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Genome-Wide Patterns of Codon Usage in the Pacific Oyster Genome

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Journal of Ocean University of China 2021年第5期20卷 1175-1182页

作者： song kai School of Mathematics and Statistics Qingdao UniversityQingdao 266071China

The use of synonymous codons with varying frequencies has been observed in many species,and the magnitude varies among closely related species and genes within the same *** processes or natural selective pressures affect this ***,a systematic investigation of codon usage pattern for molluscan species and its association with the two factors hasn’t been *** this study,the whole genome codon usage patterns in oyster genome is investigated using the relative synonymous codon usage(RSCU)method,and 17 putative optimal codons were identified,wherein most had either a cytosine(C)or guanine(G)residue at the third *** showed that codon bias was positively associated with gene expression levels and *** codons had different mutational bias patterns compared with nonoptimal ***,the results show that codon bias is negatively associated with nucleotide *** the oyster genome,the fourfold degenerate codons are affected by different selective pressures,which can be regarded as an evidence that natural selection shapes codon usage *** research will help to understand how natural selection and mutation bias affect codon usage in Mollusca genomes.

关键词： codon bias synonymous codons gene expression nucleotide diversity Crassostrea gigas

Identification of Non-Coding RNAs Based on Alignment-Free Features in Crassostrea gigas(Pacific Oyster)Transcriptome

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Journal of Ocean University of China 2022年第6期21卷 1633-1640页

作者： CHAI Wenjing song kai School of Mathematics and Statistics Qingdao UniversityQingdao 266071China

Non-coding RNAs(ncRNAs)play important roles in the regulation of many biological processes,such as transcription initiation and epigenetic modifications that occur after transcription and *** novel transcripts have been identified via high-throughput ***,identifying ncRNAs among the transcripts of novel species using alignment-based features is ***,developing a fast and accurate method based on alignment-free features to identify ncRNAs among novel transcripts is *** this study,we proposed a new approach,namely,coding potential prediction based on alignment-free features(CPAF),to identify ncRNAs among a large number of *** used four types of features:Fickett score;Hexamer score;composition,transition,and distribution features;and modified *** the results,CPAF performed better than previous state-of-the-art methods in predicting ncRNA transcripts,with particular reference to small ***,we applied CPAF to identify ncRNAs in Pacific oyster *** approach identified more ncRNAs than other previously used methods.

关键词： Non-coding RNA alignment-free k-mer transcripts

Shared decision-making in the management of patients with inflammatory bowel disease

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World Journal of Gastroenterology 2022年第26期28卷 3092-3100页

作者： kai song Dong Wu Department of Gastroenterology State Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical SciencesPeking Union Medical CollegeBeijing 100730China

The rapid progress of research into inflammatory bowel disease(IBD)has resulted in increasingly more treatment *** options have different advantages and disadvantages,and the preferences of patients may also *** patients can be invited to the formulation of medical decision-making,their compliance and satisfaction would be improved,thus possibly achieving better therapeutic *** present review aims to summarize the current literature on shared decision-making(SDM)in the management of IBD,with the goal of promoting the application of SDM.

关键词： Inflammatory bowel diseases Decision making Shared Therapeutics

Random Forest-Based Fatigue Reliability-Based Design Optimization for Aeroengine Structures

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Computer Modeling in Engineering & Sciences 2024年第7期140卷 665-684页

作者： Xue-Qin Li Lu-kai song School of Energy and Power Engineering Beihang UniversityBeijing100191China Department of Mechanical Engineering The Hong Kong Polytechnic UniversityKowloonHong Kong999077China Research Institute of Aero-Engine Beihang UniversityBeijing100191China

Fatigue reliability-based design optimization of aeroengine structures involves multiple repeated calculations of reliability degree and large-scale calls of implicit high-nonlinearity limit state function,leading to the traditional direct Monte Claro and surrogate methods prone to unacceptable computing efficiency and *** this case,by fusing the random subspace strategy and weight allocation technology into bagging ensemble theory,a random forest(RF)model is presented to enhance the computing efficiency of reliability degree;moreover,by embedding the RF model into multilevel optimization model,an efficient RF-assisted fatigue reliability-based design optimization framework is *** the low-cycle fatigue reliability-based design optimization of aeroengine turbine disc as a case,the effectiveness of the presented framework is *** reliabilitybased design optimization results exhibit that the proposed framework holds high computing accuracy and computing *** current efforts shed a light on the theory/method development of reliability-based design optimization of complex engineering structures.

关键词： Random forest reliability-based design optimization ensemble learning machine learning

A novel Q-based online model updating strategy and its application in statistical process control for rubber mixing

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Chinese Journal of Chemical Engineering 2015年第5期23卷 796-803页

作者： Chunying Zhang Sun Chen Fang Wu kai song School of Chemical Engineering and Technology Tianjin University

To overcome the large time-delay in measuring the hardness of mixed rubber, rheological parameters were used to predict the hardness. A novel Q-based model updating strategy was proposed as a universal platform to track time-varying properties. Using a few selected support samples to update the model, the strategy could dramat- ically save the storage cost and overcome the adverse influence of low signal-to-noise ratio samples. Moreover, it could be applied to any statistical process monitoring system without drastic changes to them, which is practical for industrial practices. As examples, the Q-based strategy was integrated with three popular algorithms （partial least squares （PIE）, recursive PIE （RPLS）, and kernel PIE （KPIE）） to form novel regression ones, QPLS, QRPIE and QKPLS, respectively. The applications for predicting mixed rubber hardness on a large-scale tire plant in east China prove the theoretical considerations.

关键词： Online model updating Rubber mixingQ statistic Hardness Rheological parameters Statistical process control

Theoretical investigations of transport properties of organic solvents in cation-functionalized graphene oxide membranes： Implications for drug delivery

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Nano Research 2018年第1期11卷 254-263页

作者： kai song Yong Long Xun Wang Gang Zhou State Key Laboratory of Chemical Resource Engineering Beijing University of Chemical Technology Beijing 100029 China Key Lab of Organic Optoelectronics and Molecular Engineering Department of Chemistry Tsinghua University Beijing 100084 China

We perform detailed quantum chemical calculations to elucidate the origin and mechanism of the selective permeability of alkali and alkaline earth cation- decorated graphene oxide （M-GO） membranes to organic solvents. The results show that the selectivity is associated mainly with the transport properties of solvents in the membranes, which depends on two regions of the flow path： the sp3 C-O matrix of the GO sheets and the cation at the center of the hexagon rather than the sp~ region. According to the delocalization of ~ states in sp2 regions, we propose a design guide for high-quality M-GO membranes. The solvent-cation interaction essentially causes directional transport of molecules in the M-GO membranes under the transmembrane pressure, indicating a site-to-site mech- anism. The solvent-sp3 C-O matrix interaction may inhibit molecular transport between two fixed cations by consuming energy. The competition between energy consumption by the solvent-cation interaction and energy expenditure by the solvent-sp3 C-O matrix interaction leads to various transport properties of solvents and thus allows for the selective permeability of the M-GO membranes. Findings from the study are helpful for the future design of multifunctional M-GO macro-membranes as cost-effective solution nanofilters in chemical, biological, and medical applications

关键词： alkali and alkaline earthcation-decorated grapheneoxide (M-GO) membrane organic solvent permeability transport density functional theory

Influence of Zn Addition on Microstructures and Martensitic Transformation in CuZr-based Alloys

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Journal of Iron and Steel Research International 2016年第1期23卷 31-36页

作者： kai-kai song Dian-yu WU Feng WAN Xiao-jun BAI Chong-de CAO Department of Physics School of ScienceNorthwestern Polytechnical University School of Mechanical Electrical &Information EngineeringShandong University(Weihai)

Compositional dependences on microstructures and martensitic transformation behaviors in（Cu_（0.5）Zr_（0.5））_（100-x）Zn_x（x=1.5,2.5,4.5,7.0,10.0,and 14.0at.%）alloys were *** was found that CuZr martensites were present in the present *** increasing Zn content,the volume fractions of CuZr martensitic crystals and B2 CuZr phase gradually decrease and increase,*** the addition of high Zn contents（i.e.,7.0,10.0,and 14.0at.%）,the matrix proves to be *** analysis results show that the initial martensitic transformation temperature（M_s）decreases from（412±5）K to（329±5）K as the Zn content increases from 1.5at.% to14.0at.%.The values of Msof Cu-Zr-Zn shape memory alloys are inversely proportional to the number and concentrations of valence electrons（i.e.,e_v/a and c_v）,respectively,implying that the martensitic transformation in CuZrZn alloys could be of electronic nature.

关键词： CuZr-based alloy Zn microstructure phase transition rapid solidification

Microstructural Features and Mechanical Behaviors of Al_(0.5)Cr_(0.8)CoFeNi_(2.5)V_(0.2) High-Entropy Alloys Fabricated by Selective Laser Melting Technique

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Acta Metallurgica Sinica(English Letters) 2022年第10期35卷 1591-1606页

作者： Yao Yan Wei-Dong song Ke-Feng Li Kang Zhao Tong-Tong Sun kai-kai song Jian-Hong Gong Li-Na Hu Shenzhen Research Institute of Shandong University Shenzhen518057China State Key Laboratory of Explosion Science and Technology Beijing Institute of TechnologyBeijing100081China Guangdong Institute of Materials and Processing Guangdong Academy of SciencesGuangdong UniversityGuangzhou510650China School of Mechanical Electrical and Information EngineeringShandong UniversityWeihai264209China Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials(Ministry of Education) Shandong UniversityJinan250061China

In this work,high strength and ductile Al_(0.5)Cr_(0.8)CoFeNi_(2.5)V_(0.2) high-entropy alloys(HEAs)were fabricated by the selective laser melting(SLM)*** orthogonal experiments,it was verified that a wide SLM processing parameter window can be used to produce crack-free samples for the investigated *** the printed HEA samples exhibit good densification higher than 98.3%.It was found that obvious epitaxial growth leads to the formation of the cylindrical and equiaxed ordered face-centered cubic(FCC)crystals,displaying the characteristics of sub-cylindrical and sub-cellular *** low-angle grain boundaries(LAGBs)prefer appearing around subgrain structures,while the high-angle grain boundaries(HAGBs)tend to form around coarse *** HEA samples with high and low apparent densities were selected to observe their mechanical properties,which exhibit Vickers hardness higher than 263 HV and do not fail during *** increasing densification,the strength gradually *** to the engineering stress–strain curves during compression,the yield strength is higher than 530 MPa,while the strength near 40%engineering strain is larger than 1840 *** deformation,a large density of dislocations becomes popular within subgrain structures together with the pre-existing dislocations from rapid solidification,leading to the formation of planar and cross slip *** coarse cylindrical crystals,some deformation twins are also induced together with the appearance of a distinct copper-type texture during *** a result,the as-printed samples display better mechanical properties than the as-cast *** present studies provide a very good HEA candidate for the SLM process,but more work should be conducted to achieve excellent comprehensive properties.

关键词： High-entropy alloys Selective laser melting Mechanical properties Microstructures

Linear and Nonlinear Spectra in Photosynthetic Light Harvesting Complexes: Benchmark Tests of Modified Redfield Method

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Chinese Journal of Chemical Physics 2015年第4期28卷 -页

作者： Yuan-yuan Jing kai song Shu-ming Bai Qiang Shi Beijing National Laboratory for Molecular Sciences State Key Laboratory for Structural Chemistry of Unstable and Stable Species Institute of Chemistry Chinese Academy of Sciences Beijing 100190China

We employ the numerically exact hierarchical equations of motion (HEOM) method to perform benchmark tests for the popular modified Redfield method in calculating linear and nonlinear spectroscopic signals of molecular aggregates in photosynthetic light harvesting complexes. It is currently well known that the perturbative and Markovian approximations involved in the modified Redfield equation may give inappropriate description of the excitation energy transfer processes in the intermediate coupling regime. An interesting topic is thus to test the validity of the modified Redfield method in calculating various types of spectroscopic signals. By using model dimers with different sets of parameters and a model of the Fenna-Matthews-Olson complex, we calculate and compare the absorption, emission, and 2D spectra using the modified Redfield and HEOM methods. It is found that results from the modified Redfield method agree well with the HEOM ones in a wide range of parameter regimes. The comparison also helps to understand the quantum beating signals in the 2D spectra of the photosynthetic light harvesting complexes.

关键词： Linear spectra Nonlinear spectra Light harvesting complexes Modified Redfield method