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Staged-probability strategy of processing shotgun proteomic data to discover more functionally important proteins

Protein & Cell 2012年第2期3卷 140-147页

作者： Hong Xu Guijun Ma Qingqiao Tan qiang Zhou wen Su Rongxiu li State Key Laboratory of Microbial Metabolism(Shanghai Jiao Tong University)and School of life Sciences&Biotechnology Shanghai Jiao Tong UniversityShanghai 200240China Department of Bioinformatics and Biostatistics College of Life Sciences&BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Software Engineering Institute East China Normal UniversityShanghai 200062China

Biologically important proteins related to membrane receptors,signal transduction,regulation,transcription,and translation are usually low in abundance and identified with low probability in mass spectroscopy(MS)-based *** valuable proteomics information on them were hitherto discarded due to the application of excessively strict data filtering for accurate *** this study,we present a stagedprobability strategy for assessing proteomic data for potential functionally important protein ***-based protein identifications from the second(L2)and third(L3)layers of the cascade affinity fractionation using the Trans-Proteomic Pipeline software were classified into three probability stages as 1.00–0.95,0.95–0.50,and 0.50–0.20 according to their distinctive identification correctness rates(i.e.100%–95%,95%–50%,and 50%–20%,respectively).We found large data volumes and more functionally important proteins located at the previously unacceptable lower probability stages of 0.95–0.50 and 0.50–0.20 with acceptable correctness *** importantly,low probability proteins in L2 were verified to exist in *** with some MS spectrogram examples,comparisons of protein identifications of L2 and L3 demonstrated that the stagedprobability strategy could more adequately present both quantity and quality of proteomic information,especially for researches involving biomarker discovery and novel therapeutic target screening.

关键词： lower minimum probability threshold probability grade TPP low-abundant protein

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Combination of olfactory ensheathing cells and human umbilical cord mesenchymal stem cell-derived exosomes promotes sciatic nerve regeneration

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Neural Regeneration Research 2020年第10期15卷 1903-1911页

作者： Yang Zhang wen-Tao Wang Chun-Rong Gong Chao li Mei Shi Department of Radiation Oncology Xijing HospitalAir Force Medical UniversityXi’anShaanxi ProvinceChina Department of Orthopedics Changhai HospitalNaval Medical UniversityShanghaiChina Rehabilitation Center North District Hospital of the People’s Hospital of Lin Yi CityLinyiShandong ProvinceChina Department of Orthopedics The Eighth Medical Center of Chinese PLA general HospitalBeijingChina

Olfactory ensheathing cells(OECs)are promising seed cells for nerve ***,their application is limited by the hypoxic environment usually present at the site of *** derived from human umbilical cord mesenchymal stem cells have the potential to regulate the pathological processes that occur in response to *** ability of OECs to migrate is unknown,especially in hypoxic conditions,and the effect of OECs combined with exosomes on peripheral nerve repair is not *** understanding of these issues will enable the potential of OECs for the treatment of nerve injury to be *** this study,OECs were acquired from the olfactory bulb of Sprague Dawley *** umbilical cord mesenchymal stem cell-derived exosomes(0–400μg/mL)were cultured with OECs for 12–48 *** culture with 400μg/mL exosomes for 24 hours,the viability and proliferation of OECs were significantly *** observed changes to OECs subjected to hypoxia for 24 hours and treatment with *** significantly promoted the survival and migration of OECs in hypoxic conditions,and effectively increased brain-derived neurotrophic factor gene expression,protein levels and ***,using a 12 mm left sciatic nerve defect rat model,we confirmed that OECs and exosomes can synergistically promote motor and sensory function of the injured sciatic *** findings show that application of OECs and exosomes can promote nerve regeneration and functional *** study was approved by the Institutional Ethical Committee of the Air Force Medical University,China(approval ***-20181004)on October 7,2018;and collection and use of human umbilical cord specimens was approved by the Ethics Committee of the linyi People’s Hospital,China(approval No.30054)on May 20,2019.

关键词： brain-derived neurotrophic factor cell migration cell viability functional recovery hypoxia nerve regeneration sciatic functional index sciatic nerve injury

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Technology for Simulating Crowd Evacuation Behaviors

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International Journal of Automation and computing 2009年第4期6卷 351-355页

作者： wen-Hu Qin Guo-Hui Su Xiao-Na li School of Instrument Science and Engineering Southeast University Nanjing 210096 PRC

This paper presents a model for simulating crowd evacuation and investigates three widely recognized problems. For the space continuity problem, this paper presents two computation algorithms： one uses grid space to evaluate the coordinates of the obstacle＇s bounding box and the other employs the geometry rule to establish individual evacuation routes. For the problem of collision, avoidance, and excess among the individuals, this paper computes the generalized force and friction force and then modifies the direction of march to obtain a speed model based on the crowd density and real time speed. For the exit selection problem, this paper establishes a method of selecting the exits by combining the exit＇s crowd state with the individuals. Finally, a particle system is used to simulate the behavior of crowd evacuation and produces useful test results.

关键词： Crowd evacuation behavior simulation particle system social force model

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Comparison of two great Chile tsunamis in 1960 and 2010 using numerical simulation

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Earthquake Science 2011年第5期24卷 475-483页

作者： Ruizhi wen Yefei Ren Xiaojun li Rong Pan Institute of Engineering Mechanics China Earthquake Administration Harbin 150080 China Institute of Geophysics China Earthquake Administration Beijing 100081 China Nuclear and Radiation Safety Center Ministry of Environmental Protection Beijing 100082 China

Great differences in hazard and losses were shown from two tsunamis, both generated in Chile, one in 1960 and the other in 2010. Numerical simulation was applied to the tsunami analysis. The fault dislocation of the seafioor was assumed to equal to the initial tsunami wave field, which can be calculated by the formula of fault dislocation in the elastic isotropic half-space. The linear long wave theory was used as the tsunami hydrodynamic model, and the finite difference method and leap-frog scheme were selected for solving the equations. The accuracy of the simulated results was verified by the observed data in five tide gauges. By means of two scenario tsunamis, the analytical results show that the earthquake magnitude, bathymetry in rupture zone and rapid release of warning information in 2010 tsunami are the main explanations of the aforementioned great difference.

关键词： Chile earthquake tsunami numerical simulation

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Peracetic acid catalytic activation using Co_(3)O_(4) nanocluster decorated graphitic carbon nitride for cefapirin degradation in water

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Science China(Technological Sciences) 2024年第10期67卷 3103-3115页

作者： YIN ShiMei GAO YiXuan CHEN Long li Fan liU XiaoNa QI Fei liU wen Beijing Key Lab for Source Control Technology of Water Pollution College of Environmental Science and EngineeringBeijing Forestry UniversityBeijing 100083China Key Laboratory of Water and Sediment Sciences(Ministry of Education) College of Environmental Sciences and EngineeringPeking UniversityBeijing 100871China School of Environmental Science and Engineering Taiyuan University of TechnologyTaiyuan 030024China State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems Peking UniversityBeijing 100871China Beijing National Laboratory for Molecular Sciences Peking UniversityBeijing 100871China

This study innovated cobalt-based catalytic nanocomposites(CCNs)for the heterogeneous activation of peracetic acid(PAA),a green and efficient advanced oxidation process for removing antibiotics from *** Co_(3)O_(4) catalysts exhibit limited activity due to stable electronic *** overcome this,CCNs were synthesized using a one-step condensation method,incorporating a size control strategy that anchors Co_(3)O_(4) nanoclusters within 4‒5 nm onto six-fold cavity of g-C3N4,simultaneously modifying the coordination environment of *** alteration significantly enhances the adsorption energy of PAA and catalytic activity compared to commercial Co_(3)O_(4).The improved performance of CCN2,in particular,is attributed to a shift in the cobalt d band center towards the Fermi level,facilitating electron delocalization and transfer,enhancing Co‒O bonding,and accelerating PAA ***2’s superior activity,with a cefapirin(CFP)degradation kinetic rate constant(k1=0.760 min^(−1))~11 times that of PAA direct oxidation(k1=0.070 min^(−1))and~5 times that of commercial Co_(3)O_(4)/PAA system(k1=0.164 min^(−1)),is due to its ability to generate dominant reactive species for antibiotic degradation,including alkoxy radicals(CH3C(=O)OO•),high valence metal(Co^(Ⅳ)(=O)^(2+)),and singlet oxygen(^(1)O_(2)),with the latter two being crucial for the degradation *** degradation of CFP involved three mechanisms,including direct oxidation by PAA,decarboxylation,and open-ring reactions at nitrogen *** research provides insights into developing high-activity catalysts for efficient PAA activation and antibiotic removal,leveraging the strategy of shifting the transition metal d band center.

关键词： peracetic acid Co_(3)O_(4)nanocluster high valence metal singlet oxygen cefapirin

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Numerical simulation study of the failure evolution process and failure mode of surrounding rock in deep soft rock roadways

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International Journal of Mining Science and Technology 2016年第2期26卷 209-221页

作者： Meng Qingbin Han lijun Xiao Yu li Hao wen Shengyong Zhang Jian State Key Laboratory for Geomechanics and Deep Underground Engineering China University of Mining and TechnologyXuzhou 221116China Shandong Provincial Key Laboratory of Depositional Mineralization&Sedimentary Minerals Shangdong University of Science and TechnologyQingdao 266590China

Based on the safety coefficient method,which assigns rock failure criteria to calculate the rock mass unit,the safety coefficient contour of surrounding rock is plotted to judge the distribution form of the fractured zone in the *** will provide the basis numerical simulation to calculate the surrounding rock fractured zone in a *** the single factor and multi-factor orthogonal test method,the evolution law of roadway surrounding rock displacements,plastic zone and stress distribution under different conditions is *** reveals the roadway surrounding rock burst evolution process,and obtains five kinds of failure modes in deep soft rock *** the fuzzy mathematics clustering analysis method,the deep soft surrounding rock failure model in Zhujixi mine can be classified and patterns *** to the identification results and the results detected by geological radar of surrounding rock loose circle,the reliability of the results of the pattern recognition is verified and lays the foundations for the support design of deep soft rock roadways.

关键词： Deep soft rock roadway Evolutionary process Failure model Numerical simulation Model recognition

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Phylogenomic conflict analyses in the apple genus Malus *** widespread hybridization and allopolyploidy driving diversification,with insights into the complex biogeographic history in the Northern Hemisphere

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Journal of Integrative Plant Biology 2022年第5期64卷 1020-1043页

作者： Bin-Bin liu Chen Ren Myounghai Kwak Richard GJHodel Chao Xu Jian He wen-Bin Zhou Chien-Hsun Huang Hong Ma Guan-Ze qian De-Yuan Hong Jun wen State Key Laboratory of Systematic and Evolutionary Botany Institute of Botanythe Chinese Academy of SciencesBeijing 100093China Department of Botany National Museum of Natural HistorySmithsonian InstitutionPO Box 37012Washington 20013–7012DCUSA Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical GardenThe Chinese Academy of SciencesGuangzhou 510650China Guangdong Provincial Key Laboratory of Applied Botany South China Botanical GardenThe Chinese Academy of SciencesGuangzhou 510650China National Institute of Biological Resources Incheon 22689South Korea School of Ecology and Nature Conservation Beijing Forestry UniversityBeijing 100083China Department of Plant and Microbial Biology North Carolina State UniversityRaleigh 27965NCUSA State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200433China Department of Biology Huck Institutes of the Life SciencesPennsylvania State University510D Mueller LaboratoryUniversity ParkPennsylvania 16802USA College of life Sciences Liaocheng UniversityLiaocheng 252059China

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting *** this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy *** nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid *** ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear *** conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree *** deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus ***,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus *** the Eocene,followed by several extinction and dispersal events in the Northern *** also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

关键词： deep genome skimming genomic discordance historical biogeography massive extinction reticulate evolution single-copy nuclear genes

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Nematode Diversity in Phaeozem Agroecosystems of Northeast China

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Pedosphere 2009年第5期19卷 597-605页

作者： li Qi JIANG Yong liANG wen-Ju WANG He JIANG Si-Wei Key Laboratory of Terrestrial Ecological Process Institute of Applied Ecology Chinese Academy of Sciences Shenyang110016 (China) Institute of Agricultural Resources and Regional Planning Chinese Academy of Agricultural Sciences Beijing 100081(China)

The diversity and distribution patterns of soil nematode communities in phaeozem agroecosystems of Northeast China were assessed to evaluate nematode taxonomic diversity and functional diversity in relation to climatic condition and soil characteristics in human modified landscape. Along the latitudinal gradient, soil samples were collected from north （Hailun） to south （Gongzhuling） down to a depth of 100 cm with intervals of 030, 20-40, 40-60, 60-80, and 80-100 cm. The nematode abundance and taxonomic diversity （generic richness） were lower at Hailun than at other sites, and higher values of evenness were observed at Hailun and Harbin than at Dehui and Gongzhuling. Nematode faunal analysis revealed that soil food web at Hailun was sueeessionally more mature or structured, and the environment little disturbed, while at Harbin and Gongzhuling, the soil food web was degraded with stressed environment. The environmental variables relevant in explaining the patterns of nematode distribution and diversity in phaeozem agroecosystems, using canonical correspondence analysis （CCA）, were the mean annual temperature, total nitrogen, electrical conductivity, mean annual precipitation, and other soil properties. Among these variables, the mean annual temperature was a relatively important factor, which could explain 29.05% of the variations in nematode composition.

关键词： agricultural disturbance canonical correspondence analysis maize field nematode faunal analysis soil biodiversity

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Manganese removal from the qiantang River source water by pre-oxidation:A case study

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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2009年第3期10卷 450-457页

作者： Jian-wen ZHU Zhen ZHANG Xiao-min li Xin-hua XU Da-hui WANG Department of Environmental Engineering Zhejiang University Hangzhou 310027 China Hangzhou Water Group Company Ltd. Hangzhou 310009 China School of Bioscienee Taizhou University Linhai 317000 China

We evaluated several different pre-oxidation treatments, namely the introduction of either potassium permanganate (KMnO4), chlorine (Cl2), or both to remove manganese (Mn) from the qiantang River source water. Our results showed that Mn removal percentages were 12.7%, 71.0%, 17.4% and 58.7% when none of the oxidants, KMnO4 only, Cl2 only, or both oxidants were added, respectively. Furthermore, a field study showed that when the available Mn concentration in the source water was 0.14 mg/L, it could be reduced to less than 0.05 mg/L when a solution of KMnO4 (0.47 mg/L) was added as the oxidant.

关键词： Pre-oxidation Potassium permanganate (KMnO2) Chlorine (Cl2) Manganese (Mn) removal

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On two actuarial quantities for the compound Poisson risk model with tax and a threshold dividend strategy

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Applied Mathematics(A Journal of Chinese Universities) 2013年第1期28卷 27-39页

作者： WANG wen-yuan XIAO li-qun MING Rui-xing HU Yi-jun College of Science Shantou University School of Mathematics and Statistics Wuhan University School of Mathematical Sciences University of Science and Technology of China School of Statistics and Mathematics Zhejiang Gongshang University

In this paper, we consider a compound Poisson risk model with taxes paid according to a loss-carry-forward system and dividends paid under a threshold strategy. First, the closed-form expression of the probability function for the total number of taxation periods over the lifetime of the surplus process is derived. Second, analytical expression of the expected accumulated discounted dividends paid between two consecutive taxation periods is provided. In addition, explicit expressions are also given for the exponential individual claims.

关键词： Compound Poisson risk model total number of taxation periods expected accumulated discounted dividends.

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