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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 *** 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

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Preparation and Rheological Characterization of Long Chain Branching Polyglycolide

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Chinese Journal of Polymer Science 2024年第8期42卷 1177-1184页

作者： Wei-Lin liu Ming-Fu Lyu Heng-Yuan Zhang Jian-ye liu Shi-Jun Zhang Beijing University of Chemical Technology Beijing 100029China SINOPEC(Beijing)Research Institute of Chemical Industry Co. Ltd.Beijing 100013China

The long chain branching(LCB)polyglycolide(PGA)was successfully prepared by the successive reactions of the terminal hydroxyl groups of PGA with triglycidyl isocyanurate(TGIC)and pyromellitic dianhydride(PMDA).The influence of LCB produced by functional group reaction on rheological and crystallization behavior was studied and discussed through linear rheology,uniaxial elongation and DSC(differential scanning calorimetry).The much higher viscosity and the more notable strain hardening behavior of modified PGA indicates the LCB with high degree of entanglements are *** melt strength of PGA is finally improved greatly and can make su re that the supercritical CO_(2)foaming can be carried out successfully.

关键词： Polyglycolide(PGA) Long chain branching(LCB) Rheology

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Synergistic effects of multiscale TiC and dual-phase structure on tensile properties of particle-reinforced steel

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Journal of Iron and Steel Research(International) 2024年第5期31卷 1232-1245页

作者： ye Jia Xiang-tao Deng qi Wang Cheng-ru Li Hao Wu Zhao-dong Wang State Key Laboratory of Rolling and Automation Northeastern UniversityShenyang110819LiaoningChina

The conventional melting methods were used to obtain in situ TiC particle-reinforced dual-phase steel,followed by hot rolling and heat treatment *** aim was to investigate the effect of TiC particles on the fracture behavior of dual-phase steel at different annealing temperatures,by analyzing the microstructure and tensile behavior of the multiscale TiC particle-reinforced dual-phase *** results showed that TiC particles precipitated in the as-cast microstructure of dual-phase steel were distributed along the grain *** hot rolling,the grain boundary-like morphology of the micron-sized TiC particles was disrupted,and the particles became more refined and evenly distributed in the *** tensile tests revealed that the strength of the TiC particle-reinforced dual-phase steel increased with increasing martensite content,while the elongation *** results were similar to those of conventional *** addition of 1 vol.%multiscale TiC particles improved the strength of the dual-phase steel but did not affect elongation of the *** and holes were primarily concentrated around the TiC particles rather than at the interface of martensite and *** main causes of crack sprouting were TiC particle interface cracking and TiC particle internal ***,the study demonstrated the potential of multiscale TiC particle-reinforced dual-phase steel as a strong and tough *** refined distribution of TiC particles in the matrix improved the strength of the material without compromising its *** results also highlighted the importance of careful selection of reinforcement particles to avoid detrimental effects on the fracture behavior of the material.

关键词： TiC particle Dual-phase structure TiC-reinforced dual-phase steel Tension Fracture behavior

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Clinical Value of the Quantitative Flow Ratio to Predict Long-term Target Vessel Failure in Patients with In-stent Restenosis after Drug-coated Balloon Angioplasty

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Current Medical Science 2024年第3期44卷 561-567页

作者： Xiang-qi WU Long-bo LI Wei YOU Zhi-ming WU Lei ZHAO Zhi-hui WANG Pei-na MENG Bin liu Fei ye Department of Cardiology Nanjing First HospitalNanjing Medical UniversityNanjing210006China Department of Cardiology The Second Hospital of Jilin UniversityJilin130000China

Objective The study sought to investigate the clinical predictive value of quantitative flow ratio(QFR)for the long-term target vessel failure(TVF)outcome in patients with in-stent restenosis(ISR)by using drug-coated balloon(DCB)treatment after a long-term *** This was a retrospective study.A total of 186 patients who underwent DCB angioplasty for ISR in two hospitals from March 2014 to September 2019 were *** QFR of the entire target vessel was measured *** primary endpoint was TVF,including target vessel-cardiac death(TV-CD),target vessel-myocardial infarction(TV-MI),and clinically driven-target vessel revascularization(CD-TVR).Results The follow-up time was 3.09±1.53 years,and 50 patients had *** QFR immediately after percutaneous coronary intervention(PCI)was significantly lower in the TVF group than in the no-TVF *** Cox regression analysis indicated that the QFR immediately after PCI was an excellent predictor for TVF after the long-term follow-up[hazard ratio(HR):5.15×10−5(6.13×10−8−0.043);P<0.01].Receiver-operating characteristic(ROC)curve analysis demonstrated that the optimal cut-off value of the QFR immediately after PCI for predicting the long-term TVF was 0.925(area under the curve:0.886,95%confidence interval:0.834–0.938;sensitivity:83.40%,specificity:88.00;P<0.01).In addition,QFR≤0.925 post-PCI was strongly correlated with the TVF,including TV-MI and CD-TVR(P<0.01).Conclusion The QFR immediately after PCI showed a high predictive value of TVF after a long-term follow-up in ISR patients who underwent DCB angioplasty.A lower QFR immediately after PCI was associated with a worse TVF outcome.

关键词： percutaneous coronary intervention in-stent restenosis target vessel failure quantitative flow ratio

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Meta-Auto-Decoder:a Meta-Learning-Based Reduced Order Model for Solving Parametric Partial Differential Equations

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Communications on Applied Mathematics and Computation 2024年第2期6卷 1096-1130页

作者： Zhanhong ye Xiang Huang Hongsheng liu Bin Dong Beijing International Center for Mathematical Research Peking UniversityBeijing 100871China School of Computer Science and Technology University of Science and Technology of ChinaHefei 230027AnhuiChina Central Software Institute Huawei Technologies Co.LtdHangzhou 310007ZhejiangChina Center for Machine Learning Research Peking UniversityBeijing 100871China

Many important problems in science and engineering require solving the so-called parametric partial differential equations(PDEs),i.e.,PDEs with different physical parameters,boundary conditions,shapes of computational domains,*** reduced order modeling techniques accelerate the solution of the parametric PDEs by projecting them onto a linear trial manifold constructed in the ofline *** methods often need a predefined mesh as well as a series of precomputed solution snapshots,and may struggle to balance between the efficiency and accuracy due to the limitation of the linear *** the nonlinear representation of neural networks(NNs),we propose the Meta-Auto-Decoder(MAD)to construct a nonlinear trial manifold,whose best possible performance is measured theoretically by the decoder *** on the meta-learning concept,the trial manifold can be learned in a mesh-free and unsupervised way during the pre-training *** adaptation to new(possibly heterogeneous)PDE parameters is enabled by searching on this trial manifold,and optionally fine-tuning the trial manifold at the same *** numerical experiments show that the MAD method exhibits a faster convergence speed without losing the accuracy than other deep learning-based methods.

关键词： Parametric partial differential equations(PDEs) Meta-learning Reduced order modeling Neural networks(NNs) Auto-decoder

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A new species of Discostella guiyangensis ***.(Bacillariophyta,Stephanodiscales)from Guiyang,China:morphology and phylogeny

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Journal of Oceanology and Limnology 2024年第4期42卷 1312-1324页

作者： Yandan XIANG Fangru NAN Xudong liu Shulian XIE John Patrick KOCIOLEK qi liu School of Life Science Shanxi UniversityTaiyuan 030006China Department of Ecology and Evolutionary Biology and Museum of Natural History University of ColoradoBoulder CO 80309USA

We describe a new species of Discostella from Guiyang based on light and scanning electron microscopic observations,as well as molecular *** species is morphologically distinguished from other species by a relatively smooth and slightly recessed central area with marginal striae of unequal lengths forked near the *** fultoportulae and a single rimoportula are situated between every two costae or on the *** morphological characters and the concatenated data of rbc L and SSU rDNA indicate that Discostella guiyangensis is a unique and new *** to divergence time estimation analysis,Discostella guiyangensis is the oldest species among the Discostella species sequenced *** addition,we complement molecular data of Discostella asterocostata and Discostella stelligera.

关键词： Discostella morphology molecular analysis divergence time estimation new species

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Advances in memristor based artificial neuron fabrication-materials,models,and applications

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International Journal of Extreme Manufacturing 2024年第1期6卷 27-50页

作者： Jingyao Bian Zhiyong liu ye Tao Zhongqiang Wang Xiaoning Zhao Ya Lin Haiyang Xu Yichun liu Key Laboratory for UV Light-Emitting Materials and Technology(Northeast Normal University) Ministry of Education5268 Renmin StreetChangchunPeople’s Republic of China

Spiking neural network(SNN),widely known as the third-generation neural network,has been frequently investigated due to its excellent spatiotemporal information processing capability,high biological plausibility,and low energy consumption *** to the working mechanism of human brain,the SNN system transmits information through the spiking action of ***,artificial neurons are critical building blocks for constructing SNN in *** are drawing growing attention due to low consumption,high speed,and nonlinearity characteristics,which are recently introduced to mimic the functions of biological *** have proposed multifarious memristive materials including organic materials,inorganic materials,or even two-dimensional *** advantage of the unique electrical behavior of these materials,several neuron models are successfully implemented,such as Hodgkin–Huxley model,leaky integrate-and-fire model and integrate-and-fire *** this review,the recent reports of artificial neurons based on memristive devices are *** addition,we highlight the models and applications through combining artificial neuronal devices with sensors or other electronic ***,the future challenges and outlooks of memristor-based artificial neurons are discussed,and the development of hardware implementation of brain-like intelligence system based on SNN is also prospected.

关键词： artificial neuron memristor memristive materials neuron model micro-nano manufacturing spiking neural network

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Targeting FAPα-positive lymph node metastatic tumor cells suppresses colorectal cancer metastasis

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Acta Pharmaceutica Sinica B 2024年第2期14卷 682-697页

作者： Shuran Fan Ming qi qi qi Qun Miao Lijuan Deng Jinghua Pan Shenghui qiu Jiashuai He Maohua Huang Xiaobo Li Jie Huang Jiapeng Lin Wenyu Lyu Weiqing Deng Yingyin He Xuesong liu Lvfen Gao Dongmei Zhang Wencai ye Minfeng Chen State Key Laboratory of Bioactive Molecules and Druggability Assessment Jinan UniversityGuangzhou 510632China Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research College of PharmacyJinan UniversityGuangzhou 510632China School of Medicine Jinan UniversityGuangzhou 510632China School of Traditional Chinese Medicine Jinan UniversityGuangzhou 510630China The First Affiliated Hospital of Jinan University Guangzhou 510632China State Key Laboratory of Chemical Oncogenomics Guangdong Provincial Key Laboratory of Chemical BiologyTsinghua Shenzhen International Graduate SchoolShenzhen 518055China

Lymphatic metastasis is the main metastatic route for colorectal cancer, which increases the risk of cancer recurrence and distant metastasis. The properties of the lymph node metastatic colorectal cancer(LNM-CRC) cells are poorly understood, and effective therapies are still lacking. Here, we found that hypoxia-induced fibroblast activation protein alpha(FAPα) expression in LNM-CRC cells. Gain-or loss-function experiments demonstrated that FAPα enhanced tumor cell migration, invasion, epithelial-mesenchymal transition, stemness, and lymphangiogenesis via activation of the STAT3 pathway. In addition, FAPα in tumor cells induced extracellular matrix remodeling and established an immunosuppressive environment via recruiting regulatory T cells, to promote colorectal cancer lymph node metastasis(CRCLNM). Z-GP-DAVLBH, a FAPα-activated prodrug, inhibited CRCLNM by targeting FAPα-positive LNM-CRC cells. Our study highlights the role of FAPα in tumor cells in CRCLNM and provides a potential therapeutic target and promising strategy for CRCLNM.

关键词： Lymphaticmetastasis Colorectal cancer Fibroblastactivation proteinα FAPα-activated prodrug Epithelial-mesenchymal

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Geobacter sulfurreducens promoted the biosynthesis of reduced graphene oxide and coupled it for nitrobenzene reduction

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Journal of Environmental Sciences 2024年第4期138卷 458-469页

作者： Shoujuan Zhang qi liu Linrui Zhong Jianhong Jiang Xiaozhe Luo Xingxin Hu qian liu Yue Lu College of Environmental Science and Engineering Hunan UniversityChangsha 410082China Shenzhen Research Institute Hunan UniversityShenzhen 510082China Key Laboratory of Environment Biology and Pollution Control Hunan UniversityMinistry of EducationChangsha 410082China China Machinery International Engineering Design&Research Institute Co. LtdChangsha 410007China Hunan Engineering Research Center for Water Treatment Process&Equipment Changsha 410007China

In order to explore an efficient and green method to deal with nitrobenzene(NB)pollutant,reduced graphene oxide(r GO)as an electron shuttle was applied to enhance the extracellular electron transfer(EET)process of Geobacter sulfurreducens,which was a typical electrochemically active bacteria(EAB).In this study,r GO biosynthesis was achieved via the reduction of graphene oxide(GO)by *** PCA within 3 ***,the r GOPCA combining system completely reduced 50-200μmol/L of NB to aniline as end product within one *** characterization revealed that PCA cells were partly wrapped by rGO,and therefore the distance of electron transfer between strain PCA and r GO material was ***,the ID/IGof GO,r GO,and r GO-PCA combining system were 0.990,1.293 and 1.31,***,highest currents were observed in r GO-PCA-NB as 12.950μA/-12.560μA at -408 m V/156 m V,attributing to the faster electron transfer efficiency in EET ***,the NB reduction was mainly due to:(I)direct EET process from *** PCA to NB;(II)r GO served as electron shuttle and accelerated electron transfer to NB,which was the main degradation ***,the biosynthesis of r GO via GO reduction by Geobacter promoted the NB removal process,which provided a facile strategy to alleviate the problematic nitroaromatic pollution in the environment.

关键词： Reduced graphene oxide Geobacter Nitrobenzene Removal Extracellular electron transfer

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Exploring hidden-charm and hidden-strange hexaquark states from lattice QCD

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Science China(Physics,Mechanics & Astronomy) 2024年第1期67卷 30-37页

作者： Hang liu Jinchen He liuming liu Peng Sun Wei Wang Yi-Bo Yang qi-An Zhang INPAC Key Laboratory for Particle Astrophysics and Cosmology(MOE)Shanghai Key Laboratory for Particle Physics and CosmologySchool of Physics and AstronomyShanghai Jiao Tong UniversityShanghai 200240China Maryland Center for Fundamental Physics Department of PhysicsUniversity of MarylandCollege ParkMaryland 20742USA Institute of Modern Physics Chinese Academy of SciencesLanzhou 730000China University of Chinese Academy of Sciences Beijing 100049China Department of Physics and Institute of Theoretical Physics Nanjing Normal UniversityNanjing 210023China Southern Center for Nuclear-Science Theory(SCNT) Institute of Modern PhysicsChinese Academy of SciencesHuizhou 516000China CAS Key Laboratory of Theoretical Physics Institute of Theoretical PhysicsChinese Academy of SciencesBeijing 100190China School of Fundamental Physics and Mathematical Sciences Hangzhou Institute for Advanced StudyUCASHangzhou 310024China International Centre for Theoretical Physics Asia-Pacific Beijing 100049/Hangzhou 310024China School of Physical Sciences University of Chinese Academy of SciencesBeijing 100049China School of Physics Beihang UniversityBeijing 102206China

Based on five different ensembles of newly generated(2+1)-flavor configurations with pion mass of approximately mπ■(140-310)MeV,we present a lattice analysis of hidden-charm and hidden-strange hexaquarks with the quark content■.The correlation matrices of two types of operators with JPC=0++,0-+,1++and 1--are simulated to extract the masses of the hexaquark candidates,which are subsequently extrapolated to the physical pion mass and continuum *** results indicate that ground state masses are below the■threshold and provide a characteristic signal for the experimental discovery of hexaquark candidates,which may enrich the versatile structure of multiquarks;moreover,it is an indispensable step to decipher the nonperturbative nature of the fundamental interactions of quarks and gluons.

关键词： quantum chromodynamics lattice QCD multiquark states

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