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National Cancer Data linkage Platform of China:Design,Methods,and Application

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China CDC weekly 2022年第13期4卷 271-275页

作者： Hongmei Zeng Yunning Liu Lijun Wang Peng Yin Baohua Wang Ruiying Fu Xianhui Ran Rongshou Zheng Siwei Zhang Jiangmei Liu Jinling You Kexin Sun Shaoming Wang Li Li Ru Chen Wenqiang Wei Maigeng Zhou Jing Wu Jie He National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina National Center for Chronic and Non-communicable Disease Control and Prevention China CDCBeijingChina

Background:The National Cancer Center(NCC)and China CDC cooperatively designed a National Cancer Data linkage(NCDL)Platform to fulfill the task of sharing cancer outcome data through an automatic web-based system.Methods:NCC and China CDC established a web-based NCDL Platform to link death information from China CDC with the cancer database from NCC.Overall,76,708 cancer patients’data were analyzed to assess the feasibility and match rate of the NCDL Platform for 7 major cancers.Results:The function of the platform includes a data application and approval system,data linkage module,and results visualization system.Through the platform,38.9%cases were identified as deaths cases from the NCDL Platform in the first 3 years after cancer diagnosis.The linkage rate was highest in liver cancer and lowest in breast cancer.Conclusions:The NCDL Platform provides a powerful and efficient way to link national vital statistics with national cancer programs’data.Expanding cancer outcome data linkage may not only improve data collection efficiency,but also improve data use.

关键词： linkage Platform approval

From n-alkane to polyacetylene on Cu(110):linkage modulation in chain growth

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Science China Chemistry 2022年第4期65卷 733-739页

作者： Zhengming Hao Junjie Zhang Miao Xie Xuechao Li Lina Wang Ye Liu Kaifeng Niu Junbo Wang Luying Song Tao Cheng Haiming Zhang Lifeng Chi Institute of Functional Nano and Soft Materials(FUNSOM)and Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices Soochow UniversitySuzhou 215123China Department of Physics Chemistry and BiologyLinköping UniversityLinköping 58183Sweden

Direct coupling or transformation of inert alkanes based on the selective C-H activation is of great importance for both chemistry and chemical engineering.Here,we report the coupling of polyenes that are transformed from n-dotriacontane(n-C_(22)H_(66))through on-surface cascade dehydrogenation on Cu(110)surface,leading to the formation of polyacetylene(PA).Three distinct linkages have been resolved by scanning tunneling microscope(STM)and noncontact atomic force microscope(nc-AFM).Apart from the α-type linkage which is the stemless coupling of the terminal C-C double bond in trans-configuration,β-and γ-type linkages appear as knots or defects which are,in fact,the C-C couplings in cis-configurations.Interestingly,the“defects”can be effectively suppressed by adjusting the surface coverage,thus making it of general interest for uniform structure modulation.

关键词： on-surface chemistry scanning tunneling microscope all-trans polyacetylene linkage chain growth

Disk based pay-as-you-go record linkage

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Frontiers of Computer Science 2022年第4期16卷 227-229页

作者： Chenchen Sun Derong Shen Key Laboratory of Computer Vision and System(Ministry of Education) Tianjin University of TechnologyTianjin300384China College of Intelligence and Computing Tianjin UniversityTianjin300350China School of Computer Science and Engineering Northeastern UniversityShenyang110189China

1Introduction Record linkage(RL)groups_records corresponding to the same entities in datasets,and is a long-standing topic in data management and mining communities[1-2].In big data era,real-time data applications become popular,and callfor payas-you-go RL(PRL),which produces as many match pairs as possible in very limited time(much shorter than the overall RLruntime).

关键词： record linkage mining

A genetic linkage map of the threatened catfish Lophiosilurus alexandri:Inferences on effective population size

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Aquaculture and Fisheries 2023年第6期8卷 689-694页

作者： M.Raquel M.Coimbra Renata da S.Farias Bruno C.N.Rda Silva Andres Blanco Miguel Hermida Armando Caballero Michael Bekaert Paulino Martinez Department of Fisheries and Aquaculture Federal Rural University of PernambucoRua Dom Manuel de MedeirosS/nDois IrmaosRecifePE52171-900Brazil Department of Zoology Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversity of Santiago de Compostel1Campus of LugoLugo27002Spain Center of Marine Research University of VigoFaculty of BiologyVigo36310Spain Institute of Aquaculture University of StirlingScotlandFK94LAUnited Kingdom

We report the first genetic linkage map of the catfish Lophiosilurus alexandri,a South American threatened and promising aquaculture catfish species.Using the progeny of three full-sib families,with 141,74,and 49 offspring,respectively,we could genotype 2351 SNP markers using the ddRAD technology,shared by the male and the female maps constructed.The averaged,female and male maps spanned a total length of 2201.3 cM,2481.9 cM,and 1872.8 cM,respectively,and comprehended the expected 27 linkage groups according to the karyotype information of the species(2n=54).The recombination rate was nearly twice higher in the female than in the male map.The average map was used to estimate the historical effective population size(Ne)of the species from linkage disequilibrium between pairs of SNPs using parental individuals and revealed a remarkable drop in Ne about 20-25 generations in the past.The construction of the biggest artificial reservoir in Latin America and associated nutrient retention is pointed as a possible reason for such a reduction and suggests a reevaluation of the conservation status of the species.The current map lays the groundwork for understanding the genetic basis of economically important traits in breeding programs and will be useful for the genome assembly of this important commercial species.

关键词： breeding linkage size

A pentaploid-based linkage map of the ancestral octoploid strawberry Fragaria virginiana reveals instances of sporadic hyper-recombination

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Horticulture Research 2020年第1期7卷 1796-1810页

作者： Thomas M.Davis Yilong Yang Lise L.Mahoney Daniel C.Frailey Department of Agriculture Nutritionand Food SystemsUniversity of New HampshireDurhamNH 03824USA

The first high-resolution genetic linkage map of the ancestral octoploid(2n=8x=56)strawberry species,Fragaria virginiana,was constructed using segregation data obtained from a pentaploid progeny population.This novel mapping population of size 178 was generated by crossing highly heterozygous F.virginiana hybrid“LB48”as a paternal parent with diploid(2n=2x=14)Fragaria vesca“Hawaii 4”.The LB48 linkage map comprises 6055 markers genotyped on the Axiom®IStraw90 strawberry SNP array.The map consists of 28 linkage groups(LGs)organized into seven homoeology groups of four LGs each,and excludes a small 29th LG of undefined homoeology.One member of each homoeology group was assignable to an“A”subgenome associated with ancestral diploid Fragaria vesca,while no other subgenomes were defined.Despite an intriguing discrepancy within homoeology group VI,synteny comparisons with the previously published Fragaria×ananassa DA×MO linkage map revealed substantial agreement.Following initial map construction,examination of crossover distributions revealed that six of the total 5162(=29 chromosomes/individual×178 individuals)chromosomes making up the data set exhibited abnormally high crossover counts,ranging from 15 to 48 crossovers per chromosome,as compared with the overall mean of 0.66 crossovers per chromosome.Each of these six hyper-recombinant(HypR)chromosomes occurred in a different LG and in a different individual.When calculated upon exclusion of the six HypR chromosomes,the canonical(i.e.,broadly representative)LB48 map had 1851 loci distributed over a total map length of 1873 cM,while their inclusion increased the number of loci by 130,and the overall map length by 91 cM.Discovery of these hyper-recombinant chromosomes points to the existence of a sporadically acting mechanism that,if identified and manipulable,could be usefully harnessed for multiple purposes by geneticists and breeders.

关键词： Fragaria straw linkage

Hepatitis C Screening: Barriers to linkage to Care

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Journal of Clinical and Translational Hepatology 2019年第3期7卷 226-231页

作者： Sammy Saab Youssef PChallita Lisa MNajarian Rong Guo Satvir SSaggi Gina Choi Departments of Surgery University of California at Los AngelesLos AngelesCAUSA Departments of Medicine University of California at Los AngelesLos AngelesCAUSA Departments of Medicine Statistics Core University of California at Los AngelesLos AngelesCAUSA

Background andAims:Hepatitis C(HCV)is a medical and public health concern.Once infected individuals are identified,management includes not only education but also the use of antiviral therapy.Although screening for HCV is readily available,barriers exist which prevent assessment and treatment in individuals potentially infected with HCV.Methods:This is a retrospective study of patients screened for HCV within the University of California,Los Angeles Health Care System between February 22 and July 9,2018.We defined linkage to care as:1)confirmatory HCV RNA test after screening HCV antibody test found a positive result;and 2)follow-up appointment for treatment was established with a specialist.Demographic and baseline laboratory values were collected.Factors potentially associated with prohibiting linkage of care were evaluated.Results:During the study period,17,512 individuals were screened for HCV.A total of 238(1.35%)were found to have detectable HCV antibodies.Of the individuals with detectable HCV antibodies,48(20%)did not undergo confirmatory testing with viral levels.Of the 190 individuals who underwent further testing,70 patients were noted to be viremic.Among them,17 of the 70(24%)were not linked to a specialist for further care.Younger patients(p=0.02)and people who inject drugs(p=0.02)were less likely to be referred for specialty care.Conclusions:The results of our study highlight that younger patients and people who inject drugs are less likely to be referred to specialty care for HCV treatment.Efforts are needed to engage these populations.

关键词： Hepatitis C Screening linkage

Construction of an anchoring SSR marker genetic linkage map and detection of a sex-linked region in two dioecious populations of red bayberry

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Horticulture Research 2020年第1期7卷 2262-2270页

作者： Yan Wang Hui-Min Jia Yu-Tong Shen Hai-Bo Zhao Qin-Song Yang Chang-Qing Zhu De-Li Sun Guo-Yun Wang Chao-Chao Zhou Yun Jiao Chun-Yan Chai Li-Ju Yan Xiong-Wei Li Hui-Juan Jia Zhong-Shan Gao Fruit Science Institute College of Agriculture and BiotechnologyZhejiang University310058 HangzhouChina Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of Sciences201602 ShanghaiChina Yuyao Forestry Technology Extension Center 315400 NingboChina Institute of Forestry Ningbo Academy of Agricultural ScienceNingboChina Cixi Forestry Technology Extension Center 315300 CixiChina Linhai Forestry Technology Extension Center 317000 TaizhouChina Forest&Fruit Tree Institute Shanghai Academy of Agricultural Sciences201403 ShanghaiChina

Red bayberry(Morella rubra)is an evergreen fruit tree found in southern China whose whole-genome sequence has recently been published.We updated the linkage map of the species by adding 118 SSR markers and the femalespecific marker MrFT2_BD-SEX.The integrated map included eight linkage groups and spanned 491 cM.Eleven sexassociated markers were identified,six of which were located in linkage group 8,in agreement with the previously reported location of the sex-determining region.The MrFT2_BD-SEX marker was genotyped in 203 cultivated accessions.Among the females of the accessions,we found two female-specific alleles,designated W-b(151 bp)and W-d(129 bp).We previously found that‘Dongkui’,a female cultivar,could produce viable pollen(we refer to such plants‘Dongkui-male’)and serve as the paternal parent in crosses.The genotypes of the MrFT2_BD-SEX marker were W-b/Z in‘Biqi’and W-d/Z in‘Dongkui-male’.The progeny of a cross between these parents produced a 3:1 female(W-)to male(ZZ)ratio and the expected 1:1:1:1 ratio of W-b/W-d:W-b/Z:W-d/Z:Z/Z.In addition,the flowering and fruiting phenotypes of all the F1 progeny fit their genotypes.Our results confirm the existence of ZW sex determination and show that the female phenotype is controlled by a single dominant locus(W)in a small genomic region(59 kb and less than 3.3 cM).Furthermore,we have produced a homozygous“super female”(WW)that should produce all-female offspring in the F2 generation,providing a foundation for commercial use and presenting great potential for use in modern breeding programs.

关键词： breeding cultivar linkage

User Account linkage Across Multiple Platforms with Location Data

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Journal of Computer Science & Technology 2020年第4期35卷 751-768页

作者： Wei Chen Weiqing Wang Hongzhi Yin Jun-Hua Fang Lei Zhao Institute of Artificial Intelligence School of Computer Science and TechnologySoochow UniversitySuzhou 215006China Faculty of Information Technology Monash UniversityMelbourne 3000Australia School of Information Technology and Electrical Engineering The University of QueenslandBrisbane 4072Australia

Linking user accounts belonging to the same user across different platforms with location data has received significant attention,due to the popularization of GPS-enabled devices and the wide range of applications benefiting from user account linkage(e.g.,cross-platform user profiling and recommendation).Different from most existing studies which only focus on user account linkage across two platforms,we propose a novel model ULMP(i.e.,user account linkage across multiple platforms),with the goal of effectively and efficiently linking user accounts across multiple platforms with location data.Despite of the practical significance brought by successful user linkage across multiple platforms,this task is very challenging compared with the ones across two platforms.The major challenge lies in the fact that the number of user combinations shows an explosive growth with the increase of the number of platforms.To tackle the problem,a novel method GTkNN is first proposed to prune the search space by efficiently retrieving top-k candidate user accounts indexed with well-designed spatial and temporal index structures.Then,in the pruned space,a match score based on kernel density estimation combining both spatial and temporal information is designed to retrieve the linked user accounts.The extensive experiments conducted on four real-world datasets demonstrate the superiority of the proposed model ULMP in terms of both effectiveness and efficiency compared with the state-of-art methods.

关键词： user account linkage multiple platform check-in record

A Sequencing-Based linkage Map of Cucumber

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Molecular Plant 2015年第6期8卷 961-963页

作者： Zhou, Qian Miao, Han Li, Shuai Zhang, Shengping Wang, Ye Weng, Yiqun Zhang, Zhonghua Huang, Sanwen Gu, Xingfang Chinese Acad Agr Sci Key Lab Biol & Genet Improvement Hort Crops Inst Vegetables & Flowers Minist AgrSino Dutch Joint Lab Hort Gen Beijing 10081 Peoples R China Chinese Acad Agr Sci Agr Genom Inst Shenzhen Shenzhen 518120 Peoples R China Univ Wisconsin Vegetable Crops Res Unit Dept Hort USDAARS Madison WI 53706 USA

Cucumber （Cucumis sativus L., 2n = 2x = 14） is an economically important vegetable worldwide and has served as a model sys- tem for plant vascular biology and sex determination studies. We reported the draft genome assembly of the North China type cucumber line 9930 in 2009 （Huang et al., 2009a） and constructed a single-base resolution map of cucumber genomic variation by resequencing of the genomes of 115 core germplasm lines （Qi et al., 2013）, which enabled genome-wide association studies of important traits in cucumber （Shang et al., 2014）.

关键词： Sequencing-Based linkage Map