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Framework to Identify Protein Complexes Based on Similarity Preclustering

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Tsinghua Science and Technology 2017年第1期22卷 42-51页

作者： Xiaoqing Peng xiaodong yan Jianxin Wang the School of Information Science and Engineering Central South UniversityChangsha 410083China

Proteins interact with each other to form protein complexes, and cell functionality depends on both protein interactions and these complexes. Based on the assumption that protein complexes are highly connected and correspond to the dense regions in Protein-protein Interaction Networks（PINs）, many methods have been proposed to identify the dense regions in PINs. Because protein complexes may be formed by proteins with similar properties,such as topological and functional properties, in this paper, we propose a protein complex identification framework（KCluster）. In KCluster, a PIN is divided into K subnetworks using a K-means algorithm, and each subnetwork comprises proteins of similar degrees. We adopt a strategy based on the expected number of common neighbors to detect the protein complexes in each subnetwork. Moreover, we identify the protein complexes spanning two subnetworks by combining closely linked protein complexes from different subnetworks. Finally, we refine the predicted protein complexes using protein subcellular localization information. We apply KCluster and nine existing methods to identify protein complexes from a highly reliable yeast PIN. The results show that KCluster achieves higher Sn and Sp values and f-measures than other nine methods. Furthermore, the number of perfect matches predicted by KCluster is significantly higher than that of other nine methods.

关键词： protein complex similarity preclustering protein-protein interaction networks K-means

Emerging low-dimensional materials for mid-infrared detection

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Nano Research 2021年第6期14卷 1863-1877页

作者： Jiangbin Wu Nan Wang xiaodong yan Han Wang Ming Hsieh Department of Electrical and Computer Engineering University of Southern CaliforniaLos AngelesCA90089USA Mork Family Department of Chemical Engineering and Material Science University of Southern CaliforniaLos AngelesCA90089USA

Mid-infrared(IR)detectors based on the emerging low-dimensional(two-dimensional and quasi one-dimensional)materials offer unique characteristics including large bandgap tunability,optical polarization sensitivity and integrability with typical silicon process,which are not available in the mid-IR detectors based on traditional compound ***,we review the recent progress in study of mid-IR detectors based on the low-dimensional materials,including black phosphorus,black arsenic phosphorus,tellurene and BaTiS3,from the perspectives of crystal structure,material synthesis,optical properties,and the detector *** detector gain and detectivity are benchmarked,and the unique properties,such as the polarization sensitivity,are *** also provide our perspective about key future research directions in this field.

关键词： mid-infrared detector anisotropy low-dimensional gain detectivity

Simulating Net Carbon Budget of Forest Ecosystems and Its Response to Climate Change in Northeastern China Using Improved FORCCHN

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Chinese Geographical Science 2012年第1期22卷 29-41页

作者： ZHAO Junfang yan xiaodong JIA Gensuo Chinese Academy of Meteorological Sciences Beijing 100081 China Beijing Normal University Beijing 100875 China Institute of Atmospheric Physics Chinese Academy of Sciences Beijing 100029 China

As dominant biomes,forests play an important and indispensable role in adjusting the global carbon balance under climate ***,there are scientific and political implications in investigating the carbon budget of forest ecosystems and its response to climate *** we synthesized the most recent research progresses on the carbon cycle in terrestrial ecosystems,and applied an individual-based forest ecosystem carbon budget model for China(FORCCHN) to simulate the dynamics of the carbon fluxes of forest ecosystems in the northeastern *** FORCCHN model was further improved and applied through adding variables and modules of precipitation(rainfall and snowfall) interception by tree crown,understory plants and *** results showed that the optimized FORCCHN model had a good performance in simulating the carbon budget of forest ecosystems in the northeastern *** 1981 to 2002,the forests played a positive role in absorbing carbon ***,the capability of forest carbon sequestration had been gradually declining during the the same *** for the average spatial distri-bution of net carbon budget,a majority of the regions were carbon *** scattered areas in the Heilongjiang Province and the Liaoning Province were identified as carbon *** net carbon budget was apparently more sensitive to an increase of air temperature than change of precipitation.

关键词： net carbon budget climate change northeastern China improved FORCCHN

Generalized spatial representation for digital modulation and its potential application

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Science China Earth Sciences 2016年第12期59卷 47-58页

作者： Hao HUAN Pengfei SHI xiaodong yan Ran TAO School of Information and Electronics Beijing Institute of TechnologyBeijing 100081China Key Lab for Spacecraft TT&C and Communication under the Ministry of Education Chongqing 400044China

Constellation mapping has provided a great convenience to measure the performance of digital signal modulation in Euclid space. However, traditional in-phase and quadrature(IQ) plane is difficult to express the frequency modulation scheme such as minimum shift keying(MSK) and the time domain modulation such as cyclic code shift keying(CCSK). How to represent the digital signal modulation visually through constellation mapping is an attractive problem. To address this issue, in this paper, the combined frequency and phase modulation are utilized to define a new kind of constellation mapping, where the phase and frequency are quantized to the same elements. The uniform geometric construction for combined phase and frequency modulation is redefined in the 3D cylindrical coordinate system based on frequency(f), in-phase component(I) and quadrature component(Q). In the new coordinates, the quadrature frequency-phase shift keying(QFPSK) is produced by the QPSK with dimensional rotation matrix and denoted by the reduced dual quaternion. Furthermore, the spatial extension from QFPSK to chirp cyclic shift keying(Chirp CSK) is analyzed with bandwidth efficiency and energy efficiency. At last, the QFPSK is combined with the 2D OFDM, yielding the image OFDM *** results verify the effectiveness of QFPSK in the proposed system with the time-varying wireless channel and frequency selective fading channel respectively.

关键词： quadrature frequency-phase shift keying (QFPSK) chirp cyclic shift keying spatial constellation mapping image OFDM system wireless communication

Non-equilibrium and stochasticity influence the activation process of the yeast DNA damage pathway

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Science China(Physics,Mechanics & Astronomy) 2018年第2期61卷 76-79页

作者： ChenZi Jin xiaodong yan FangTing Li School of Physics Center for Quantitative Biology Peking University

Living cells are open systems that exist far away from a state of thermodynamical equilibrium. They utilize the high-grade chemical energy provided by food to produce ATP and re- lease ADP and Pi together with heat dissipation. Living cells exist in a non-equilibrium steady state （NESS）, they replicate themselves and respond to various environmental changes via signal transduction pathways. Because the majority of cells exist at room temperature, the stochasticity of chemical reac- tions in the cells is unavoidable. Recent research into fluores- cent proteins and microscopy techniques have enabled us to observe the dynamic process of mRNA and proteins in single living bacterial cells [1], and these have resulted in new in- sights into regulation mechanisms in molecular biology, i.e., in cellular signal transduction pathways.

关键词： Non-equilibrium stochasticity influence DNA damage pathway

Testing the ability of RIEMS2.0 to simulate multi-year precipitation and air temperature in China

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Chinese Science Bulletin 2009年第17期54卷 3101-3111页

作者： ZHAO DeMing FU CongBin yan xiaodong Key Laboratory of Regional Climate-Environment for Temperate East Asia Institute of Atmospheric Physics Chinese Academy ofSciences Beijing 100029 China

RIEMS2.0 (Regional Integrated Environment Modeling System, Version 2.0) is now being developed starting from RIEMS1.0 by the Key Laboratory of Regional Climate Environment Research for Temperate East Asia, Institute of Atmospheric Physics, Chinese Academy of Sciences, China. In order to test RIEMS2.0’s ability to simulate long-term climate and its changes, as well as provide a basis for further development and applications, we compare simulated precipitation and air temperature from 1980 to 2007 (simulation duration from Jan. 1, 1979 to Dec. 31, 2007) under different cumulus parameterization schemes with the observed data. The results show that RIEMS2.0 can reproduce the spatial distribution of precipitation and air temperature, but that the model overestimates precipitation with the rainfall center moving northwestward and underestimates air temperature for annual simulations. Annual and interannual variations in precipitation and air temperature for different climate subregions are well captured by the model. Further analysis of summer and winter simulations shows that precipitation is overestimated, except for the Jianghuai-Jiangnan subregions in the winter, and the air temperature bias in the summer is weaker than in the winter. There are larger biases for precipitation and air temperature in semiarid subregions. Anomalies in precipitation and air temperature are also well captured by the model. Although a similar distribution can be found between observed data and simulated results under different cumulus parameterization schemes, these show differences in intensity and location. In sum, RIEMS2.0 shows good stability and does well in simulating the long-term climate and its changes in China.

关键词：空气温度年降水量中国模拟能力检验

Simulation of the climatic effects of natural forcings during the pre-industrial era

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Chinese Science Bulletin 2007年第11期52卷 1545-1558页

作者： YIN ChongHua yan xiaodong SHI ZhengGuo WANG ZhaoMin Key Laboratory of Climate-Environment for Temperate East Asia Institute of Atmospheric Physics Chinese Academy of Sciences Beijing 100029 China British Antarctic Survey High Cross Madingling Road Cambridge CB3 0ET UK Graduate University of Chinese Academy of Sciences Beijing 100049 China

The MPM-2,an Earth system model of intermediate complexity,is employed to study the climate sys-tem response to natural forcings during the pre-industrial era (1000-1800 AD),with a special focus on the surface air temperature (SAT) evolution. Solar radiation and volcanism are the primary natural forcings during this period. In the MPM-2,the solar radiation forcing determines the long-term trend of the climate system change,and the volcanic forcing intensifies (weakens) this trend. Ultimately,the combination of solar and volcanic forcings dominates the long-term changes of the climate system. These results are in good agreement with other model data or temperature reconstructions. Natural forcings can well explain the Little Ice Age (LIA) and the Medieval Warm Period (MWP). At the large regional scale,the SAT response to natural forcings is almost coincident with that of the Northern Hemisphere. Based on MPM-2 model results,it is concluded that the global climate gradually became cold during the pre-industrial era. However,MPM-2 model results substantially correlate with recon-structed solar and volcanic forcings. Namely,to some great extent,these results strongly rely on the forcing series data we choose. Therefore,in order to accurately simulate the secular variation of the historical climate,it is very important to reconstruct well the solar radiation change and volcanic forc-ing data are well reconstructed for the past 10000 years,at least for the past 2000 years,in addition to the model improvements. The sensitivity study on the abrupt solar radiation change indicates that the increased solar radiation not only strengthens the nonlinear response of SAT,but intensifies the global hydrological cycle. At the same time,the biosphere is also affected obviously.

关键词：冰河时代火山作用仿真模拟日光气候因素前工业时代

Effects of historical land cover changes on climate

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Chinese Science Bulletin 2007年第18期52卷 2575-2583页

作者： SHI ZhengGuo yan xiaodong YIN ChongHua WANG ZhaoMin Key Laboratory of Regional Climate-Environment Research for Temperate East Asia Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China British Antarctic Survey Cambridge CB30ET UK

In order to explore the influence of anthropogenic land use on the climate system during the last mil- lennium, a set of experiments is performed with an Earth system model of intermediate complexity—— the McGill Paleoclimate Model (MPM-2). The present paper mainly focuses on biogeophysical effects of historical land cover changes. A dynamic scenario of deforestation is described based on changes in cropland fraction (RF99). The model simulates a decrease in global mean annual temperature in the range of 0.09-0.16℃, especially 0.14-0.22℃ in Northern Hemisphere during the last 300 years. The responses of climate system to GHGs concentration changes are also calculated for comparisons. Now, afforestation is becoming an important choice for the enhancement of terrestrial carbon sequestration and adjustment of regional climate. The results indicate that biogeophysical effects of land cover changes cannot be neglected in the assessments of climate change.

关键词：气候变化陆地覆盖森林开伐气候-生物圈相互作用

Microstructure evolution of Al-Zn-Mg-Cu-Zr alloy during hot deformation

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Rare Metals 2010年第4期29卷 426-432页

作者： yan Liangming,SHEN Jian,LI Zhoubing,LI Junpeng,and yan xiaodong General Research Institute for Nonferrous Metals,Beijing 100088,China General Research Institute for Nonferrous Metals Beijing China

Compression tests of the Al-Zn-Mg-Cu-Zr（7055） alloy were performed at various strains and temperatures from 300 to 450℃ under a con- stant strain rate between 10^-2 s^-1and 1 s^-1. Microstructures during hot deformation were studied by transmission electron microscopy （TEM）. Dislocation density, dislocation cells and subgrains of the deformed samples were investigated in detail and compared to make a better understanding of the microstructure evolution. The results showed that stress-strain curves under the experimental conditions belonged to the type of dynamic recovery. When the alloy deformed at various strains and 300℃, the microstructure underwent a process of disordered dislocations to cell structure, subgrain structure and subgrain coarsening. With the temperature increasing, subgrains grew and dislocation density in the interior decreased at a strain rate of 1 s^-1. At the temperature of 350℃, the average diameter of subgrains decreased, sub-boundaries broadened and dislocation density in the interior decreased when the strain rate was increased. The deformed samples of 7055 alloy had smaller subgrains than that of 7005 alloy at the same compression condition because of high alloy content.

关键词： aluminum alloy microstructure evolution dynamic recovery subgrain