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

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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 *** spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising *** this paper,we proposed an untargeted analysis method,Dear-DIA^(XMBD),for direct analysis of DIA ***-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 *** 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

Some Simple Groups Which are Determined by Their Orders and Degree-Patterns

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Algebra colloquium 2024年第2期31卷 341-346页

作者： Qinghong guo Weijun Liu Genghua Fan School of Mathematics and Statistics HNP-LAMACentral South University Changsha 410083China college of General Education Guangdong University of Science and Technology DongguanGuangdong 523083China 不详

Let G be a finite group and Irr(G)the set of all irreducible complex characters of *** cd(G)be the set of all irreducible complex character degrees of G and denote byρ(G)the set of all primes which divide some character degree of *** character-prime graphΓ(G)associated to G is a simple undirected graph whose vertex set isρ(G)and there is an edge between two distinct primes p and q if and only if the product p q divides some character degree of *** show that the finite nonabelian simple groups A_(7),j_(1),j_(3),j_(4),L_(3)(3)and U_(3)(4)are uniquely determined by their degree-patterns and orders.

关键词： irreducible complex character character-prime graph finite nonabelian simple group

Body size induced changes in metabolic carbon of soil nematodes under N deposition and precipitation regime change in a temperate grassland

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Ecological Processes 2024年第1期13卷 120-131页

作者： Shuyan cui Xiaomei Mo guo Zheng college of Life Science Shenyang Normal University

Background Global climate change has resulted in precipitation regimes exhibiting an increasing trend in rainfall intensity but a reduction in its frequency. Nitrogen(N) deposition is a crucial component of the global N cycling. Nematode body size is a trait that responds to climate change and is used as a standard trait-based indicator in soil community analysis. Variations in body size influence metabolic carbon(c). We examined the ways by which body size and metabolic c of nematodes respond to changing precipitation regimes and how N deposition regulates these responses by an 8-year manipulative *** Nematode body size was indicated by the community-weighted mean(cWM) mass. We quantified c metabolism components of soil nematodes including production c, respiration c, and corresponding c use efficiency(cUE) under different precipitation intensities and N addition in a semi-arid steppe on the Mongolian Plateau. The Mantel test was used to determine the correlations between cWM, cUE and environmental factors. The partial least squares path modeling(PLS-PM) was conducted to quantify direct or indirect contributions among latent *** We found that heavy precipitation intensity increased the cWM mass of total nematodes and omnivorespredators without N addition. N addition decreased cWM mass of bacterivores across all the precipitation intensity treatments. Stronger precipitation intensities might be favorable for nematode production and respiration c. Variations in the nematode cWM mass drove the cUE to change with N *** Our findings provide new insights into the mechanisms underlying nematode body size and c metabolism, and highlight that explorative studies, such as manipulative experiments, are needed to identify traits underlying size-related effects and to investigate how they affect cUE of nematodes. These efforts may increase our understanding of how changes in precipitation regimes and N deposition may alter soil nema

关键词： community-weighted mean Metabolic footprint Nitrogen addition Precipitation intensity

Traditional chinese medicine for the treatment of immune-related nephropathy:A review

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Acta Pharmaceutica Sinica B 2024年第1期14卷 38-66页

作者： Pu jiang changliang Yao De-an guo School of Pharmacy Nanjing University of Chinese MedicineNanjing 210023China Shanghai Research center for Modernization of Traditional chinese Medicine National Engineering Research Center of TCM Standardization TechnologyShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China

Immune-related nephropathy(IRN)refers to immune-response-mediated glomerulonephritis and is the main cause of end-stage renal *** pathogenesis of IRN is not fully understood;therefore,treatment is *** chinese medicines(TcMs)have potent clinical effects in the treatment of the IRN conditions immunoglobulin A nephropathy,lupus nephropathy,and diabetic *** underlying mechanisms mainly include its inhibition of inflammation;improvements to renal interstitial fibrosis,oxidative stress,autophagy,apoptosis;and regulation of *** this review,we summarize the clinical symptoms of the three IRN subtypes and the use of TcM prescriptions,herbs,and bioactive compounds in treating IRN,as well as the potential mechanisms,intending to provide a reference for the future study of TcM as IRN treatments.

关键词： IgA nephropathy Diabetic nephropathy Lupus nephritis Traditional chinese medicine Immunity Pathogenesis Mechanism Pathophysiology

HDPairFinder:A data processing platform for hydrogen/deuterium isotopic labeling-based nontargeted analysis of trace-level amino-containing chemicals in environmental water

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journal of Environmental Sciences 2024年第2期136卷 583-593页

作者： Tingting Zhao Kristin carroll caley B.craven Nicholas j.P.Wawryk Shipei Xing jian guo Xing-Fang Li Tao Huan Department of chemistry Faculty of ScienceUniversity of British ColumbiaVancouver Campus2036 Main MallVancouverBritish ColumbiaV6T 1Z1Canada Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlberta T6G 2G3Canada

The combination of hydrogen/deuterium(H/D)formaldehyde-based isotopic methyl labeling with solid-phase extraction and high-performance liquid chromatography–high resolution mass spectrometry(HPLc-HRMS)is a powerful analytical solution for nontargeted analysis of trace-level amino-containing chemicals in water *** the huge amount of chemical information generated in HPLc-HRMS analysis,identifying all possible H/Dlabeled amino chemicals presents a significant challenge in data *** address this,we designed a streamlined data processing pipeline that can automatically extract H/D-labeled amino chemicals from the raw HPLc-HRMS data with high accuracy and ***,we developed a cross-correlation algorithm to correct the retention time shift resulting from deuterium isotopic effects,which enables reliable pairing of H-and D-labeled ***,we implemented several bioinformatic solutions to remove false chemical features generated by in-source fragmentation,salt adduction,and natural13c ***,we used a data mining strategy to construct the AMINES library that consists of over 38,000 structure-disjointed primary and secondary amines to facilitate putative compound ***,we integrated these modules into a freely available R program,*** rationale of each module was justified and its performance tested using experimental H/D-labeled chemical standards and authentic water *** further demonstrated the application of HDPairFinder to effectively extract N-containing contaminants,thus enabling the monitoring of changes of primary and secondary N-compounds in authentic water *** is a reliable bioinformatic tool for rapid processing of H/D isotopic methyl labeling-based nontargeted analysis of water samples,and will facilitate a better understanding of N-containing chemical compounds in water.

关键词： Isotope labeling Nontargeted analysis Reactive N-compounds HPLc-HRMS Source water

Dual-salt poly(tetrahydrofuran)electrolyte enables quasi-solid-state lithium metal batteries to operate at−30℃

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journal of Energy chemistry 2024年第9期96卷 456-463页

作者： Zhiyong Li Zhuo Li Rui Yu Xin guo School of Materials Science and Engineering State Key Laboratory of Material Processing and Die&Mould TechnologyHuazhong University of Science and TechnologyWuhan 430074HubeiChina The State Key Laboratory of Refractories and Metallurgy and Institute of Advanced Materials and Nanotechnology Wuhan University of Science and TechnologyWuhan 430081HubeiChina

The stable operation of solid-state lithium metal batteries at low temperatures is plagued by severe restrictions from inferior electrolyte-electrode interface compatibility and increased energy barrier for Li^(+)***,we prepare a dual-salt poly(tetrahydrofuran)-based electrolyte consisting of lithium hexafluorophosphate and lithium difluoro(oxalato)borate(LiDFOB).The Li-salt anions(DFOB−)not only accelerate the ring-opening polymerization of tetrahydrofuran,but also promote the formation of highly ion-conductive and sustainable interphases on Li metal anodes without sacrificing the Li^(+)conductivity of electrolytes,which is favorable for Li^(+)transport kinetics at low *** of this polymer electrolyte in Li||LiFePO_(4)cells show 82.3%capacity retention over 1000 cycles at 30℃and endow stable discharge capacity at−30℃.Remarkably,the Li||LiFePO4 cells retain 52%of their room-temperature capacity at−20℃and 0.1 *** rational design of dual-salt polymer-based electrolytes may provide a new perspective for the stable operation of quasi-solid-state batteries at low temperatures.

关键词： Poly(tetrahydrofuran) Dual-salt electrolyte Solidel ectrolyte interphase Low-temperature operation Quasi-solid-state battery

comparative Experimental Study on Heat Transfer characteristics of Building Exterior Surface at High and Low Altitudes

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journal of Thermal Science 2024年第3期33卷 1119-1131页

作者： jIA Yonghong guo Shurui LI jin guo Lei cHENG Zhu ZHANG Yin YANG Hanyu LONG Enshen Institute for Disaster Management and Reconstruction Sichuan UniversityChengdu610065China MOE Key Laboratory of Deep Earth Science and Engineering College of Architecture and EnvironmentSichuan UniversityChengdu610065China

The external surface heat transfer coefficient of building envelope is one of the important parameters necessary for building energy saving design,but the basic data in high-altitude area are ***,the authors propose a modified measurement method based on the heat balance of a model building,and use the same model building to measure its external surface heat transfer coefficient under outdoor conditions in chengdu city,china at an altitude of 520 m and Daocheng city at an altitude of 3750 m *** results show that the total heat transfer coefficient(h_(t))of building surface in high-altitude area is reduced by 34.48%.The influence of outdoor wind speed on the convective heat transfer coefficient(h_(c))in high-altitude area is not as significant as that in low-altitude *** fitting relation between convection heat transfer coefficient and outdoor wind speed is also *** the same heating power,the average temperature rise of indoor and outdoor air at highaltitude is 41.9%higher than that at low altitude,and the average temperature rise of inner wall is 25.8%higher than that at low *** shows that high-altitude area can create a more comfortable indoor thermal environment than low-altitude area under the same energy consumption *** is not appropriate to use the heat transfer characteristics of the exterior surface of buildings in low-altitude area for building energy saving design and related heating equipment selection and system terminal matching design in high-altitude area.

关键词： altitude heat transfer characteristics convective heat transfer coefficient(h_(c)) radiative heat transfer coefficient(h_(r)) external building envelope

Adaptive Sparse Grid Discontinuous Galerkin Method:Review and Software Implementation

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communications on Applied Mathematics and computation 2024年第1期6卷 501-532页

作者： juntao Huang Wei guo Yingda cheng Department of Mathematics and Statistics Texas Tech UniversityLubbockTX79409USA Department of computational Mathematics Science and EngineeringMichigan State UniversityEast LansingMI48824USA Department of Mathematics Michigan State UniversityEast LansingMI48824USA

This paper reviews the adaptive sparse grid discontinuous Galerkin(aSG-DG)method for computing high dimensional partial differential equations(PDEs)and its software *** c++software package called AdaM-DG,implementing the aSG-DG method,is available on GitHub at https://***/juntaoHuang/*** package is capable of treating a large class of high dimensional linear and nonlinear *** review the essential components of the algorithm and the functionality of the software,including the multiwavelets used,assembling of bilinear operators,fast matrix-vector product for data with hierarchical *** further demonstrate the performance of the package by reporting the numerical error and the cPU cost for several benchmark tests,including linear transport equations,wave equations,and Hamilton-jacobi(Hj)equations.

关键词： Adaptive sparse grid Discontinuous Galerkin High dimensional partial differential equation Software development

Numerical Simulation of the Seismic Response of a Horizontal Storage Tank Based on a SPH-FEM coupling Method

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computer Modeling in Engineering & Sciences 2024年第5期139卷 1655-1678页

作者： Peilei Yan Endong guo HouliWu Liangchao Zhang Key Laboratory of Earthquake Engineering and Engineering Vibration Institute of Engineering MechanicsChina Earthquake AdministrationHarbin150080China Key Laboratory of Earthquake Disaster Mitigation Ministry of Emergency ManagementHarbin150080China

A coupled numerical calculation method combining smooth particle hydrodynamics(SPH)and the finite element method(FEM)was implemented to investigate the seismic response of horizontal storage *** of a horizontal storage tank featuring a free liquid surface under seismic action was constructed using the SPH–FEM coupling *** stored liquid was discretized using SPH particles,while the tank and supports were discretized using the *** interaction between the stored liquid and the tank was simulated by using the meshless particle contact ***,the numerical simulation results were compared and analyzed against seismic simulation shaking table test data to validate the ***,a series of numerical models,considering different liquid storage volumes and seismic effects,were constructed to obtain time history data of base shear and top center displacement,which revealed the seismic performance of horizontal storage *** simulation results and experimental data showed good agreement,with an error rate of less than 18.85%.And this conformity signifies the rationality of the SPH-FEM coupling *** base shear and top center displacement values obtained by the coupled SPH-FEM method were only 53.3% to 69.1% of those calculated by the equivalent mass method employed in the current *** the stored liquid volume increased,the seismic response of the horizontal storage tank exhibited a gradual upward trend,with the seismic response increasing from 73% to 388% for every 35% increase in stored liquid *** maximum von Mises stress of the tank and the supports remained below the steel yield strength during the *** coupled SPH-FEM method holds certain advantages in studying the seismic problems of tanks with complex structural forms,particularly due to the representation of the flow field distribution during earthquakes by involving reservoir fluid participation.

关键词： SPH-FEM coupling method horizontal storage tank seismic response sloshing