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Chasing Sequencing Perfection:Marching Toward Higher Accuracy and Lower Costs

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 1-12页

作者： Hangxing Jia Shengjun Tan Yong e.zhang CAS Key Laboratory of Zoological Systematics and evolution&State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China CAS Center for excellence in Animal evolution and Genetics Chinese Academy of SciencesKunming 650223China

Next-generation sequencing(NGS),represented by Illumina platforms,has been an essential cornerstone of basic and applied ***,the sequencing error rate of 1 per 1000 bp(10^(−3))represents a serious hurdle for research areas focusing on rare mutations,such as somatic mosaicism or microbe *** examining the high-fidelity sequencing methods developed in the past decade,we summarized three major factors underlying errors and the corresponding 12 strategies mitigating these *** then proposed a novel framework to classify 11 preexisting representative methods according to the corresponding combinatory strategies and identified three trends that emerged during methodological *** further extended this analysis to eight long-read sequencing methods,emphasizing error reduction ***,we suggest two promising future directions that could achieve comparable or even higher accuracy with lower costs in both NGS and long-read sequencing.

关键词： Sequencing error High-fidelity sequencing Consensus sequencing Single-molecule sequencing Rare mutation

Classification of knowledge graph completeness measurement techniques

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Journal of Systems engineering and electronics 2024年第1期35卷 154-162页

作者： zhang ying XIAO Gang Institute of Systems engineering Academy of Military SciencesBeijing 100107China

At present,although knowledge graphs have been widely used in various fields such as recommendation systems,question and answer systems,and intelligent search,there are always quality problems such as knowledge omissions and *** assessment and control,as an important means to ensure the quality of knowledge,can make the applications based on knowledge graphs more complete and more accurate by reasonably assessing the knowledge graphs and fixing and improving the quality problems at the same ***,as an indispensable part of the knowledge graph construction process,the results of quality assessment and control determine the usefulness of the knowledge *** them,the assessment and enhancement of completeness,as an important part of the assessment and control phase,determine whether the knowledge graph can fully reflect objective phenomena and reveal potential connections among *** this paper,we review specific techniques of completeness assessment and classify completeness assessment techniques in terms of closed world assumptions,open world assumptions,and partial completeness *** purpose of this paper is to further promote the development of knowledge graph quality control and to lay the foundation for subsequent research on the completeness assessment of knowledge graphs by reviewing and classifying completeness assessment techniques.

关键词： quality assessment completeness assessment closed world assumptions open world assumption partial completeness assumption

Deep Guided Attention Network for Joint Denoising and Demosaicing in Real Image

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Chinese Journal of electronics 2024年第1期33卷 303-312页

作者： Tao zhang ying FU Jun zhang School of Computer Science and Technology Beijing Institute of Technology Advanced Reasearch Institute of Multidisciplinary Science Beijing Institute of Technology

Denoising(DN) and demosaicing(DM) are the first crucial stages in the image signal processing pipeline. Recently, researches pay more attention to solve DN and DM in a joint manner, which is an extremely undetermined inverse problem. existing deep learning methods learn the desired prior on synthetic dataset, which limits the generalization of learned network to the real world data. Moreover, existing methods mainly focus on the raw data property of high green information sampling rate for DM, but occasionally exploit the high intensity and signalto-noise(SNR) of green channel. In this work, a deep guided attention network(DGAN) is presented for real image joint DN and DM(JDD), which considers both high SNR and high sampling rate of green information for DN and DM, respectively. To ease the training and fully exploit the data property of green channel, we first train DN and DM sub-networks sequentially and then learn them jointly, which can alleviate the error accumulation. Besides, in order to support the real image JDD, we collect paired raw clean RGB and noisy mosaic images to conduct a realistic dataset. The experimental results on real JDD dataset show the presented approach performs better than the state-of-the-art methods, in terms of both quantitative metrics and qualitative visualization.

关键词： Training Visualization Inverse problems Green products Noise reduction Pipelines Signal processing

An effective nonlinear dynamic formulation to analyze grasping capability of soft pneumatic robotic gripper

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International Journal of Smart and Nano Materials 2024年第3期15卷 405-431页

作者： Qiping Xu Chenhang ying Kehang zhang Huiyu Xie Shiju e Department of Robotics engineering Key Laboratory of Urban Rail Transit Intelligent Operation and Maintenance Technology&Equipment of Zhejiang ProvinceCollege of EngineeringZhejiang Normal UniversityJinhuaP.R.China

Soft pneumatic robotic grippers have found extensive applica-tions across various engineering domains,which prompts active research due to their splendid compliance,high flex-ibility,and safe human-robot interaction over conventional stiff *** simplified rod-based models prin-cipally focused on clarifying overall large deformation and bending postures of soft grippers from static or quasi-static perspectives,whereas it is challenging to elaborate grasping characteristics of soft grippers without considering contact interaction and nonlinear large deformation *** address this,based on absolute nodal coordinate formulation(ANCF),comprehensively allowing for structural complexity,geometric,material and boundary nonlinearities,and incorpor-ating Coulomb’friction law with a multiple-point contact method,we put forward an effective nonlinear dynamic mod-eling approach for exploring grasping capability of soft ***,we solved the established dynamic equations using Generalized-αscheme,and conducted thorough numer-ical simulation analysis on a three-jaw soft pneumatic gripper(SPG)in terms of grasping configurations,displacements and contact *** proposed dynamic approach can accurately both describe complicated deformed configurations along with stress distribution and provide a feasible solution to simulate grasping targets,whose effectiveness and precision were analyzed theoretically and verified experimentally,which may shed new light on devising and optimizing other multi-functional SPGs.

关键词： Nonlinear dynamic formulation soft pneumatic robotic grippers contact interaction grasping capability configuration variations

Microstructure evolution and strengthening mechanism of high -performance powder metallurgy TA15 titanium alloy by hot rolling

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International Journal of Minerals,Metallurgy and Materials 2024年第6期31卷 1426-1436页

作者： ying Gao Ce.zhang Jiazhen zhang Xin Lu Beijing Advanced Innovation Center for Materials Genome engineering State Key Laboratory for Advanced Metals and MaterialsInstitute for Advanced Ma-terials and TechnologyUniversity of Science and Technology BeijingBeijing 100083China National engineering Research Center for Advanced Rolling Technology National Engineering Research Center for Flat Rolling EquipmentInstitute of Engin-eering TechnologyUniversity of Science and Technology BeijingBeijing 100083China

Hot deformation of sintered billets by powder metallurgy(PM)is an effective preparation technique for titanium alloys,which is more significant for high-alloying *** this study,Ti–6.5Al–2Zr–Mo–V(TA15)titanium alloy plates were prepared by cold press-ing sintering combined with high-temperature hot *** microstructure and mechanical properties under different process paramet-ers were *** microscope,electron backscatter diffraction,and others were applied to characterize the microstructure evolution and mechanical properties strengthening *** results showed that the chemical compositions were uniformly dif-fused without segregation during sintering,and the closing of the matrix craters was accelerated by increasing the sintering *** block was hot rolled at 1200℃ with an 80%reduction under only two passes without *** strength and elongation of the plate at 20–25℃ after solution and aging were 1247 MPa and 14.0%,respectively,which were increased by 24.5%and 40.0%,respect-ively,compared with the as-sintered alloy at 1300℃.The microstructure was significantly refined by continuous dynamic recrystalliza-tion,which was completed by the rotation and dislocation absorption of the substructure surrounded by low-angle grain *** hot rolling combined with heat treatment,the strength and plasticity of PM-TA15 were significantly improved,which resulted from the dense,uniform,and fine recrystallization structure and the synergistic effect of multiple slip systems.

关键词： elemental powder powder metallurgy titanium alloy hot rolling strength and plasticity

Identification of human microRNA-disease association via low-rank approximation-based link propagation and multiple kernel learning

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Frontiers of Computer Science 2024年第2期18卷 217-229页

作者： Yizheng WANG Xin zhang ying JU Qing LIU Quan ZOU Yazhou zhang Yijie DING ying zhang Institute of Fundamental and Frontier Sciences University of Electronic Science and Technology of ChinaChengdu 610054China Yangtze Delta Region Institute(Quzhou) University of Electronic Science and Technology of ChinaQuzhou 324000China Beidahuang Industry Group General Hospital Harbin 150088China School of Informatics Xiamen UniversityXiamen 361005China Department of Anesthesiology Hospital(T.C.M)Affiliated to Southwest Medical UniversityLuzhou 646000China Software engineering College Zhengzhou University of Light IndustryZhengzhou 450002China

Numerous studies have demonstrated that human microRNAs(miRNAs)and diseases are associated and studies on the microRNA-disease association(MDA)have been *** developed a model using a low-rank approximation-based link propagation algorithm with Hilbert–Schmidt independence criterion-based multiple kernel learning(HSIC-MKL)to solve the problem of the large time commitment and cost of traditional biological experiments involving miRNAs and diseases,and improve the model *** constructed three kernels in miRNA and disease space and conducted kernel fusion using *** propagation uses matrix factorization and matrix approximation to effectively reduce computation and time *** results of the experiment show that the approach we proposed has a good effect,and,in some respects,exceeds what existing models can do.

关键词： human miRNA-disease association multiple kernel learning link propagation miRNA similarity disease similarity

Microscale spherical TiO_(2)powder prepared by hydrolysis of TiCl_(4)solution:Synthesis and kinetics

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Particuology 2024年第1期84卷 60-71页

作者： Peiyi Yan ying zhang Shili Zheng School of Rare earths University of Science and Technology of ChinaHefei230026China Ganjiang Innovation Academy Chinese Academy of SciencesGanzhou341119China Key Laboratory of Green Process and engineering National Engineering Research Center of Green Recycling for Strategic Metal ResourcesInstitute of Process EngineeringChinese Academy of SciencesBeijing100190China State Key Laboratory of Vanadium and Titanium Resources Comprehensive Utilization Panzhihua617000China

Hydrolysis of TiCl_(4)solution is capable of preparing microscale TiO_(2)*** research studied the synthesis of microscale spherical TiO_(2)powders and the hydrolysis *** effects of the flow field generated by different agitators and baffles in the crystallizer,the initial free acid concentration,the initial equivalent TiO_(2)concentration,and the temperature on the hydrolysis progress and powder morphology were systematically *** results show that the flow field in a crystallizer can significantly affect the morphology and particle size of the powders,and the axial flow can improve the sphericity of the *** increased free HCl and equivalent TiO_(2)concentrations in the pregnant solution inhibit the forward hydrolysis reaction,prolong the time to reach equilibrium,and reduce the *** appropriate temperature matching the compositions of the pregnant solution is crucial for the powder morphology and *** with sizes ranging from around 5 um-40μm can be tuned under controlled flow field,solution compositions,and temperature *** addition,the Cheng and Wunderlich modified Avrami equation was used for the crystallization kinetic *** effects of the free HCl concentration,equivalent TiO_(2)concentration,and hydrolysis temperature are reflected in the reaction rate constant and active nuclei reduction *** the free HCl and equivalent TiO_(2)concentrations will reduce the reaction rate constant and accelerate the deactivation of the active nuclei,thus increasing the final powder size,while increasing the temperature will lead to the opposite results.

关键词： TiCl_(4) Hydrolysis Microscale TiO_(2) Spherical Kinetics

Gene therapy for monogenic disorders: challenges, strategies, and perspectives

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Journal of Genetics and Genomics 2024年第2期51卷 133-143页

作者： Yi zhang Zhi-ying Wu Department of Medical Genetics and Center for Rare Diseases Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang 310009China Department of Neurology Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang 310009China Key Laboratory of Medical Neurobiology of Zhejiang Province HangzhouZhejiang 310009China

Monogenic disorders refer to a group of human diseases caused by mutations in single genes. While disease-modifying therapies have offered some relief from symptoms and delayed progression for some monogenic diseases, most of these diseases still lack effective treatments. In recent decades, gene therapy has emerged as a promising therapeutic strategy for genetic disorders. Researchers have developed various gene manipulation tools and gene delivery systems to treat monogenic diseases. Despite this progress, concerns about inefficient delivery, persistent expression, immunogenicity, toxicity, capacity limitation, genomic integration, and limited tissue specificity still need to be addressed. This review gives an overview of commonly used gene therapy and delivery tools, along with the challenges they face and potential strategies to counter them.

关键词： Gene therapy Monogenic diseases Geneediting Genedelivery Challenges

Feeding prehistoric coastal community:A study of marine faunal remains at the Jingtoushan site

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Science China earth Sciences 2024年第5期67卷 1574-1590页

作者： endong WU Guoping SUN ying zhang School of Culture History and LanguageAustralian National UniversityCanberra 2600Australia Zhejiang Provincial Institute of Cultural Relics and Archaeology Hangzhou 310012China National Centre for Archaeology Beijing 100013China

This article examines the abundant marine mollusc,and fish remains at the Jingtoushan shell midden(8,300 to7,800 cal a BP)in Zhejiang Province,China,to investigate the fishing economy,community development,the palaeoenvironment,and their interactions among the prehistoric populations in the lower Yangtze River Basin and southeastern coastal *** also attempts to explore the prosperity and decline of coastal settlements in China during the Neolithic Age and the potential reasons for their rise and fall,*** on the ecological and biological principles of marine animals,standard zooarchaeological methods and radiocarbon dating analysis are used for sampling,identification,measurement,and *** show that at least 11 mollusc taxa and 14 fish taxa can be identified from the Jingtoushan faunal *** ancient Jingtoushan residents possibly lived in a settlement close to the coast and engaged in inshore and offshore fishing,hunting,and gathering as their primary subsistence strategies,with low-level rice cultivation as a supplementary means of ***,the changes in the coastal environment could be one of the reasons why the Jingtoushan residents abandoned their *** research contributes to Chinese Neolithic archaeology with new evidence of the exploitation of marine resources around 8000 a BP in the eastern coastal areas and the relationship between Neolithic community development and environmental changes.

关键词： Neolithic Age Marine faunal remains Fishing economy Palaeoenvironment Community development