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GTB-PPI:Predict Protein-protein Interactions Based on L1-regularized Logistic Regression and Gradient Tree Boosting

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Genomics, Proteomics & Bioinformatics 2020年第5期18卷 582-592页

作者： Bin Yu cheng chen hongyan Zhou Bingqiang Liu Qin ma School of Life Sciences University of Science and Technology of ChinaHefei 230027China College of mathematics and Physics Qingdao University of Science and TechnologyQingdao 266061China Artificial Intelligence and Biomedical Big Data Research Center Qingdao University of Science and TechnologyQingdao 266061China School of mathematics Shandong UniversityJinan 250100China Department of Biomedical Informatics College of MedicineThe Ohio State UniversityColumbusOH 43210USA

Protein-protein interactions(PPIs)are of great importance to understand genetic mechanisms,delineate disease pathogenesis,and guide drug *** the increase of PPI data and development of machine learning technologies,prediction and identification of PPIs have become a research hotspot in *** this study,we propose a new prediction pipeline for PPIs based on gradient tree boosting(GTB).First,the initial feature vector is extracted by fusing pseudo amino acid composition(Pse AAC),pseudo position-specific scoring matrix(Pse PSSM),reduced sequence and index-vectors(RSIV),and autocorrelation descriptor(AD).Second,to remove redundancy and noise,we employ L1-regularized logistic regression(L1-RLR)to select an optimal feature ***,GTB-PPI model is ***-fold cross-validation showed that GTB-PPI achieved the accuracies of 95.15% and 90.47% on Saccharomyces cerevisiae and Helicobacter pylori datasets,*** addition,GTB-PPI could be applied to predict the independent test datasets for Caenorhabditis elegans,Escherichia coli,Homo sapiens,and Mus musculus,the one-core PPI network for CD9,and the crossover PPI network for the Wnt-related signaling *** results show that GTB-PPI can significantly improve accuracy of PPI *** code and datasets of GTB-PPI can be downloaded from https://***/QUST-AIBBDRC/GTB-PPI/.

关键词： Protein-protein interaction Feature fusion L1-regularized logistic regression Gradient tree boosting machine learning

Effect of particle-particle interaction on dielectrophoretic single particle trap in a sudden contraction flow

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Nanotechnology and Precision Engineering 2018年第4期1卷 236-241页

作者： Haihang Cui Rui ma Li chen hongyan Zhang School of Environment and Municipal Engineering Xi'an University of Architecture and Technology

Dielectrophoretic(DEP) force is significant in manipulating tiny objects in micro/nano scale. To study the effect of electric interaction force on particle manipulation, a microstructure consisting of a pair of strip electrodes and a sudden contraction micro-channel was constructed. Besides DEP force and hydrodynamic force acting on single particle, the numerical model also involved electric interaction force and force moment on two particles. The analyses revealed that the particle-particle interaction force was in the same order as that of DEP force on single trapped particle. The interaction force resulted in trapping single particle failure under continuous DEP ***, pulsed DEP force, turning on/off DEP force at a given time interval, was suggested. During the "off" period,the velocity difference of the two particles located at sudden contraction micro-channel enlarged the gap between them and further weakened the particle-particle interaction. By a proof-of-concept experiment, both the trapping behavior of single particle and that of two particles were in good agreement with the *** carefully controlled parameters, the reliable function of retaining single particle was realized by pulsed DEP.

关键词： DEP Single particle Interaction force Pulsed DEP

Hot electron assisted photoelectrochemical water splitting from Audecorated ZnO@TiO_(2) nanorods array

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Nano Research 2022年第7期15卷 5824-5830页

作者： Hongdong Li hongyan Liu Fei Wang Guodong Li xiaoli Wang Zhiyong Tang CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyBeijing 100190China Center of materials Science and Optoelectronics Engineering University of Chinese Academy of SciencesBeijing 100049China Key Laboratory of Eco-chemical Engineering College of Chemistry and Molecular EngineeringQingdao University of Science and TechnologyQingdao 266042China Beijing Institute of Aeronautical materials Beijing 100095China

Engineering of semiconductor nanomaterials is critical to enhance the photoelectrochemical(PEC)performance for water ***,semiconductors often show the low light absorption,slow charge transfer,and easy recombination of carriers,thus leading to the low catalytic *** this work,we show facile synthesis of ZnO@TiO_(2) core–shell nanorods(NRs)arrays modified with Au nanoparticles(NPs)as the photoelectrode for PEC water ***,the obtained ZnO@TiO_(2)(15 nm)/Au(8 nm)array shows the maximum photocurrent density of 3.14 ma/cm^(2) at 1.2 V *** hydrogen electrode(RHE),2.6 times and 1.7 times higher than those obtained from ZnO NRs and ZnO@TiO_(2)(15 nm)*** electric-field simulation and transient absorption spectroscopy show that the Au-decorated core–shell nanostructures have an enhanced hot electron generation and prolonged decay time,indicating effective charge transfer and recombination inhibition of *** work provides an efficient preparation strategy for photoelectrodes as well as great potential for the large-scale development of this technology.

关键词： surface plasmon resonance energy transfer transient absorption hot electron water splitting

Response of phytoplankton functional group to spring drought in a large subtropical reservoir

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Journal of Oceanology and Limnology 2024年第5期42卷 1586-1596页

作者： Yue WU Qi YE Siwen chen Kaining chen Shuzhan ma Yiheng CHANG xiaoli SHI State Key Laboratory of Lake Science and Environment Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjing 210008China University of Chinese Academy of Sciences Beijing 100049China State Environmental Protection Key Laboratory of Aquatic Ecosystem Health in the Middle and Lower Reaches of Yangtze River Jiangsu Provincial Academy of Environmental ScienceNanjing 210036China

Global warming has caused an increase in the frequency and duration of droughts *** could trigger large changes in physico-chemical conditions and phytoplankton community in waterbodies,resulting in a shift in the phytoplankton *** diatom blooms in reservoirs have been increasingly observed in the past decade in the Taihu Lake *** aim of the present study is to elucidate the impacts of droughts on aquatic environment and to determine the driving factors for the succession of the phytoplankton functional groups based on the analysis of data collected during spring from 2009 to 2020 in the Daxi *** unimodal relationship between 1-month aggregated precipitation index and phytoplankton species richness indicated the competitive exclusion occurred in extremely drought *** structural equation modeling indicated that drought-related low water level conditions intensified sediment resuspension,and increased the phosphorus-enriched nonalgal turbidity in the Daxi ***,a steady shift in the Reynolds phytoplankton functional groups from L 0,TD,J,X 2,and A(phytoplankton taxa preferring low turbidity and nutrient conditions)to TB(pennate diatoms being adapt to turbid and nutrient-rich conditions)was *** increased TP and non-algal turbidity in addition to the lowered disturbance contribute to the prevalence of Group *** the difficulties in nutrient control,timely water replenishment is often a feasible method of controlling the dominance of harmful algae for reservoir ***,alternative water sources are in high demand for ensuring ecological safety and water availability when dealing with drought.

关键词： drought reservoir sediments resuspension phytoplankton functional group diatom

The impact of the accumulation of algal blooms on reed wetlands in the littoral zones of Chaohu Lake

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Journal of Oceanology and Limnology 2022年第5期40卷 1750-1763页

作者： Shuzhan ma Yue WU Siwen chen Bingfa chen cheng LIU Xiaozhi GU xiaoli SHI Kaining chen State Key Laboratory of Lake Science and Environment Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjing 210008China University of Chinese Academy of Sciences Beijing 100049China Institute of Agricultural Resources and Environmental Sciences Jiangsu Academy of Agricultural SciencesNanjing 210014China Jiangsu Collaborative Innovation Center of Technology and material of Water Treatment Suzhou University of Science and TechnologySuzhou 215009China

In a large eutrophic lake,the littoral zone is normally an area with high-density elevated aquatic plant life,including algal blooms,where the presence of reed wetlands allows the accumulation of *** this study,the impact of accumulated algal blooms in reed wetlands in the littoral zone s of Chaohu Lake was investigated seasonally from 2018 to *** concentrations of chlorophyll a(Chl a),total nitrogen(TN),and total phosphorus(TP)were much higher in the reed-covered littoral zones(RCLZ)than in the unvegetated littoral zones(ULZ),indicating that more algal biomass was trapped and accumulated in the *** biomass could be horizontally transported to downwind littoral zones under low wind speeds,favoring the establishment of *** accumulation levels were highest in summer due to high water temperatures and algal ***,the northern littoral zones were conducive to the development of large algal blooms because of the wind *** values of TN,TP,Chl a,and loss on ignition in surface sediments were higher in the RCLZ than in the ***,the diffusive fluxes of ammonium and soluble reactive pho sphorus were also higher in the RCLZ than in the *** the capability of reed wetlands to trap algae,mechanical salvage and other physical methods should be adopted to eliminate algal biomass when massive blooms accumulate in the RCLZ.

关键词： Chaohu Lake littoral zone reed wetlands algal blooms

Dual-Tone Radio Interferometric Positioning Systems for Multi-Target Localization Using a Single Mobile Anchor

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China Communications 2015年第1期12卷 25-35页

作者： LI Li'an WANG Yiyin ma xiaoli chen Cailian GUAN Xinping Department of Automation Shanghai Jiao Tong Universityand Key Laboratory of System Control and Information ProcessingMinistry of Education of China School of Electrical & Computer Engineering Georgia Institute of Technology

In this paper, a low-cost dualtone radio interferometric positioning system using a single mobile anchor is proposed to locate multiple targets at the same time. We name it mDRIPS. In mDRIPS, each target continuously transmits a dual-tone signal with its dedicated frequencies, and the mobile anchor receives the signals at different positions along its trajectory, Neither time synchronization between the mobile anchor and the targets nor time synchronization among the targets is required. We take the instability of targets clocks into consideration and develop an ESPRIT-type algorithm to estimate frequencies of each dual-tone signal. Furthermore, the time of arrival （TOA） of each target signal is extracted from the phase estimates of the received dual-tone signals. After measuring several TOAs at different locations along the anchor＇s trajectory, each target can be located. Since the frequency difference of the two tones of each dualtone signal is designed to be smaller than the channel coherence bandwidth, the same fading effect on these two tones can be eliminated. Moreover, the integer ambiguity problem due to phase wrapping is investigated, and a localization algorithm to deal with a simplified ambiguity problem is proposed. Numerical results demonstrate the efficiency of the proposed mDRIPS.

关键词： ranging localization mobile anchor radio interferometry oscillator instability

Highly sensitive fluorescent sensing and photocatalytic degradation performance of two-dimensional Tb-organic network

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Journal of Rare Earths 2024年第2期42卷 303-313,I0003页

作者： Ting Gao Zhihu ma Yixia Ren Zhixiang Wang Meili Zhang xiaoli chen Jijiang Wang Laboratory of New Energy and New Function materials Shaanxi Key Laboratory of Chemical Reaction EngineeringCollege of Chemistry and Chemical EngineeringYan'an UniversityYan'an716000China

A novel tetra-nuclear Tb-organic network,named as [Tb_(4)(2-pyia)_(6)(HAc)_(0.5)(2,2'-bipy)(H_(2)O)_(4.5)]·2,2'-bipy·H_(2)O(1),was synthesized hydrothermally based on 5-(pyridin-2-ylmethoxy) isophthalic acid(H_(2)pyia) and 2,2'-bipyridine(2,2'-bipy) ligands,and characterized by single crystal X-ray diffraction,thermogravimetric(TG) analyses,powder X-ray diffraction(PXRD) and infrared(IR) technology.1 possesses a two-dimensional network based on the tetra-nuclear inorganic building units,and the π-πstacking interactions between the pyia^(2-) ligands and the guest 2,2'-bipy molecules play an important role in the forming of 3D supramolecular structure.1 exhibits excellent fluorescent sensing performance for Fe^(3+)(1.26×10^(-8) mol/L),Cr_(2)O_(7)^(2-)(8.1×10^(-7) mol/L),2,4,6-trinitrophenol(TNP)(2.71×10^(-8) mol/L)and tetracycline(TCT)(2.76×10^(-7) mol/L) in aqueous solution with lower detection *** sensing mechanisms of 1 were investigated by density functional theory(DFT) calculations,ultraviolet-visible(UV-Vis) diffuse reflectance spectroscopy,PXRD and fluorescent lifetime *** activated product of 1 was prepared by heating at 255℃ under constant pressure and used to photo-catalytically degrade *** 1 and the activated one have good photocatalytic degradation performance for TCT with degradation rates of 84.29% and 96.07%,*** photocatalytic mechanisms were discovered by UV-Vis diffuse reflectance spectroscopy and radical trap *** Tb-organic framework might be an excellent multifunctional fluorescent sensor and a good photocatalytic agent for TCT degradation in the future.

关键词： Tb-organic network Fluorescent sensing Photocatalytic degradation Rare earths

Comparison of three flocculants for heavy cyanobacterial bloom mitigation and subsequent environmental impact

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Journal of Oceanology and Limnology 2022年第5期40卷 1764-1773页

作者： Kaixuan LIU Lei JIANG Jinsheng YANG Shuzhan ma Kaining chen Yufeng ZHANG xiaoli SHI Department of Environmental Science and Engineering Nanjing Tech UniversityNanjing 211816China State Key Laboratory of Lake Science and Environment Nanjing Institute of Geography and LimnologyChinese Academy of SciencesNanjing 210008China University of Chinese Academy of Sciences Beijing 100049China Jiangsu Collaborative Innovation Center of Regional Modern Agriculture&Environmental Protection Huaiyin Normal UniversityHuaiyin 223001China

Cyanobacteria can accumulate as a heavy biomass on the leeward side of large eutrophic lakes,posing a potential threat to public *** mitigating capacity of three flocculants and their potential impacts on the major environmental features of water and sediments was *** indicate that polyaluminum chloride(PAC)and ferric chloride(FeCl)are efficient flocculants that can rapidly mitigate cyanobacterial blooms with chlorophyll-a concentrations higher tnan 1500 ug/L within 15 *** comparison,cationic starch with chitosan could only treat cyanobacterial blooms in chlorophyll-a concentrations of less than 200μg/*** addition of FeClcaused a decline in the pH value,while dissolved oxygen in the water column dropped to 2 mg/L during cationic starch with chitosan treatment for a high cyanobacterial biomass ***,a combination of flocculants and oxygenators should be considered when treating high-concentration cyanobacterial blooms for emergency ***,the cell lysis of cyanobacteria caused by cationic starch with chitosan can result in an increase in total dissolved phosphorus and total dissolved ***,the high accumlation of nutrients in sediments after the settling of cyanobacteria can cause high internal phosphorus *** increase in the total organic carbon of the sediments can threaten lake restoration achieved by planting submerged macrophytes.

关键词： cyanobacterial bloom emergency control flocculants lake restoration

Identification and Characterization of a Distinct Strain of Beak and Feather Disease Virus in Southeast China

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Virologica Sinica 2020年第1期35卷 43-51页

作者： Yanmei ma Xiaoyong chen Keyuan chen Xiancheng Zeng Shili Yang Wei Chang Yao Tang xiaoli chen Song Wang Ji-Long chen Fujian Agriculture and Forestry University Fuzhou 350002China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of Sciences(CAS)Beijing 100101China Fuzhou Zoo Fuzhou 350012China

Beak and feather disease virus(BFDV) is an infectious agent responsible for feather degeneration and beak deformation in birds. In march 2017, an epidemic of psittacine beak and feather disease(PBFD) struck a farm in Fuzhou in the Fujian Province of southeast China, resulting in the death of 51 parrots. In this study, the disease was diagnosed and the pathogen was identified by PCR and whole genome sequencing. A distinct BFDV strain was identified and named as the FZ *** BFDV strain caused severe disease symptoms and pathological changes characteristic of typical PBFD in parrots, for example, loss of feathers and deformities of the beak and claws, and severe pathological changes in multiple organs of the infected birds. Phylogenetic analysis showed that the FZ strain was more closely related to the strain circulating in New Caledonia than the strains previously reported in China. Nucleotide homology between the FZ strain and other 43 strains of BFDV ranged from 80.0% to 92.0%. Blind passage experiment showed that this strain had limited replication capability in SPF Chicken Embryos and DF-1 Cells. Furthermore, the capsid(Cap) gene of this FZ strain was cloned into the p GEX-4 T-1 expression vector to prepare the polyclonal anti-Cap antibody. Western blotting analysis using the anti-Cap antibody further confirmed that the diseased parrots were infected with BFDV. In this study, a PBFD and its pathogen was identified for the first time in Fujian Province of China, suggesting that future surveillance of BFDV should be performed.

关键词： Beak and feather disease virus(BFDV) Parrot FZ strain Capsid protein(Cap) Phylogenetic analysis