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Genomes of major fishes in world fisheries and aquaculture: Status, application and perspective

Aquaculture and Fisheries 2020年第4期5卷 163-173页

作者： Guoqing Lu Mingkun luo Department of Biology University of Nebraska at OmahaOmaha68182USA Wuxi Fisheries College Nanjing Agricultural UniversityJiangsuWuxi214081China

Capture fisheries and aquaculture provide a significant amount of high-quality protein to human beings and thus play an essential role in ending global hunger and malnutrition.The availability of tens of hundreds of fish genomes and the advances of genomics have allowed addressing many challenging issues such as overfishing and germplasm degradation faced by fisheries and aquaculture.In this review,we describe the current status of genomics in fisheries and aquaculture,with an emphasis on 14 species of fish that are considerably important to global fisheries and aquaculture,in the context of genome sequencing and assembly,annotation,GC contents,and repeats.The majority of these genomes are assembled at the chromosome level and annotated with proteins and pathways,with functional relevance to fisheries and aquaculture,such as environmental adaptation and phenotypic variation.We summarize potential genomic applications in fisheries and aquaculture that are related to assessment and use of genetic resources,disease resistance,growth and development,sexual determination,and fisheries management.Although much progress has been achieved in genomic application to fisheries and aquaculture,the full potential remains to be explored and reaped.We discuss the challenges and perspectives of genomics in translational aquaculture and fisheries,which include genome assembly and annotation,genomic selection and breeding,genomics in fisheries management,and integrated artificial intelligence systems.In the coming decades,we anticipate the applications of genomic techniques such as genome editing and genomic selection,along with the use of emerging intelligence systems,in aquaculture and fisheries will contribute significantly to genetic improvements of farmed fish and sustainable exploitation of fishery resources,which consequently lead to eradicating global poverty by 2030,an ambitious goal set by the United Nations.

关键词： Fish genomics World aquaculture Fisheries management Genomic selection Intelligent system

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CRISPR-Cas9 sgRNA design and outcome assessment: Bioinformatics tools and aquaculture applications

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Aquaculture and Fisheries 2022年第2期7卷 121-130页

作者： Mingkun luo Jun Wang Zaijie Dong Chenghui Wang Guoqing Lu Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization Freshwater Fisheries Research Centre of Chinese Academy of Fishery SciencesMinistry of Agriculture and Rural AffairsWuxi214081China Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of AquacultureShanghai Ocean UniversityShanghai201306China Department of Biology University of Nebraska at OmahaOmahaNE68182USA

The CRISPR-Cas9 genome editing has many advantages over its counterparts and could ultimately assist in disease control and molecular breeding in aquaculture.Single-guide RNA(sgRNA)design is presumably the most crucial task in a typical CRISPR-Cas9 experiment;an understanding of algorithms behind sgRNA design programs is thus essential for improved efficacy and specificity.We focus this review on the bioinformatics aspects in genome editing experiments and describe commonly used computational approaches and tools of sgRNA design and outcome assessment.We show an example of sgRNA design with optimal parameter settings and appropriate interpretation of results and present a brief overview of CRISPR-Cas9 applications,such as genetic improvement and sustainability in aquaculture.We discuss challenging issues,particularly in the context of computational biology,in the use of computational tools in CRISPR-based genome editing.This review provides a synthesis of bioinformatics tools used for CRISPR-Cas9 sgRNA design and outcome assessment and offers a general view of CRISPR-based applications in farmed fish,which are expected to facilitate genome editing programs and hence improve aquaculture breeding,production,and sustainability.

关键词： CRISPR-Cas9 Genome editing sgRNA design Outcome assessment Bioinformatics tools Aquaculture applications

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Deep Hashing Based on VAE-GAN for Efficient Similarity Retrieval

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Chinese Journal of Electronics 2019年第6期28卷 1191-1197页

作者： JIN guoqing ZHANG Yongdong lu Ke Institute of Computing Technology Chinese Academy of Sciences University of Chinese Academy of Sciences

Inspired by the recent advances in generative networks, we propose a VAE-GAN based hashing framework for fast image retrieval. The method combines a Variational autoencoder(VAE) with a Generative adversarial network(GAN) to generate content preserving images for pairwise hashing learning. By accepting real image and systhesized image in a pairwise form, a semantic perserving feature mapping model is learned under a adversarial generative process. Each image feature vector in the pairwise is converted to a hash codes, which are used in a pairwise ranking loss that aims to preserve relative similarities on images. Extensive experiments on several benchmark datasets demonstrate that the proposed method shows substantial improvement over the state-of-the-art hashing methods.

关键词： Image retrieval Learning to hash Variational autoencoder(VAE) Generative adversarial network(GAN)

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Angle of repose in the numerical modeling of ballast particles focusing on particle-dependent specifications:Parametric study

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Particuology 2022年第6期20卷 39-50页

作者： Peyman Aela lu Zong Morteza Esmaeili Mohammad Siahkouhi guoqing Jing School of Civil Engineering Beijing Jiaotong UniversityBeijing 100044China School of Railway Engineering Iran University of Science and TechnologyTehran 16846-13114Iran

The discrete element method(DEM)is widely used in the realistic simulation of the shapes of particles.Researchers have considered the simplification of particle shapes owing to the high computational cost of such simulation.In this regard,the modeling of calibrated particles is a major challenge owing to the simultaneous effects of particle properties.The angle-of-repose test is a standard test method used to calibrate the bulk behavior of simulated particles.In the present study,the hollow-cylinder(slump)test was modeled for the verification of discrete element simulations.In this regard,a sensitivity analysis was conducted for all effective parameters,namely the static friction,rolling friction,restitution coefficient,sphericity,roundness,particle size distribution,and number of ballast particles.The results indicate that the rolling friction,roundness,number of particles,and size of particles are the most important parameters in the determination of the angle of repose(AOR).For particles in the range of ballast(20-60 mm),the effect of the number of particles on the angle of repose is reduced when the number is greater than 426.Additionally,it is concluded that angular particles can be replaced with sub-angular particles(R≈0.2-0.45)with a higher rolling friction coefficient(μ_(r)>0.14).

关键词： Ballast Angle of repose Calibration Hollow cylinder test Friction coefficients Shape factors

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Intra-Organizational Social Media and Employee Idea Generation:Analysis based on the Spanning-Relevance Framework

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Journal of Systems Science and Systems Engineering 2022年第6期31卷 649-676页

作者： Benjiang lu Xunhua Gu Nianlong luo Xueli Wang guoqing Chen School of Business Nanjing UniversityNanjing 210093China School of Economics and Management Tsinghua UniversityBeijing 10084China Information Technology Center Tsinghua University Beijing 100084China China Retail Research Center School of Economics and ManagementTsinghua UniversityBeijing 100084China

Intra-organizational social media platforms are expected to help build a flexible corporate stage that facilitates employees'communication and leverages creative idea generation.However,whether and how these systems can expedite the creativity of employees remains unclear.This paper attempts to address the impacts of employees'social relationships on intra-organizational social media on their idea generation quantity and quality.Drawn upon the extant literature in the fields of information systems and organizational behavior,a theoretical model is postulated on the basis of analyzing the attributes of social ties and exchanged information content in light of a two-dimensional framework that juxtaposes boundary spanning and work relevance.The model is empirically tested using data obtained from two internal application systems of a large telecommunications company.Test results validate that employees'online social relationships with different attributes are discriminably associated with their group identification and proactive creativity.Meanwhile,proactive creativity and group identification both show the positive impacts on idea generation quantity,whereas only proactive creativity has a significant positive impact on idea generation quality.These findings contribute to the literature on intra-organizational social media and employee idea generation,by uncovering the links among employees'online social relationships,mental processes,and idea generation.

关键词： Intra-organizational social media online social relationship idea generation group identification proactivecreativity

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2019nCoVR—A comprehensive genomic resource for SARS-CoV-2 variant surveillance

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The Innovation 2021年第4期2卷 1-2页

作者： Guoqing Lu Etsuko N.Moriyama Department of Biology University of Nebraska at OmahaOmahaNE 68182USA School of Biological Sciences and Center for Plant Science Innovation University of Nebraska-LincolnLincolnNE 68588USA

The coronavirus disease 2019(COVID-19)is a once-in-a-century pandemic,and the virus,the severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2,has infected more than 180 million people and claimed almost 4 million lives worldwide(as of July 5,2021)since the first case was reported in Wuhan,China,on December 31,2019.The China National Center for Bioinformation(CNCB)responded promptly and launched the 2019 Novel Coronavirus Resource(2019nCoVR;https://***/ncov/)in January 2020 for rapid release and public sharing of SARS-CoV-2 genomic data and analysis tools(Figure 1A).

关键词： Figure prompt VR

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Leakage and wear characteristics of carbon seals for aero-engines

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Chinese Journal of Aeronautics 2022年第11期35卷 389-400页

作者： guoqing LI Shen ZHANG Zhong KANG Yanfeng ZHANG Xingen lu Junqiang ZHU Institute of Engineering Thermophysics Chinese Academy of SciencesBeijing 100190China School of Aeronautics and Astronautics University of Chinese Academy of SciencesBeijing 100190China School of Energy Power and Mechanical EngineeringNorth China Electric Power UniversityBejing 102206China

Experimental investigation has been performed to study the leakage and wear characteristics of carbon seal working at high circumferential speed. To expand the scope of application, two newly designed carbon seals were compared: #1 Carbon Seal(CS1) with the inner diameter of136 mm and including 4 segments, #2 Carbon Seal(CS2) with the inner diameter of 212 mm and including 6 segments. Air leakage tests were firstly conducted in the Medium-speed Seal Test Rig. The pressure ratio changed from 1.04 to 2.02 with the rotating speed varying from 0 to18300 r/min. Of paramount concern was the durability test, including 300 h running time accumulated by three different working conditions, which was separately implemented on each carbon seal.The morphology variation of the friction surface, wear and leakage were recorded. Results indicated that the leakage monotonously increases with the pressure ratio and decreases with the rotating speed. Comparing with CS1, more typical features exist on the friction surface of CS2, which are generated by more severe wear. Continually, leakage characteristics deteriorate. Furthermore, fitted formula has been educed for the life prediction of carbon seal, which could provide some supports for aero-engine design.

关键词： Aero-engine Carbon seal Durability test Leakage Rotating Wear

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UAV cooperative air combat maneuver decision based on multi-agent reinforcement learning

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Journal of Systems Engineering and Electronics 2021年第6期32卷 1421-1438页

作者： ZHANG Jiandong YANG Qiming SHI guoqing lu Yi WU Yong School of Electronics and Information Northwestern Polytechnical UniversityXi’an 710072China Shenyang Aircraft Design Institute Shenyang 110035China

In order to improve the autonomous ability of unmanned aerial vehicles(UAV)to implement air combat mission,many artificial intelligence-based autonomous air combat maneuver decision-making studies have been carried out,but these studies are often aimed at individual decision-making in 1 v1 scenarios which rarely happen in actual air combat.Based on the research of the 1 v1 autonomous air combat maneuver decision,this paper builds a multi-UAV cooperative air combat maneuver decision model based on multi-agent reinforcement learning.Firstly,a bidirectional recurrent neural network(BRNN)is used to achieve communication between UAV individuals,and the multi-UAV cooperative air combat maneuver decision model under the actor-critic architecture is established.Secondly,through combining with target allocation and air combat situation assessment,the tactical goal of the formation is merged with the reinforcement learning goal of every UAV,and a cooperative tactical maneuver policy is generated.The simulation results prove that the multi-UAV cooperative air combat maneuver decision model established in this paper can obtain the cooperative maneuver policy through reinforcement learning,the cooperative maneuver policy can guide UAVs to obtain the overall situational advantage and defeat the opponents under tactical cooperation.

关键词： decision-making air combat maneuver cooperative air combat reinforcement learning recurrent neural network

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Evolutionary direction of processed pseudogenes

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中国科学：生命科学英文版 2016年第8期59卷 839-849页

作者： guoqing Liu Xiangjun Cui Hong Li lu Cai School of Life Science and Technology Inner Mongolia University of Science and TechnologyBaotou 014010China 1nstitute of Bioengineering and Technology lnner Mongolia University of Science and TechnologyBaotou 014010China School of Physical Science and Technology Inner Mongolia UniversityHohhot 010021China Computational Systems Biology Lab Department of Biochemistry and Molecular BiologyInstitute of BioinformaticsUniversity of GeorgiaAthens GA 30602USA

While some pseudogenes have been reported to play important roles in gene regulation, little is known about the possible relationship between pseudogene functions and evolutionary process of pseudogenes, or about the forces responsible for the pseudogene evolution. In this study, we characterized human processed pseudogenes in terms of evolutionary dynamics. Our results show that pseudogenes tend to evolve toward: lower GC content, strong dinucleotide bias, reduced abundance of transcription factor binding motifs and short palindromes, and decreased ability to form nucleosomes. We explored possible evolutionary forces that shaped the evolution pattern of pseudogenes, and concluded that mutations in pseudogenes are likely determined, at least partially, by neighbor-dependent mutational bias and recombination-associated selection.

关键词： GC content mutual information transcription factor binding motifs mutational bias recombination

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Robust UV/moisture dual curable PDMS-microcapsule-silica functional material for self-healing,antifouling,and antibacterial applications

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Nano Research 2023年第5期16卷 7810-7819页

作者： Nan Zheng Jie Liu guoqing Wang Pan Yao Lihong Dang Ze Liu Jiufu lu Wenge Li Shaanxi Key Laboratory of Catalysis School of Chemical and Environmental ScienceShaanxi University of TechnologyHanzhong 723001China State Key Laboratory of Marine Resource Utilization in South China Sea School of Materials Science and EngineeringHainan UniversityHaikou 570228China School of Biological Sciences and Engineering Shaanxi University of TechnologyHanzhong 723001China Merchant Marine College Shanghai Maritime UniversityShanghai 201306China

Polydimethylsiloxane containing methacryloyloxy and methoxy silane groups(MAPDMS)-microcapsule-SiO_(2)(MPMS)functional materials were prepared by constructing micro-nano hierarchical structures on the surface of MAPDMS matrix.Herein,MAPDMS@1,1-stilbene-modified hydrolyzed polyglycidyl methacrylate/graphene oxide/dimethyloctadecyl[3-(trimethoxysilyl)propyl]ammonium chloride(MAPDMS@PGMA_(m)/GO/QC18)self-healing microcapsules with compact multi-shell structure were synthesized and combined with nano-SiO_(2)to construct the hierarchical structures.Furthermore,ultraviolet(UV)/moisture dual curing mode was introduced into deep curing reaction and efficient self-healing reaction of the MPMS.The results show that the introduction of UV/moisture dual curing mode and micro-nano hierarchical structure gives MPMS functional materials excellent mechanical properties,antifouling properties,self-healing properties,antibacterial properties.The shear strength and tensile strength of MPMS increase from 3.32 and 4.26 MPa of MAPDMS to 3.81 and 5.06 MPa,respectively.Its static contact angle increases from 115.9°of MAPDMS to 156.5°,its slide angle decreases from 68.5°of MAPDMS to 7.8°,respectively.The antifouling performance of MPMS against seawater,soy sauce,juice,coffee,protein,other contaminants is effectively improved compared with MAPDMS matrix.At the same time,the tensile strength and elongation at break of MPMS after healing reach 98.22%and 96.57%of those in original state,respectively.In addition,the antibacterial rates of MPMS against Escherichia coli and Staphylococcus aureus reach 99.85%and 100%,respectively.The MPMS prepared in this paper is expected to be widely used in marine antifouling,pipeline network,anti-icing,microfluidics,wearable devices,medical devices,electrochemical biosensors,other fields.

关键词： ultraviolet(UV)/moisture dual curing mechanism self-healing microcapsules micro-nano hierarchical structure antifouling antibacterial

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