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Computational prediction of cleavage using proteasomal in vitro digestion and MHC I ligand data

Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2013年第9期14卷 816-828页

作者： Yu-feng lu Hao sheng Yi ZHANG Zhi-yang LI School of Mathematical Sciences Dalian University of Technology College of Science Hebei University of Science and Technology School of Information Science and Technology Dalian Maritime University

Proteasomes are responsible for the production of the majority of cytotoxic T lymphocyte(CTL) ***,it is important to identify correctly which peptides will be generated by proteasomes from an unknown ***,the pool of proteasome cleavage data used in the prediction algorithms,whether from major histocompatibility complex(MHC) I ligand or in vitro digestion data,is not identical to in vivo proteasomal digestion ***,the accuracy and reliability of these models still need to be *** this paper,three types of proteasomal cleavage data,constitutive proteasome(cCP),immunoproteasome(iCP) in vitro cleavage,and MHC I ligand data,were used for training cleave-site predictive methods based on the kernel-function stabilized matrix method(KSMM).The predictive accuracies of the KSMM+pair coefficients were 75.0%,72.3%,and 83.1% for cCP,iCP,and MHC I ligand data,respectively,which were comparable to the results from support vector machine(SVM).The three proteasomal cleavage methods were combined in turn with MHC I-peptide binding predictions to model MHC I-peptide processing and the presentation *** integrations markedly improved MHC I peptide identification,increasing area under the receiver operator characteristics(ROC) curve(AUC) values from 0.82 to *** results suggested that both MHC I ligand and proteasomal in vitro degradation data can give an exact simulation of in vivo processed *** information extracted from cCP and iCP in vitro cleavage data demonstrated that both cCP and iCP are selective in their usage of peptide bonds for cleavage.

关键词： Cytotoxic T lymphocyte epitopes Kernel function Proteasome Stabilized matrix method

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Machine-learning-assisted prediction of surgical outcomes in patients undergoing gastrectomy

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Chinese Journal of Cancer Research 2019年第5期31卷 797-805页

作者： sheng lu Min Yan Chen Li Chao Yan Zhenggang Zhu Wencong lu Department of General Surgery Rui Jin HospitalShanghai Jiao Tong University School of MedicineShanghai Institute of Digestive SurgeryShanghai 200025China Department of Chemistry College of SciencesShanghai UniversityShanghai 200444China

Objective: Postoperative complications adversely affected the prognosis in patients with gastric cancer. This study intends to investigate the feasibility of using machine-learning model to predict surgical outcomes in patients undergoing ***: In this study, cancer patients who underwent gastrectomy at Shanghai Rui Jin Hospital in 2017 were randomly assigned to a development or validation cohort in a 9:1 ratio. A support vector classification(SVC) model to predict surgical outcomes in patients undergoing gastrectomy was developed and further ***: A total of 321 patients with 32 features were collected. The positive and negative outcomes of postoperative complication after gastrectomy appeared in 100(31.2%) and 221(68.8%) patients, respectively. The SVC model was constructed to predict surgical outcomes in patients undergoing gastrectomy. The accuracy of 10-fold cross validation and external verification was 78.17% and 78.12%, respectively. Further, an online web server has been developed to share the SVC model for machine-learning-assisted prediction of surgical outcomes in patients undergoing gastrectomy in the future procedures, which is accessible at the web address:http://47.***.47.97:5005/r_model_***: The SVC model was a useful predictor for measuring the risk of postoperative complications after gastrectomy, which may help stratify patients with different overall status for choice of surgical procedure or other treatments. It can be expected that machine-learning models in cancer informatics research are possibly shareable and accessible via web address all over the world.

关键词： Gastric cancer postoperative complications machine-learning models support vector classification

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Microstructure and Mechanical Properties of AZ31 Mg Alloy Fabricated by Pre-compression and Frustum Shearing Extrusion

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Acta Metallurgica Sinica(English Letters) 2019年第2期32卷 235-244页

作者： Kun sheng Li-Wei lu Yao Xiang Min Ma Zhong-Chang Wang Hunan Provincial Key Laboratory of High Efficiency and Precision Machining of Difficult-to-Cut Material Hunan University of Science and Technology College of Materials Science and Engineering Hunan University of Science and Technology Department of Quantum Materials Science and Technology International Iberian Nanotechnology Laboratory(INL)

The AZ31 Mg alloys were processed by 6% pre-compression and frustum shearing extrusion at various temperatures, and the microstructure, texture and mechanical properties of the resulting alloys are systematically investigated. The results show that the grain size monotonically increases from 6.4 to 12.6 lm and the texture intensity increases from 6.7 to 9.6with the increase in the extrusion temperature. The combining effect of the pre-twinning and the frustum shearing deformation is found to contribute to the development of the weak basal texture in Mg alloys. The Mg alloy sheet produced at the extrusion temperature of 563 K exhibits excellent mechanical properties. The yield strength, ultimate tensile strength and elongation for the extruded alloys are 189.6 MPa, 288.4 MPa and 24.9%, respectively. Such improved mechanical properties are comparable or even superior to those of the alloys subjected to other deformation techniques, rendering the pre-compression and frustum shearing extrusion a promising way for further tailoring properties of Mg alloys.

关键词： AZ31 magnesium alloy Frustum shearing extrusion Microstructure Mechanical property Dynamic recrystallization

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Anodic dissolution of a crack tip at AA2024-T351 in 3.5wt% NaCl solution

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International Journal of Minerals,Metallurgy and Materials 2012年第10期19卷 939-944页

作者： Hai sheng Chao-fang Dong Kui Xiao Xiao-gang Li Lin lu School of Materials Science and Engineering University of Science and Technology BeijingBeijing 100083China

The anodic dissolution process of a crack tip at 2024-T351 aluminium alloy （AA2024-T351） was determined by means of scanning Kelvin probe （SKP）. Wedge-open loading （WOL） specimens were immersed in a 3.5wt% NaCl solution. After various durations of immersion, the Volta potential distributions around the crack were measured by SKP and the surface morphologies were observed by scanning electron microscopy （SEM）. It is found that there is a nonuniform distribution of Volta potential around the crack. Before immersion, the Volta potential at crack tip is more negative than that in other regions. However, after immersion, a converse result occurs with the most positive Volta potential measured at the crack tip. SEM observations demonstrate that the noticeable positive shift of Volta potential results fi：om the formation of corrosion products which deposit around the crack tip. Energy-dispersive spectrometry （EDS） analysis shows that the corrosion products are mainly A1 oxide and Cu-rich particles. These observations implicate that the applied stress contributes to the preferential anodic dissolution of the crack tip and the redistribution of Cu.

关键词： aluminium alloys crack tips dissolution brines stress corrosion cracking

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Cryosphere water resources supply function and service in China

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Advances in Climate Change Research 2022年第3期13卷 408-420页

作者： Kai-lu LI Ren-sheng CHEN Guo-Hua LIU Yong YANG Northwest Institute of Eco-Environment and Resources Chinese Academy of SciencesLanzhou 730000China College of Resources and Environment University of Chinese Academy of SciencesBeijing 100049China College of Urban and Environmental Sciences Northwest UniversityXi’an 710000China

With global warming and rapid shrinkage of the cryosphere,the decreasing cryosphere water resources(CWR)supply function would weaken its service and then affect local economic development and implement of United Nations Sustainable Development Goals(SDGs)in the world,but how does the CWR supply affect its service and their variations in the past and future are still not clear at *** this study,the past dynamics(1960-2020),current situation(2010s)and projected changes(2020-2100)of CWR in China were assessed by calculating the meltwater from glacier,snow cover and the ground ice of permafrost under Representative Concentration Pathways scenarios(RCP2.6,RCP4.5,and RCP8.5).Combined with projected data of population and economy,the CWR service potential was also estimated in the 2030s,2050s and 2090s under scenarios of Shared Socioeconomic Pathways(SSP1,SSP2,and SSP5).The annual CWR in China is about 310.7×10^(9)m^(3) in the 2010s,with glacier runoff,snowmelt,and ground ice meltwater accounting for 24.1%,72.7%and 3.2%,*** SSP1-RCP2.6,the quantity of CWR was projected to decline by 14%-18%over the next 80 years,and the service potential would reach the peak in *** under SSP5-RCP8.5,CWR would be reduced by 40%by 2100,and the service would gradually decline from *** study of CWR is of great significance for water security,sustainable development and risk avoidance in the arid endorheic region.

关键词： Cryosphere water resources Glaciers Snow cover Permafrost Function and service

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Retrogression characteristics of a novel Al-Cu-Li-X alloy

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International Journal of Minerals,Metallurgy and Materials 2010年第5期17卷 624-628页

作者： Zhi-shan Yuan Zheng lu Xiu-liang Wu You-hua Xie sheng-long Dai Chang-sheng Liu Grikin Advanced Materials Co. Ltd. General Research Institute for Non-Ferrous Metals Beijing 100088 China Beijing Institute of Aeronautical Materials Beijing 100095 China School of Materials ＆ Metallurgy Northeastern University Shenyang 110004 China

Retrogression characteristics of a novel Al-Cu-Li-X alloy of 2A97 were studied by hardness testing, transmission electron microscopy （TEM）, and differential scanning calorimetry （DSC）. The retrogression treatments of aging at 155°C for 12 h followed by aging at 220 and 240°C were chosen by determining the peak temperature of δ＇ precipitation at 230°C by DSC. The retrogression treatment at a lower temperature of 220°C causes the precipitation and coarsening of δ＇ and θ＇ phases in the matrix, resulting in an increase in hardness. Retrogression at a higher temperature of 240°C causes the dissolution and coarsening of δ＇ and θ＇ precipitates in the matrix and on the grain boundaries, resulting in a decrease in hardness. Microstructural changes upon retrogression including the appearance of equilibrium precipitates such as T1, T2, δ＇, and θ are confirmed by the selected area electron diffraction and the bright and dark field image analysis.

关键词： retrogression artificial aging aluminum-lithium alloy microstructure

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CO_2-sensitive Amphiphilic Triblock Copolymer Self-assembly Morphology Transition and Accelerating Drug Release from Polymeric Vesicle

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Chinese Journal of Polymer Science 2018年第1期36卷 18-24页

作者： Xian-Wu Jing Zhi-Yu Huang Hong-sheng lu Bao-Gang Wang College of Chemistry and Chemical Engineering Southwest Petroleum University Engineering Research Center of Oilfield Chemistry Ministry of Education

A series of triblock copolymers, containing a CO_2-switchable block poly（2-（dimethylamino）ethyl methacrylate）（PDM） block and two symmetrical hydrophilic blocks polyacrylamide（PAM）, were synthesized using atom transfer radical polymerization（ATRP） method. The p H and conductivity tests showed that the triblock copolymer exhibited switchable responsiveness to CO_2, i.e. a relatively low conductivity of solution could be switched on and off by bubbling and removing of CO_2, and the triblock copolymer aqueous solution displayed a CO_2-switchable viscosity variation. The changes were all attributed to protonation of tertiary amine groups in PDM blocks and proven by 1 H-NMR. Cryogenic transmission electron microscopy and dynamic light scattering characterization demonstrated that the viscosity variation was the result of a unilamellar vesicle-network aggregate structure transition. The release of rhodamine B from the vesicles with and without CO_2 stimuli showed the potential application in drug delivery domains; after CO_2 bubbling, the drug release rate could be accelerated. Finally, reasonable mechanism of CO_2-switchable morphology changes and CO_2-induced drug release was proposed.

关键词： ATRP CO_2-sensitive Polymeric vesicles Drug release

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Syntheses and Characterizations of Cyanido-bridged Dinuclear Ru-complexes and Their MMCT Properties in the One-electron Oxidation State

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Chinese Journal of Structural Chemistry 2021年第10期40卷 1253-1264页

作者： LIU Yang ZHU Xiao-Quan WU Xin-Tao sheng Tian-lu College of Chemistry Fuzhou UniversityFuzhou 350002China State Key Laboratory of Structural Chemistry Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhou 350002China University of Chinese Academy of Sciences Beijing 100049China

We have designed and synthesized a family of dinuclear cyanido-bridged complexes[PY5Me_(2)Ru(μ-CN)Ru(dppe)CpMe_(n)][PF_(6)]_(2) (PY5Me_(2)=2,6-bis (1,1-bis(2-pyridyl)ethyl) pyridine,Cp=cyclopentadienyl,n=0,2[PF6]_(2);n=1,3[PF6]_(2);n=5,4[PF6]_(2)) by using a mononuclear complex[PY5Me_(2)Ru(μ-CN)][PF_(6)](1) as the *** the three complexes have been fully characterized by including single-crystal X-ray diffraction *** one-electron oxidation complexes 2^(3+),3^(3+) and 4^(3+) obtained in situ all show a MMCT absorption band in the visible *** MMCT energy increases as the redox potential of the N-terminal fragments decreases,and the redox potential decreases as the number of methyl groups on the cyclopentadiene of the cyanido-nitrogen coordinated Ru metal increases,supported by the TDF/TDDFT calculations.

关键词： electron transfer mixed-valence metal to metal charge transfer(MMCT) cyanide bridge

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Tailoring Cationic Helical Polypeptides for Efficient Cytosolic Protein Delivery

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Chemical Research in Chinese Universities 2020年第1期36卷 134-138页

作者： WANG Ruijue sheng Kai HOU Yingqin SUN Jialing lu Hua Beijing National Laboratory for Molecular Sciences Center for Soft Matter Science and EngineeringKey Laboratory of Polymer Chemistry and Physics of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871P.R.China

Protein delivery is of central importance for both diagnostic and therapeutic ***,protein delivery faces challenges including poor endosomal escape and thus limited ***,we report the facile construction and screening of a small library of cationic helical polypeptides for cytosolic protein *** library is based on a random copolymer poly(γ-{2-[2-(2-methoxyethoxy)ethoxy]ethoxy}esteryl-L-glutamate)-randompoly(γ-6-chlorohexyl-L-glutamate)[P(EG3-r-ClC6)Glu],which is then modified with various pyridine derivatives and alkyl *** Cytometry,confocal laser scanning microscopy,and viability assay collaboratively identify two leading polymers,showing efficient delivery of enhanced green fluorescent protein(eGFP)and low *** finding is further validated by the cytosolic delivery of RNase A and cytochrome C(Cyt C)to HeLa cells in the viability ***,this work demonstrates that high-throughput screening is an effective and viable approach to the selection of cationic helical polypeptides for the cytosolic delivery of functional proteins.

关键词： Cationic helical polypeptide Protein delivery Cytosolic protein

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Interacted Effect of Arbuscular Mycorrhizal Fungi and Polyamines on Root System Architecture of Citrus Seedlings

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Journal of Integrative Agriculture 2012年第10期11卷 1675-1681页

作者： WU Qiang-sheng ZOU Ying-ning LIU Chun-yan lu Ting College of Horticulture and Gardening Yangtze University

Either arbuscular mycorrhizal fungi （AMF） or polyamines （PAs） may change root system architecture （RSA） of plants, whereas the interaction of AMF and PAs on RSA remains unclear. In the present study, we studied the interaction between AMF （Paraglomus occultum） and exogenous PAs, including putrescine （Put）, spermidine （Spd） and spermine （Spin） on mycorrhizal development of different parts of root system, plant growth, RSA and carbohydrate concentrations of 6-m-old citrus （Citrus tangerine Hort. ex Tanaka） seedlings. After 14 wk of PAs application, PA-treated mycorrhizal seedlings exhibited better mycorrhizal colonization and numbers of vesicles, arbuscules, and entry points, and the best mycorrhizal status of taproot, first-, second-, and third-order lateral roots was respectively found in mycorrhizal seedlings supplied with Put, Spd and Spm, suggesting that PAs might act as a regulated factor of mycorrhizal development through transformation of root sucrose more into glucose for sustaining mycorrhizal development. AMF usually notably increases RSA traits （taproot length, total length, average diameter, projected area, surface area, volume, and number of first-, second-, and third-order lateral roots） of only PA-treated seedlings. Among the three PA species, greater positive effects on RSA change and plant biomass increment of the seedlings generally rank as Spd〉Spm〉Put, irrespective of whether or not AMF colonization. PAs significantly changed the RSA traits in mycorrhizal but not in non-mycorrhizal seedlings. It suggests that the application of PAs （especially Spd） to AMF plants would optimize RSA of citrus seedlings, thus increasing plant growth （shoot and root dry weight）.

关键词： citrus lateral root mycorrhiza putrescine root system architecture spermidine spermine

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