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A Transformer-Based Ensemble Framework for the Prediction of Protein-Protein Interaction Sites

Research 2024年第2期2023卷 703-718页

作者： Minjie Mou Ziqi Pan Zhimeng Zhou Lingyan zheng hanyu Zhang Shuiyang Shi Fengcheng Li Xiuna Sun Feng zhu College of Pharmaceutical Sciences The Second Affliated HospitalZhejiang University School of MedicineNational Key Laboratory of Advanced Drug Delivery and Release SystemsZhejiang UniversityHangzhou 310058China Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University Alibaba-Zhejiang University Joint Research Center of Future Digital HealthcareHangzhou 330110China

The identification of protein-protein interaction (PPI) sites is essential in the research of protein function and the discovery of new drugs. So far, a variety of computational tools based on machine learning have been developed to accelerate the identification of PPI sites. however, existing methods suffer from the low predictive accuracy or the limited scope of application. Specifically, some methods learned only global or local sequential features, leading to low predictive accuracy, while others achieved improved performance by extracting residue interactions from structures but were limited in their application scope for the serious dependence on precise structure information. There is an urgent need to develop a method that integrates comprehensive information to realize proteome-wide accurate profiling of PPI sites. herein, a novel ensemble framework for PPI sites prediction, EnsemPPIS, was therefore proposed based on transformer and gated convolutional networks. EnsemPPIS can effectively capture not only global and local patterns but also residue interactions. Specifically, EnsemPPIS was unique in (a) extracting residue interactions from protein sequences with transformer and (b) further integrating global and local sequential features with the ensemble learning strategy. Compared with various existing methods, EnsemPPIS exhibited either superior performance or broader applicability on multiple PPI sites prediction tasks. Moreover, pattern analysis based on the interpretability of EnsemPPIS demonstrated that EnsemPPIS was fully capable of learning residue interactions within the local structure of PPI sites using only sequence information. The web server of EnsemPPIS is freely available at http://***/ensemppis.

关键词： residue extracting ensemble

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Technologies and studies of gas exchange in two-stroke aircraft piston engine:A review

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Chinese Journal of Aeronautics 2024年第1期37卷 24-50页

作者： Yu ZhOU Xueyu LI Shuiting DING Shuai ZhAO Kun zhu Longtao ShAO Farong DU Gerui WANG zheng XU Research Institute of Aero-Engine Beihang UniversityBeijing 100191China Aircraft/Engine Integrated System Safety Beijing Key Laboratory Beijing 100191China School of Transportation Science and Engineering Beihang UniversityBeijing 100191China Civil Aviation University of China Tianjin 300300China Aero Engine Academy of China Beijing 101304China School of Energy and Power Engineering Beihang UniversityBeijing 100191China Beihang hangzhou Innovation Institute Yuhang Hangzhou 310052China

The in-cylinder gas exchange process is crucial to the power performance of two-stroke aircraft piston engines,which is easily influenced by complex factors such as high-altitude performance variation and in-cylinder flow *** paper reviews the development history and characteristics of gas exchange types,as well as the current state of theory and the validation methods of gas exchange technology,while also discusses the trends of cutting-edge technologies in the *** paper provides a theoretical foundation for the optimization and engineering design of gas exchange systems and,more importantly,points out that the innovation of gas exchange types,the modification of theoretical models,and the technology of variable airflow organization are the key future research directions in this field.

关键词： Aircraft piston engine Aircraft power systems Gas exchange high-altitude performance In-cylinder flow Two-stroke Unmanned Aerial Vehicles(UAVs)

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MOF-derived Se doped MnS/Ti_(3)C_(2)T_(x) as cathode and Zn-Ti_(3)C_(2)T_(x) membrane as anode for rocking-chair zinc-ion battery

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Nano Research 2024年第4期17卷 2781-2789页

作者： Kaisheng Sun Zemao Xiao Yunfei Shen heng Lv Jianpeng zhu Jianxiang Pang Yang zheng Wenwen Kong Long Chen School of Chemistry and Chemical Engineering/State Key Laboratory Incubation Base for Green Processing of Chemical Engineering Shihezi UniversityShihezi 832003China CAS Key Laboratory of Functional Materials and Devices for Special Environments Xinjiang Key Laboratory of Electronic Information Materials and DevicesCenter of Materials Science and Optoelectronics EngineeringXinjiang Technical Institute of Physics and Chemistry of CASUrumqi 830011China

Mn-based zinc ion battery has the advantages of low cost and high performance,which makes it the promising energy storage ***,the poor conductivity and the agglomeration in the synthesis process of manganese-based materials restrict the performance of ***,the Se-doped MnS/Ti_(3)C_(2)T_(x)(Se-MnS/Ti_(3)C_(2)T_(x))composite material derived from Mn-based metal-organic framework is *** tests show that Se-doped could generate S defects and enhance the electrochemical activity of *** the same time,the introduction of Ti_(3)C_(2)T_(x) substrate is conducive to exposing more sulfur defects and improving the utilization rate of *** the mechanism study,it is found that Se-MnS/Ti_(3)C_(2)T_(x) is transformed into S/Se co-doped Mn3O_(4) at the first charge,which innovatively elucidated the behavior of S/Se during *** the electrochemical performance test,the specific capacity can reach 74.7 mAh·g^(-1) at 5.0 A·g^(-1).In addition,the Zn-Ti_(3)C_(2)T_(x) membrane electrode is prepared by vacuum filtration as the zinc-poor anode,which is assembled into the rocking chair full battery to avoid dendrite growth and exhibit excellent rate *** addition of Zn2+weakens the electrostatic repulsion between the interlayers of MXene,and the formation of the folded morphology aids the penetration of the *** 1.0 A·g^(-1),the capacity can reach 50.6 mAh·g^(-1).This work is helpful to promote the research and development of the reaction mechanism of manganese based rocking chair batteries.

关键词： rocking-chair zinc-ion battery MnS Zn-Ti_(3)C_(2)T_(x) membrane Se doped Ti_(3)C_(2)T_(x) composite

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Identification of reservoir types in deep carbonates based on mixedkernel machine learning using geophysical logging data

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Petroleum Science 2024年第3期21卷 1632-1648页

作者： Jin-Xiong Shi Xiang-Yuan Zhao Lian-Bo Zeng Yun-Zhao Zhang zheng-Ping zhu Shao-Qun Dong Key Laboratory of Exploration Technologies for Oil and Gas Resources of the Ministry of Education Yangtze UniversityWuhan4310HubeiChina School of Geosciences Yangtze UniversityWuhan430100HubeiChina College of Geosciences China University of Petroleum(Beijing)Beijing102249China Petroleum Exploration and Production Research Institute of SINOPEC Beijing100083China School of Earth Sciences and Engineering Xi'an Shiyou UniversityXi'an 710065ShaanxiChina

Identification of reservoir types in deep carbonates has always been a great challenge due to complex logging responses caused by the heterogeneous scale and distribution of storage *** cross-plot analysis and empirical formula methods for identifying reservoir types using geophysical logging data have high uncertainty and low efficiency,which cannot accurately reflect the nonlinear relationship between reservoir types and logging ***,the kernel Fisher discriminant analysis(KFD),a kernel-based machine learning technique,attracts attention in many fields because of its strong nonlinear processing ***,the overall performance of KFD model may be limited as a single kernel function cannot simultaneously extrapolate and interpolate well,especially for highly complex data *** address this issue,in this study,a mixed kernel Fisher discriminant analysis(MKFD)model was established and applied to identify reservoir types of the deep Sinian carbonates in central Sichuan Basin,*** MKFD model was trained and tested with 453 datasets from 7 coring wells,utilizing GR,CAL,DEN,AC,CNL and RT logs as input *** particle swarm optimization(PSO)was adopted for hyper-parameter optimization of MKFD *** evaluate the model performance,prediction results of MKFD were compared with those of basic-kernel based KFD,RF and SVM ***,the built MKFD model was applied in a blind well test,and a variable importance analysis was *** comparison and blind test results demonstrated that MKFD outperformed traditional KFD,RF and SVM in the identification of reservoir types,which provided higher accuracy and stronger *** MKFD can therefore be a reliable method for identifying reservoir types of deep carbonates.

关键词： Reservoir type identification Geophysical logging data Kernel Fisher discriminantanalysis Mixedkernel function Deep carbonates

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Rational design of natural leather-based water evaporator for electricity generation and functional applications

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Journal of Energy Chemistry 2024年第9期96卷 129-144页

作者： Bingyuan Zhang Xiaoyu Guan Qingxin han haoxiang Guo Sai zheng Xuhui Sun Afnan h.El-Gowily Mohammed A.Abosheasha Yanxia zhu Motoki Ueda Meng An haojun Fan Yoshihiro Ito College of Bioresources Chemical and Materials Engineering Key Laboratory of Auxiliary Chemistry and Technology for Chemical IndustryMinistry of EducationShaanxi Collaborative Innovation Center of Industrial Auxiliary Chemistry and TechnologyShaanxi University of Science&TechnologyXi'an 710021ShaanxiChina Nano Medical Engineering Laboratory RIKEN Cluster for Pioneering Research2-1 HirosawaWako 351-0198SaitamaJapan Key Laboratory of Leather Chemistry and Engineering(Sichuan University) Ministry of EducationChengdu 610065SichuanChina College of Mechanical and Electrical Engineering Shaanxi University of Science&TechnologyXi'an 710021ShaanxiChina Biochemistry Division Chemistry DepartmentFaculty of ScienceTanta UniversityTanta 31527Egypt

In recent years,water evaporation-induced electricity has attracted a great deal of attention as an emerging green and renewable energy harvesting *** abundant materials have been developed to fabricate hydrovoltaic devices,the limitations of high costs,inconvenient storage and transport,low environmental benefits,and unadaptable shape have restricted their wide ***,an electricity generator driven by water evaporation has been engineered based on natural biomass leather with inherent properties of good moisture permeability,excellent wettability,physicochemical stability,flexibility,and *** numerous nano/microchannels together with rich oxygen-bearing functional groups,the natural leather-based water evaporator,Leather_(Emblic-NPs-SA/CB),could continuously produce electricity even staying outside,achieving a maximum output voltage of∼3 V with six-series ***,the leather-based water evaporator has enormous potential for use as a flexible self-powered electronic floor and seawater demineralizer due to its sensitive pressure sensing ability as well as its excellent photothermal conversion efficiency(96.3%)and thus fast water evaporation rate(2.65 kg m^(−2)h^(−1)).This work offers a new and functional material for the construction of hydrovoltaic devices to harvest the sustained green energy from water evaporation in arbitrary ambient environments,which shows great promise in their widespread applications.

关键词： Energy conversion Water evaporation-induced electricity Functional leather Flexible self-powered sensor Desalination

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Is reactive oxygen species the only way for cancer inhibition over single atom nanomedicine?Autophagy regulation also works

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Chinese Chemical Letters 2024年第6期35卷 474-479页

作者： Yuanyi Zhou Ke Ma Jinfeng Liu Zirun zheng Bo hu Yu Meng Zhizhong Li Mingshan zhu Postdoctoral Innovation Practice Base The First and Fifth Affiliated Hospital of Jinan UniversityGuangzhou 510632China Guangdong Provincial Key Laboratory of Spine and Spinal Cord Reconstruction The Fifth Affiliated Hospital of Jinan University(Heyuan Shenhe People’s Hospital)Heyuan 517465China School of Environment Jinan UniversityGuangzhou 511443China Department of Nephrology The First Affiliated Hospital of Jinan UniversityGuangzhou 510632China

Exploring the therapeutic effect of single atom catalysts beyond reactive oxygen species(ROS)modulation would boost the prosperity of nanomedicine in cancer *** as a vital therapy target offers new options for the control of renal cell carcinoma(RCC)***,Fe single atom-decorated graphene oxide(Fe_(1)-GO)nanosheet is developed to be a feasible autophagy inducer in RCC *** the well-dispersed O-Fe_(1)-O active sites,Fe_(1)-GO kills AChN cells effectively but maintains acceptable cytotoxicity to the normal podocyte and hK2 ***-depth analyses ascribe the inhibition of AChN cells to the upregulated autophagy instead of the commonly known catalytic ROS *** in vivo therapeutic effect of Fe_(1)-GO nanomedicine is also validated by the RCC-bearing BALB/c mice model,realizing an 89% reduction of tumor weight and good *** work provides new insights into the design of autophagy regulators as well as potential therapeutic strategies for RCC treatment.

关键词： Fe single atom Autophagy Renal cell carcinoma Graphene oxide Cancer therapy

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Differences in vascular endothelial function and serum proteome between obese people with phlegm-dampness constitution and balanced constitution

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Journal of Traditional Chinese Medicine 2024年第1期44卷 188-196页

作者： zhu Linghui SUN Ziwei GUAN Yuanyuan LIU Meiyi zheng Yi YU Ruoxi WANG Qi LI Lingru School of Chinese Medicine Beijing University of Chinese MedicineBeijing 102488China National Institute of TCM Constitution and Preventive Medicine Beijing University of Chinese MedicineBeijing 100029China

OBJECTIVE:To evaluate the extent of vascular endothelial dysfunction and preliminary identify serum protein biomarkers associated with obese individuals at risk for cardiovascular disease(CVD).METhODS:Fifteen obese volunteers with the phlegmdampness constitution or balanced constitution were recruited for this study *** clinical baseline data was collected,and the vascular endothelial function was evaluated using the EndoPAT?.Blood samples were collected for the serum proteome *** differences in the serum protein expression levels between the two groups were detected and the protein interaction network analysis,correlation analysis,receiver operating characteristic(ROC)curve analysis,and random forest model investigation were ***:There were no statistical differences found in the baseline *** vascular endothelial function,the reactive hyperemia index(RhI)of the phlegm-dampness constitution obese group was significantly lower than that of the balanced constitution obese group(1.46±0.30 vs 2.82±0.78,Phelial *** are 66 differentially expressed serum proteins between the two *** A2(Apo A2),angiotensin-converting enzyme 2(ACE-2),interleukin-33(IL-33),and forkhead box P3(FoxP3)showed significant differences and area under curve values of their ROC curves were greater than 0.7 and correlated significantly with ***:Vascular endothelial dysfunction was present in the phlegm-dampness constitution obese ***,alterations in the expression levels of key serum proteins,including Apo A2,ACE-2,IL-33,and Fox P3 could serve as potential biomarkers in the obese population at risk of CVD.

关键词： obesity phlegm-dampness constitution vascular endothelial function proteome reactive hyperemia index

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Insufficient TRPM5 Mediates Lipotoxicity-induced Pancreaticβ-cell Dysfunction

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Current Medical Science 2024年第2期44卷 346-354页

作者： Kai-yuan WANG Shi-mei WU zheng-jian YAO Yun-xia zhu Xiao hAN Key Laboratory of human Functional Genomics of Jiangsu Province Department of Biochemistry and Molecular BiologyNanjing Medical UniversityNanjing 211166China

Objective:While the reduction of transient receptor potential channel subfamily M member 5(TRPM5)has been reported in islet cells from type 2 diabetic(T2D)mouse models,its role in lipotoxicity-induced pancreaticβ-cell dysfunction remains *** study aims to study its ***:Pancreas slices were prepared from mice subjected to a high-fat-diet(hFD)at different time points,and TRPM5 expression in the pancreaticβcells was examined using immunofluorescence ***-stimulated insulin secretion(GSIS)defects caused by lipotoxicity were mimicked by saturated fatty acid palmitate(Palm).Primary mouse islets and mouse insulinoma MIN6 cells were treated with Palm,and the TRPM5 expression was detected using qRT-PCR and Western ***-induced GSIS defects were measured following siRNA-based Trpm5 *** detrimental effects of Palm on primary mouse islets were also assessed after overexpressing Trpm5 via an adenovirus-derived Trpm5(Ad-Trpm5).Results:hFD feeding decreased the mRNA levels and protein expression of TRPM5 in mouse pancreatic *** reduced TRPM5 protein expression in a time-and dose-dependent manner in MIN6 *** also inhibited TRPM5 expression in primary mouse *** of Trpm5 inhibited insulin secretion upon high glucose stimulation but had little effect on insulin *** of Trpm5 reversed Palm-induced GSIS defects and the production of functional maturation molecules unique toβ***:Our findings suggest that lipotoxicity inhibits TRPM5 expression in pancreaticβcells both in vivo and in vitro and,in turn,drivesβ-cell dysfunction.

关键词： type 2 diabetes β-cell dysfunction lipotoxicity TRPM5

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Effective utilization of dolomitic lead-zinc waste rock by replacing dolomite as flux in iron ore sintering process

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Journal of Iron and Steel Research International 2024年第8期31卷 1861-1872页

作者： Xin Wang Cong-cong Yang Jian Pan De-qing zhu zheng-qi Guo Guang-hui Xia Shi-juan Qu School of Minerals Processing and Bioengineering Central South UniversityChangsha 410083HunanChina Low-Carbon and hydrogen Metallurgy Research Center Central South UniversityChangsha 410083HunanChina

With increasingly stringent environmental protection policies,cost-effective and value-added treatment of massive lead-zinc waste rock(LZWR)generated from the preconcentration process has attracted substantial attention.A type of dolomitic LZWR with 18 wt.%MgO,27 wt.%CaO,0.29 wt.%Zn and 1.43 wt.%S was used as a replacement flux in the iron ore sintering *** sinter pot tests were carried out based on an industrial ore *** results show that replacing 0%-60%of dolomite with LZWR does not adversely affect the sintering productivity,fuel consumption rate,and the quality of the sinter products,while the Zn and S elements contained in LZWR can be effectively removed with the residual Zn and S contents of the resultant sinter products being less than 0.02 and 0.055 wt.%,***,substituting LZWR for dolomite as a flux inevitably increases the SO_(2) concentration in the sintering flue gas due to its high sulfur *** the processing capacity of the sintering flue gas desulfurization system,the replacement ratio of dolomite can reach 40%,equal to LZWR consumption of 24.3 kg per ton of *** SO_(2) in sintering flue gas can be recovered to produce(Nh_(4))_(2)SO_(4) or hSO_(4),while the volatilized Zn collected into the zinc-containing dust can be subsequently recycled by the rotary hearth furnace ***,it is technologically and economically feasible to use the LZWR as a replacement flux in the iron ore sintering process,providing a new way for the safe,large-scale and low-cost treatment of LZWR.

关键词： Lead Zinc waste rock Dolomite Sintering Flue gas Sinter product

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Construction of millimeter-scale vascularized engineered myocardial tissue using a mixed gel

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Regenerative Biomaterials 2024年第3期3卷 56-67页

作者： Ming Ke Wenhui Xu Yansha hao Feiyang zheng Guanyuan Yang Yonghong Fan Fangfang Wang Zhiqiang Nie Chuhong zhu Department of Anatomy Third Military Medical UniversityChongqing 400038China State Key Laboratory of Trauma Burn and Combined InjuryChongqing 400038China Department of Plastic and Aesthetic Surgery Southwest HospitalThird Military Medical UniversityChongqing 400038China Engineering Research Center of Tissue and Organ Regeneration and Manufacturing Ministry of EducationChongqing 400038China

Engineering myocardium has shown great clinal potential for repairing permanent myocardial ***,the lack of perfusing blood vessels and difficulties in preparing a thick-engineered myocardium result in its limited clinical *** prepared a mixed gel containing fibrin(5 mg/ml)and collagen I(0.2 mg/ml)and verified that human umbilical vein endothelial cells(hUVECs)and human-induced pluripotent stem cell-derived cardiomyocytes(hiPSC-CMs)could fom microvascular lumens and myocardial cell clusters by harnessing the low-hardness and hyperelastic characteristics of ***-CMs and hUVECs in the mixed gel formed self-organized cell clusters,which were then cultured in different media using a three-phase *** successfully constructed vascularized engineered myocardial tissue had a spherical structure and final diameter of *** tissue exhibited autonomous beats that occured at a frequency similar to a normal human heart *** internal microvascular lumen could be maintained for 6 weeks and showed good results during preliminary surface re-vascularization in vitro and vascular remodeling in *** summary,we propose a simple method for constructing vascularized engineered myocardial tissue,through phased cultivation that does not rely on high-end manufacturing equipment and cutting-edge preparation *** constructed tissue has potential value for clinical use after preliminary evaluation.

关键词： engineered myocardium vascularized hiPSC-CM hUVEC fibrin

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