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Computational tools for plant genomics and breeding

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Science China(Life Sciences) 2024年第8期67卷 1579-1590页

作者： Hai Wang Mengjiao Chen Xin Wei Rui Xia Dong Pei Xuehui Huang Bin Han State Key Laboratory of Maize Bio-breeding Frontiers Science Center for Molecular Design BreedingJoint International Research Laboratory of Crop Molecular BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Sanya Institute of China Agricultural university Sanya 572025China Hainan Yazhou Bay Seed Laboratory Sanya 572025China State Key Laboratory of Tree Genetics and Breeding Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091China shanghai Key Laboratory of Plant Molecular Sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China College of Horticulture South China Agricultural UniversityGuangzhou 510640China National center for Gene research CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200233China

Plant genomics and crop breeding are at the intersection of biotechnology and information *** by a combination of highthroughput sequencing,molecular biology and data science,great advances have been made in omics technologies at every step along the central dogma,especially in genome assembling,genome annotation,epigenomic profiling,and transcriptome *** advances further revolutionized three directions of *** is genetic dissection of complex traits in crops,along with genomic prediction and *** second is comparative genomics and evolution,which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant *** third direction is the development of deep learning approaches for the rational design of biological sequences,especially proteins,for synthetic *** three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.

关键词： bioinformatics plant genomics breeding by design

CableSAM: an efficient automatic segmentation method for aircraft cabin cables

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Optoelectronics Letters 2024年

作者： LING Aihua WANG Junwen LU Jiaming LIU Ruyu School of Information Science and Technology， Hangzhou normal university shanghai Aircraft Manufacturing Co.，Ltd School of Computer Science and Engineering， Tianjin university of Technology

Cabin cables， as critical components of an aircraft’s electrical system， significantly impact the operational efficiency and safety of the aircraft. The existing cable segmentation methods in civil aviation cabins are limited， especially in automation， being heavily dependent on large amounts of data and resources， lacking the flexibility to adapt to different scenarios. To address these challenges， this paper introduces a novel image segmentation model， CableSAM， specifically designed for automated segmentation of cabin cables. CableSAM improves segmentation efficiency and accuracy using knowledge distillation and employs a context ensemble strategy. It accurately segments cables in various scenarios with minimal input prompts. comparative experiments on three cable datasets demonstrate that CableSAM surpasses other advanced cable segmentation methods in performance.

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CEPC Technical Design Report

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Radiation Detection Technology and Methods 2024年第1期8卷 I0003-I0016,1-1091页

作者： Waleed Abdallah Tiago Carlos Adorno de Freitas Konstantin Afanaciev Shakeel Ahmad Ijaz Ahmed Xiaocong Ai Abid Aleem Wolfgang Altmannshofer Fabio Alves Weiming An Rui An Daniele Paolo Anderle Stefan Antusch Yasuo Arai Andrej Arbuzov Abdesslam Arhrib Mustafa Ashry Sha Bai Yu Bai Yang Bai Vipul Bairathi Csaba Balazs Philip Bambade Yong Ban Tripamo Bandyopadhyay Shou-Shan Bao Desmond P.Barber Ayse Bat Varvara Batozskaya Subash Chandra Behera Alexander Belyaev Michele Bertucci Xiao-Jun Bi Yuanjie Bi Tianjian Bian Fabrizio Bianchi Thomas Biekotter Michela Biglietti Shalva Bilanishvili Deng Binglin Denis Bodrov Anton Bogomyagkov Serge Bondarenko Stewart Boogert Maarten Boonekamp Marcello Borri Angelo Bosotti Vincent Boudry Mohammed Boukidi Igor Boyko Ivanka Bozovic Giuseppe Bozzi Jean-Claude Brient Anastasiia Budzinskaya Masroor Bukhari Vladimir Bytev Giacomo Cacciapaglia Hua Cai Wenyong Cai Wujun Cai Yijian Cai Yizhou Cai Yuchen Cai Haiying Cai Huacheng Cai Lorenzo Calibbi Junsong Cang Guofu Cao Jianshe Cao Antoine Chance Xuejun Chang Yue Chang Zhe Chang Xinyuan Chang Wei Chao Auttakit Chatrabhuti Yimin Che Yuzhi Che Bin Chen Danping Chen Fuqing Chen Fusan Chen Gang Chen Guoming Chen Hua-Xing Chen Huirun Chen Jinhui Chen Ji-Yuan Chen Kai Chen Mali Chen Mingjun Chen Mingshui Chen Ning Chen Shanhong Chen Shanzhen Chen Shao-Long Chen Shaomin Chen Shiqiang Chen Tianlu Chen Wei Chen Xiang Chen Xiaoyu Chen Xin Chen Xun Chen Xurong Chen Ye Chen Ying Chen Yukai Chen Zelin Chen Zilin Chen Gang Chen Boping Chen Chunhui Chen Hok Chuen Cheng Huajie Cheng Shan Cheng Tongguang Cheng Yunlong Chi Pietro Chimenti Wen Han Chiu Guk Cho Ming-Chung Chu Xiaotong Chu Ziliang Chu Guglielmo Coloretti Andreas Crivellin Hanhua Cui Xiaohao Cui Zhaoyuan Cui Brunella D'Anzi Ling-Yun Dai Xinchen Dai Xuwen Dai Antonio De Maria Nicola De Filippis Christophe De La Taille Francesca De Mori Chiara De Sio Elisa Del Core Shuangxue Deng Wei-Tian Deng Zhi Deng Ziyan Deng Bhupal Dev Tang Dewen Biagio Di Micco Ran Ding Siqin Dingl Yadong Ding Haiyi Dong Jianin AGH university of Science and Technology Faculty of Physics and Applied Computer ScienceKrakow Anhui university HefeiAnhui Applied Physics Department Federal Urdu University of ArtsScience and TechnologyIslamabad Banaras Hindu university Institute of ScienceVaranasi Bandirma Onyedi Eylul university Bandirma Beihang university Beijing Beijing Computational Science research center Beijing Beijing Conveyi LTD Beijing Beijing Glass research Institute Co. LtdBeijing Beijing Institute of Technology Beijing Beijing normal university Beijing Brown university ProvidenceRI Budker Institute of Nuclear Physics Novosibirsk Cadi Ayyad university Laboratory of Fundamental and Applied PhysicsPolydisciplinary FacultyMarrakech Cairo university Giza center for Theory and Computation National Tsing Hua UniversityHsinchu Central China normal university WuhanHubei Central South university ChangshaHunan Centro de Fisica Teorica de Particulas Universidade Tecnica de LisboaLisboa Chengdu KaitengSifang Digital Radio&TV Equipment Co. LtdChengduSichuan China academy of engineering physics MianyangSichuan China building materials academy Beijing China center of Advanced Science and Technology Beijing China Institute of Atomic Energy Beijing China Jiliang university HangzhouZhejiang China Nuclear Instrument CO. LTDBeijing China university of Geosciences Beijing China university of Geosciences WuhanHubei China university of Mining and Technology XuzhouJiangsu China West normal university NanchongSichuan Chongqing university Department of PhysicsChongqing Chulalongkorn university Bangkok City university of Hong Kong Department of PhysicsHong Kong Cockcroft Institute Daresbury Cornell university IthacaNY CPPM(AMU/IPhU&CNRS/INP) Marseille Dalian Minzu university DalianLiaoning Dalian university of Technology Department of PhysicsDalian Deutsches Elektronen-Synchrotron DESY Hamburg Dzhelepov Laboratory of Nuclear Problems of Joint Institute for Nuclear research(DLNP JINR) Dubna East China university Of Science And Technol

The Circular Electron Positron Collider(CEPC)is a large scientific project initiated and hosted by China,fostered through extensive collaboration with international *** complex comprises four accelerators:a 30 GeV Linac,a 1.1 GeV Damping Ring,a Booster capable of achieving energies up to 180 GeV,and a Collider operating at varying energy modes(Z,W,H,and tt).The Linac and Damping Ring are situated on the surface,while the subterranean Booster and Collider are housed in a 100 km circumference underground tunnel,strategically accommodating future expansion with provisions for a potential Super Proton Proton Collider(SPPC).The CEPC primarily serves as a Higgs *** its baseline design with synchrotron radiation(SR)power of 30 MW per beam,it can achieve a luminosity of 5×10^(34)cm^(-2)s^(-1)per interaction point(IP),resulting in an integrated luminosity of 13 ab^(-1)for two IPs over a decade,producing 2.6 million Higgs *** the SR power to 50 MW per beam expands the CEPC's capability to generate 4.3 million Higgs bosons,facilitating precise measurements of Higgs coupling at sub-percent levels,exceeding the precision expected from the HL-LHC by an order of *** Technical Design Report(TDR)follows the Preliminary Conceptual Design Report(Pre-CDR,2015)and the Conceptual Design Report(CDR,2018),comprehensively detailing the machine's layout,performance metrics,physical design and analysis,technical systems design,R&D and prototyping efforts,and associated civil engineering ***,it includes a cost estimate and a preliminary construction timeline,establishing a framework for forthcoming engineering design phase and site selection *** is anticipated to begin around 2027-2028,pending government approval,with an estimated duration of 8 *** commencement of experiments and data collection could potentially be initiated in the mid-2030s.

关键词： initiated exceeding precise

Gene expression analysis of pancreatic cystic neoplasm in SV40Tag transgenic mice model

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world Journal of Gastroenterology 2007年第15期13卷 2218-2222页

作者： Jie Feng Qiang Sun Cheng Gao Juan Dong Xiao-Luan Wei Hua Xing Hou-Da Li shanghai Laboratory Animal research center Shanghai 200032 China comparative Medical center Yangzhou University Yangzhou 225009 Jiangsu Province China shanghai Institute of Brain Functional Genomics East China Normal University Shanghai 200062 China

AIM： To study the gene expression changes in pancreatic cystic neoplasm in SV40Tag transgenic mice model and to provide information about the prevention, clinical diagnosis and therapy of pancreatic cancer. METHODS： Using the pBC-SV40Tag transgenic mice model of pancreatic cystic neoplasm, we studied the gene expression changes by applying high-density microarrays. Validation of part gene expression profiling data was performed using real-time PCR.RESULTS： By using high-density oligonucleotide microarray, of 14113 genes, 453 were increased and 760 decreased in pancreatic cystic neoplasm, including oncogenes, cell-cycle-related genes, signal transduction-related genes, skeleton-related genes and metabolism-related genes. Among these, we confirmed the changes in Igf, Shh and Wnt signal pathways with real-time PCR. The results of real-time PCR showed similar expression changes in gene chip.CONCLUSION： all the altered expression genes are associated with cell cycle, DNA damage and repair, signal pathway, and metabolism. SV40Tag may cooperate with several proteins in promoting tumorigenesis.

关键词： SV40Tag Pancreatic cystic neoplasm cDNA microarray

Generation and characterization of a transgenic mouse model for pancreatic cancer

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world Journal of Gastroenterology 2006年第17期12卷 2785-2788页

作者： Qiang sun Jie Feng Xiao-Luan Wei Rong Zhang Su-Zhen Dong Qian Shen Juan Dong Hou-Da Li Ying-He Hu shanghai Institute of Brain Functional Genomics East China Normal University Shanghai 200062 Shanghai China comparative Medical center Yangzhou University Yangzhou 225009 Jiangsu Province China

AIM： To generate a SV40Tag transgenic tumor animal model and to study the mechanism underlying tumorigenesis. METHODS： A mammary gland expression vector containing SV40Tag DNA was generated. Transgene fragments were microinjeted into fertilized eggs of FVB mice. The genetically manipulated embryos were transferred into the oviducts of pseudo-pregnant female mice. PCR and Northern blot analysis were used for genotype analysis of F1 and F2 mice. Transgene expression was detected by RT-PCR and immunohistochemistry. RESULTS： SV40Tag gene was detected in two lines of transgenic mice. One of them delivered the transgene to F1 and a tumor was found in the pancreas of these mice. RT-PCR and immunohistochemistry showed that SV40Tag gene was expressed in the tumor. Pathological characterization of the transgenic mice demonstrated that the tumor belonged to pancreatic cystic neoplasm. CONCLUSION： SV40Tag transgenic mouse model can be successfully established. The transgenic mice develop a pancreatic tumor, which can be used for investigation of the molecular mechanism of tumorigenesis in vivo.

关键词： SV40Tag Transgenic mice Animal model Pancreatic neoplasms

ABM-based emergency evacuation modelling during urban pluvial floods:A“7.20”pluvial flood event study in Zhengzhou,Henan Province

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Science China Earth Sciences 2023年第2期66卷 282-291页

作者： Yuhan YANG Jie YIN Dandan WANG Yufan LIU Yi LU Weiguo ZHANG Shiyuan XU State Key Laboratory of Estuarine and Coastal research East China Normal UniversityShanghai200241China Key Laboratory of Geographic Information Science(Ministry of Education) East China Normal UniversityShanghai200241China Institute of Eco-Chongming East China Normal UniversityShanghai202162China research center for China Administrative Division East China Normal UniversityShanghai202162China National Disaster Reduction center of China Ministry of Emergency Management of People’s Republic of ChinaBeijing100124China

Increasing urban pluvial flood disasters due to climate change and rapid urbanisation have been a great challenge *** and effective emergency evacuation is important for reducing casualties and *** has become a bottleneck for emergency *** study aimed to develop a commonly used Agent-Based Mode(ABM)for pluvial flood emergency evacuation at the city scale,exploring the cascading impacts of pluvial flooding on human behaviour and emergency *** July 2021 pluvial flood event in Zhengzhou,Henan Province,claiming 380 lives and 40.9 billion yuan in direct losses,was selected as this case study.A raster-based hydraulic model(ECNU Flood-Urban)was used to predict flood inundation(extent and depth)during an event in Zhengzhou’s ***,a comparative analysis of emergency evacuations was conducted before and after the pluvial flood *** results showed that crowd behaviour plays an important role in an emergency evacuation,and extensive flooding leads to an 11-83%reduction in the number of *** study highlights the importance of risk education and contingency plans in emergency *** ABM model developed in this study is proven to be effective and practical and will provide support for decision-making in urban flood emergency management.

关键词： Pluvial flood Emergency evacuation Agent-based model Crowd behaviour Extreme rainfall in Zhengzhou

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Combinatorial knowledge dynamics,innovative performance,and transition studies

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Journal of Geographical Sciences 2023年第4期33卷 705-718页

作者： XUE Shuaijun LIU Chengliang Department of Geography Kiel UniversityKiel 24118Germany School of Urban and Regional Sciences East China Normal UniversityShanghai 200241China Institute for Global Innovation and Development East China Normal UniversityShanghai 200062China center of world Geography and Geo-strategical Studies East China Normal UniversityShanghai 200062China

Cross-domain research and development has prevailed in regional transformation and disruptive innovation in the last 15 ***,a new concept,termed combinatorial knowledge bases(CKBs),offers insights into combining knowledge dynamics and is considered a good approach to explore recombinant innovative ***,we review the literature on CKBs in Western economic geography,and we introduce a research agenda for CKBs in China’s economic *** the latter,four aspects are elaborated:the co-evolution of the innovation chain and industrial chain,the geography of innovative activiinnovative entrepreneurship and new path development,and innovation system *** paper contributes to theoretical studies of China’s geography by linking CKBs to Chinese-specific phenomena.

关键词： combinatorial knowledge bases innovation China's transformation

Experimental study on the effect of An-pressing and Rou-kneading Huantiao (GB 30) on certain brain nuclei of pleasure circuits in rats with chronic neuralgia

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Journal of Acupuncture and Tuina Science 2018年第6期16卷 360-369页

作者： Xiao Bin Li Zheng-yu Yu Zhong-yi Zhang Jin Yan Jun-jie Liu Xiao College of Acupuncture and TUina Shanghai University of Traditional Chinese MedicineShanghai 20l203China research center Shanghai University of Traditional Chinese MedicineShanghai 201203China shanghai literature Institute of Traditional Chinese Medicine Shanghai 20020China shanghai East Hospital Shanghai 200120China College of Pharmacy Fudan UniversityShanghai 200032China

Objective:To explore the central neurobiological mechanisms of pleasure effect on rats with neuralgia treated by tuina manipulations of An-pressing and Rou-kneading Huantiao (GB 30).Methods:A total of 64 male Sprague-Dawley (SD) rats were used in this *** rats were randomly selected as a normal group,and the other 46 rats were used to duplicate the chronic constriction injury (CCI) *** rats failed in modeling and 36 rats *** 36 rats were then randomly divided into a model group and a tuina group,with 18 rats in each *** rats in the normal group and the model group did not receive any interventions,while those in the tuina group received An-pressing and Rou-kneading Huantiao (GB 30),1 min for each time,once a day,3 weeks in *** tests were evaluated to observe the change of pain-sensitivity score before intervention,1 week after intervention,2 weeks after intervention,and 3 weeks after *** 1 week of intervention,2 weeks of intervention,and 3 weeks of intervention,6 rats were randomly selected from each group respectively for brain *** change of Nissl's body and β-endorphin in the accumbens nucleus as well as amygdaloid nucleus of pleasure circuits,and pro-opiomelanocortin (POMC) in the arcuate nucleus were analyzed by methods of histochemistry and molecular ***:After modeling,the pain-sensitivity scores of the tuina group and the model group were statistically different from the score of the normal group (both P<0.05).After An-pressing and Rou-kneading Huantiao (GB 30) for one week,the pain-sensitivity score of the tuina group had statistical difference compared with that of the model group (P<0.05).At each different time point:the amounts of Nissl's body in accumbens nucleus and amygdaloid nucleus of the tuina group were significantly more than those of the model group (all P<0.01).Besides,the numbers of β-endorphin immunoreactive cells in the accumbens nucleus and amygdaloid nucleus o

关键词： Tuina Massage Neuralgia Analgesia Endorphins Pro-opiomelanocortin Rats

Spectral data treatments for impervious endmember derivation and fraction mapping from Landsat ETM＋ imagery： a comparative analysis

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Frontiers of Earth Science 2015年第2期9卷 179-191页

作者： Wei WANG Xinfeng YAO Minhe JI Jiao ZHANG Key Laboratory of GIScience (Ministry of Education of China) East China Normal University Shanghai 200241 China Agricultural Information Institute of Science and Technology Shanghai Academy of Agricultural Sciences Shanghai 201403 China China East-West Cooperation research center East China Normal University Shanghai 200241 China

Various spectral data preprocessing approaches have been used to improve endmember extraction for urban landscape decomposition, yet little is known of their comparative adequacy for impervious surface mapping. This study tested four commonly used spectral data treatment strategies for endmember derivation, including original spectra, image fusion via principal component analysis, spectral normalization, and the minimum noise fraction （MNF） transformation. Land cover endmembers derived using each strategy were used to build a linear spectral mixture analysis （LSMA） model in order to unmix treated image pixels into fraction maps, and an urban imperviousness map was generated by combining the fraction maps representing imperviousness endmembers. A cross-map comparative analysis was then performed to rank the four data treatment types based on such common evaluation indices as the coefficient of determination （R2） and root mean square error （RMSE）. A Landsat 7 ETM~ multispectral image covering the metropolitan region of shanghai, China was used as the primary dataset, and the model results were evaluated using high-resolution color- infrared aerial photographs of roughly the same time period. The test results indicated that, with the highest R2 （0.812） and the lowest RMSE （0.097） among all four preprocessing treatments, the endmembers in the form of MNF-transformed spectra produced the best model output for characterizing urban impervious surfaces. The outcome of this study may provide useful guidance for future impervious surface mapping using medium-resolution remote sensing data.

关键词： impervious surface estimation linear spectral