy of SciencesBeijing 101408China

Achieving an efficient and stable heterogeneous Fenton reaction over a wide pH range is of great significance for wastewater treatment.here,a pollen-derived biochar catalyst with a unique honeycomb-like structure,coupled with the dispersion of magnetic Fe_(3)O_(4)/FeS(Fe/S)nanoparticles,was synthesized by simple impregnation precursor,followed by pyrolysis.The prepared Fe/S-biochar catalyst demonstrated outstanding phenol degradation efficiency across a wide pH range,with 98%of which eliminated even under neutral conditions(pH 7.0).The high catalytic activity was due to the multilevel porous structure of pollenderived biochar provided enough active sites and allowed for better electron transfer,then increases oxidation ability to promote the reaction.Moreover,the acid microenvironment formed by SO_(4)^(2-)group from Fe/S composite extended the pH range for Fenton reaction,and S^(2-)facilitated the conversion of≡Fe^(3+)to≡Fe^(2+),resulting in remarkable degradation efficiency.Further,biochar can effectively promote cycling stability by limiting Fe leaching.This work may provide a general strategy for designing 3D framework biochar-based Fe/S catalysts with excellent performance for heterogeneous Fenton reactions.

关键词： Biomass Biochar Fenton reaction Fe_(3)O_(4)/FeS(Fe/S) Phenol degradation

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Regulation of insect behavior by non-coding RNAs

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Science China(Life Sciences) 2024年第6期67卷 1106-1118页

作者： Jing he Le Kang State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China Beijing Institutes of Life Sciences Chinese Academy of SciencesBeijing 100101China College of Life Science Hebei UniversityBaoding 071002China

The adaptation of insects to environments relies on a sophisticated set of behaviors controlled by molecular and physiological processes.Over the past several decades,accumulating studies have unveiled the roles of non-coding RNAs(nc RNAs)in regulating insect behaviors.nc RNAs assume particularly pivotal roles in the behavioral plasticity of insects by rapidly responding to environmental stimuli.nc RNAs also contribute to the maintenance of homeostasis of insects by fine-tuning the expression of target genes.However,a comprehensive review of nc RNAs'roles in regulating insect behaviors has yet to be conducted.here,we present the recent progress in our understanding of how nc RNAs regulate various insect behaviors,including flight and movement,social behavior,reproduction,learning and memory,and feeding.We refine the intricate mechanisms by which nc RNAs modulate the function of neural,motor,reproductive,and other physiological systems,as well as gene expression in insects like fruit flies,social insects,locusts,and mosquitos.Furthermore,we discuss potential avenues for future studies in nc RNA-mediated insect behaviors.

关键词： ncRNAs insect behavior plasticity fine-tuning environmental adaptation

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Distributed Nash Equilibrium Seeking on Compact Action Sets over Jointly Strongly Connected Switching Networks

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Journal of Systems Science & Complexity 2024年第1期37卷 63-81页

作者： he Xiongnan HUANG Jie Department of Mechanical and Automation Engineering The Chinese University of Hong KongHong Kong 999077China.

This paper studies the distributed Nash equilibrium seeking(DNES)problem for games whose action sets are compact and whose network graph is switching satisfying the jointly strongly connected condition.To keep the actions of all players in their action sets all the time,one has to resort to the projected gradient-based method.Under the assumption that the unique Nash equilibrium is the unique equilibrium of the pseudogradient system,an algorithm is proposed that is able to exponentially find the Nash equilibrium.Further,the authors also consider the distributed Nash equilibrium seeking problem for games whose actions are governed by high-order integrator dynamics and belong to some compact sets.Two examples are used to illustrate the proposed approach.

关键词： Compact action sets jointly strongly connected switching graphs Nash equilibrium seeking projected gradient-based algorithm.

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Neural Stem Cell Competition

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Neuroscience Bulletin 2024年第2期40卷 277-279页

作者： Yanan Li Jie he State Key Laboratory of Neuroscience Institute of NeuroscienceCenter for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesShanghai 200031China University of Chinese Academy of Sciences Beijing 100049China

Cell competition is an adaptive surveillance mechanism to ensure the robustness of developmental outputs,maintain tissue integrity,and regulate tumor progression in multicellular organisms,which is highly conserved from invertebrates to vertebrates[1].At the cellular level,cell competition represents a non-cell-autonomous process in that cells can sense the fitness of their neighbors through cellular interactions,thereby eliminating low-fitness cells and expanding high-fitness counterparts,however,cells develop normally in homogenous populations.

关键词： thereby maintain eliminating

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The Role of Adipose Tissue-derived Exosomes in Chronic Metabolic Disorders

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Current Medical Science 2024年第3期44卷 463-474页

作者： Rui he Yong CheN Division of Endocrinology Department of Internal MedicineTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China Laboratory of Endocrinology & Metabolism Key Laboratory of Vascular Aging of the Ministry of EducationTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430030China Branch of National Clinical Research Center for Metabolic Diseases Wuhan430030China

Excessive fat deposition in obese subjects promotes the occurrence of metabolic diseases,such as type 2 diabetes mellitus(T2DM),cardiovascular diseases,and non-alcoholic fatty liver disease(NAFLD).Adipose tissue is not only the main form of energy storage but also an endocrine organ that not only secretes adipocytokines but also releases many extracellular vesicles(EVs)that play a role in the regulation of whole-body metabolism.Exosomes are a subtype of EVs,and accumulating evidence indicates that adipose tissue exosomes(AT Exos)mediate crosstalk between adipose tissue and multiple organs by being transferred to targeted cells or tissues through paracrine or endocrine mechanisms.However,the roles of AT Exos in crosstalk with metabolic organs remain to be fully elucidated.In this review,we summarize the latest research progress on the role of AT Exos in the regulation of metabolic disorders.Moreover,we discuss the potential role of AT Exos as biomarkers in metabolic diseases and their clinical application.

关键词： exosome adipose tissue obesity diabetes chronic metabolic disorder miRNA

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