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Evaluating the performance of genomic selection on purebred population by incorporating crossbred data in pigs
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作者 Jun Zhou Qing Lin +10 位作者 Xueyan Feng Duanyang Ren Jinyan Teng Xibo Wu Dan Wu Xiaoke Zhang Xiaolong Yuan Zanmou Chen Jiaqi Li Zhe Zhang Hao Zhang 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2024年第2期639-648,共10页
Genomic selection(GS)has been widely used in livestock,which greatly accelerated the genetic progress of complex traits.The population size was one of the significant factors affecting the prediction accuracy,while it... Genomic selection(GS)has been widely used in livestock,which greatly accelerated the genetic progress of complex traits.The population size was one of the significant factors affecting the prediction accuracy,while it was limited by the purebred population.Compared to directly combining two uncorrelated purebred populations to extend the reference population size,it might be more meaningful to incorporate the correlated crossbreds into reference population for genomic prediction.In this study,we simulated purebred offspring(PAS and PBS)and crossbred offspring(CAB)base on real genotype data of two base purebred populations(PA and PB),to evaluate the performance of genomic selection on purebred while incorporating crossbred information.The results showed that selecting key crossbred individuals via maximizing the expected genetic relationship(REL)was better than the other methods(individuals closet or farthest to the purebred population,CP/FP)in term of the prediction accuracy.Furthermore,the prediction accuracy of reference populations combining PA and CAB was significantly better only based on PA,which was similar to combine PA and PAS.Moreover,the rank correlation between the multiple of the increased relationship(MIR)and reliability improvement was 0.60-0.70.But for individuals with low correlation(Cor(Pi,PA or B),the reliability improvement was significantly lower than other individuals.Our findings suggested that incorporating crossbred into purebred population could improve the performance of genetic prediction compared with using the purebred population only.The genetic relationship between purebred and crossbred population is a key factor determining the increased reliability while incorporating crossbred population in the genomic prediction on pure bred individuals. 展开更多
关键词 PIGS crossbred population genomic selection reference population construction relationship
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Changes in the adult sex ratio of six duck species breeding populations over two decades
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作者 Monika Homolkova Petr Musil +4 位作者 Diego Pavon-Jordan Dorota Gajdosova Zuzana Musilova Sarka Neuzilova Jan Zouhar 《Avian Research》 SCIE CSCD 2024年第2期202-210,共9页
Despite all efforts,long-term changes in the adult sex ratios of breeding duck populations are still unclear;this uncertainty is especially true for male-bias populations,which are often under the scrutiny of research... Despite all efforts,long-term changes in the adult sex ratios of breeding duck populations are still unclear;this uncertainty is especially true for male-bias populations,which are often under the scrutiny of researchers lacking convenient results for the active protection of endangered species.Species with male-bias populations are usually strongly affected by a decline in population size that leads to a higher extinction risk.In this study,we examined our long-term data of the abundance of breeding populations in six duck species(Mallard Anas platyrhynchos,Gadwall Mareca strepera,Red-crested Pochard Netta rufina,Common Pochard Aythya ferina,Tufted Duck Aythya fuligula,and Common Goldeneye Bucephala clangula)from fishponds in South Bohemia,Czechia,between 2004 and 2022.This evidence was used to assess long-term changes in the adult sex ratio in these breeding populations and investigate the possible effects of the NAO index(North Atlantic Oscillation index)on them,indicating climate conditions in winter.We determined a long-term decrease of the proportion of females in the breeding season in two of the six examined species:Common Pochard and Red-crested Pochard,which is driven by the long-term increase in the number of males in contrast to the decreasing or stable number of females likely caused by different migration behaviours between females and males.In the case of Common Pochard,in breeding populations,we estimated 60-65%of males in the early 2000s rising to 75-80%in the early 2020s.However,we establish no significant effects linked to climate conditions of the previous winter in these species as a crucial cause of the changes of the proportion of females in the breeding population. 展开更多
关键词 Adult sex ratio Breeding population population dynamics Red-listed species WATERFOWL Winter weather conditions
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Evolution and Determinants of Population Agglomeration in Less Developed Metropolitan Areas:A Case Study of the Taiyuan Metropolitan Area,China
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作者 QIN Zhiqin LIANG Ye +1 位作者 AN Shuwei DOU Yongjing 《Chinese Geographical Science》 SCIE CSCD 2024年第4期739-751,共13页
It is of importance to enhance the urban areas'capacity for population aggregation in underdeveloped regions,aiming to rectify the imbalanced and insufficient pattern of economic development in China.Taking the Ta... It is of importance to enhance the urban areas'capacity for population aggregation in underdeveloped regions,aiming to rectify the imbalanced and insufficient pattern of economic development in China.Taking the Taiyuan Metropolitan Area(TMA)in central China as a case study,this paper examines the evolutionary process and characteristics of population agglomeration from 2000 to 2020,and identifies factors associated with agglomeration and their spatial effects.The findings indicated that:1)against the background of sustained population shrinkage in the provincial area,the TMA showed a demographic trend of steady increase,albeit with a decelerated growth rate.In the metropolitan area,urban population size continued to grow rapidly,whereas the rural areas endured sustained losses.Disparities in city size continued to widen,and the polarization of concentrated population in the core cities kept increasing.2)Agglomerations in both secondary and service industries had significant positive effects on local population agglomeration,with the former effect being stronger.Regional economic development,government fiscal expenditure,and financial advancement all contributed to facilitating local population clustering.From a spatial spillover perspective,service agglomeration and financial development promoted population agglomeration in surrounding areas.Conversely,fiscal expenditure inhibited such agglomeration.As for industrial agglomeration and regional economic development,their spatial spillover effects were non-significant.The results obtained reveal several policy implications aimed at enhancing the population agglomeration capacity of the metropolitan area in underdeveloped regions during the new era. 展开更多
关键词 population agglomeration population shrinkage spatial spillover effects Taiyuan Metropolitan Area(TMA) China
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Comparative Study of Genetic Structure and Genetic Diversity betweenWild and Cultivated Populations of Taxus cuspidata,Northeast China
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作者 Dandan Wang Xiaohong Li Yanwen Zhang 《Phyton-International Journal of Experimental Botany》 SCIE 2024年第2期355-369,共15页
Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is... Taxus cuspidata is a rare plant with important medicinal and ornamental value.Aiming at the obvious differences between wild and cultivated populations of T.cuspidata from Northeast China,a total of 61 samples,that is,33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship,genetic diversity,and genetic structure between them by specific length amplified fragment sequencing(SLAF-seq).Finally,470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained.Phylogenetic analysis showed that 61 samples were classified into 2 clusters:wild populations and cultivated populations,and some wild yews were categorized into the cultivated populations;the genetic diversity analysis showed that the Nei diversity index of wild populations(0.4068)was smaller than that of cultivated populations(0.4414),and the polymorphic information content(PIC)of wild populations(0.2861)was smaller than that of cultivated populations(0.3309).The genetic differentiation analysis showed that the total populations of gene diversity(H_(t))of cultivated and wild populations were respectively 0.8159 and 0.5685,the coefficient of gene differentiation(G_(st))of cultivated and wild populations was respectively 0.3021 and 0.1068,and the gene flow(N_(m))(2.4967)of wild populations was larger than cultivated populations(0.8199).The molecular variance(AMOVA)revealed that inter-population variation accounted for 29.57%of the total genetic variation,while intra-population variation accounted for 70.42% of the total genetic variation(p<0.001),this suggested that the genetic variation in the T.cuspidata is mainly attributed to within-population factors.In conclusion,the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations,and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations.As evident,the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T.cuspidata species.These developed SNP markers can provide a molecular foundation for T.cuspidata breeding,construction of genetic maps,variety identification,and association analysis of agronomic traits. 展开更多
关键词 T.cuspidata SLAF-seq SNP wild population cultivated population genetic structure
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KCNQ1 rs2237895 gene polymorphism increases susceptibility to type 2 diabetes mellitus in Asian populations 被引量:1
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作者 Dong-Xu Li Li-Ping Yin +4 位作者 Yu-Qi Song Nan-Nan Shao Huan Zhu Chen-Sen He Jiang-Jie Sun 《World Journal of Diabetes》 SCIE 2024年第3期552-564,共13页
BACKGROUND The association of single nucleotide polymorphism of KCNQ1 gene rs2237895 with type 2 diabetes mellitus(T2DM)is currently controversial.It is unknown whether this association can be gene realized across dif... BACKGROUND The association of single nucleotide polymorphism of KCNQ1 gene rs2237895 with type 2 diabetes mellitus(T2DM)is currently controversial.It is unknown whether this association can be gene realized across different populations.AIM To determine the association of KCNQ1 rs2237895 with T2DM and provide reliable evidence for genetic susceptibility to T2DM.METHODS We searched PubMed,Embase,Web of Science,Cochrane Library,Medline,Baidu Academic,China National Knowledge Infrastructure,China Biomedical Literature Database,and Wanfang to investigate the association between KCNQ1 gene rs2237895 and the risk of T2DM up to January 12,2022.Review Manager 5.4 was used to analyze the association of the KCNQ1 gene rs2237895 polymorphism with T2DM and to evaluate the publication bias of the selected literature.RESULTS Twelve case–control studies(including 11273 cases and 11654 controls)met our inclusion criteria.In the full population,allelic model[odds ratio(OR):1.19;95%confidence interval(95%CI):1.09–1.29;P<0.0001],recessive model(OR:1.20;95%CI:1.11–1.29;P<0.0001),dominant model(OR:1.27.95%CI:1.14–1.42;P<0.0001),and codominant model(OR:1.36;95%CI:1.15–1.60;P=0.0003)(OR:1.22;95%CI:1.10–1.36;P=0.0002)indicated that the KCNQ1 gene rs2237895 polymorphism was significantly correlated with susceptibility to T2DM.In stratified analysis,this association was confirmed in Asian populations:allelic model(OR:1.25;95%CI:1.13–1.37;P<0.0001),recessive model(OR:1.29;95%CI:1.11–1.49;P=0.0007),dominant model(OR:1.35;95%CI:1.20–1.52;P<0.0001),codominant model(OR:1.49;95%CI:1.22–1.81;P<0.0001)(OR:1.26;95%CI:1.16–1.36;P<0.0001).In non-Asian populations,this association was not significant:Allelic model(OR:1.06,95%CI:0.98–1.14;P=0.12),recessive model(OR:1.04;95%CI:0.75–1.42;P=0.83),dominant model(OR:1.06;95%CI:0.98–1.15;P=0.15),codominant model(OR:1.08;95%CI:0.82–1.42;P=0.60.OR:1.15;95%CI:0.95–1.39;P=0.14).CONCLUSION KCNQ1 gene rs2237895 was significantly associated with susceptibility to T2DM in an Asian population.Carriers of the C allele had a higher risk of T2DM.This association was not significant in non-Asian populations. 展开更多
关键词 Type 2 diabetes mellitus KCNQ1 rs2237895 Single nucleotide polymorphism Asian populations
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Heterogeneous population distribution enhances resistance to wheat lodging by optimizing the light environment
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作者 Yibo Hu Feng Qin +6 位作者 Zhen Wu Xiaoqin Wang Xiaolong Ren Zhikuan Jia Zhenlin Wang Xiaoguang Chen Tie Cai 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2024年第7期2211-2226,共16页
Lodging is still the key factor that limits continuous increases in wheat yields today,because the mechanical strength of culms is reduced due to low-light stress in populations under high-yield cultivation.The mechan... Lodging is still the key factor that limits continuous increases in wheat yields today,because the mechanical strength of culms is reduced due to low-light stress in populations under high-yield cultivation.The mechanical properties of the culm are mainly determined by lignin,which is affected by the light environment.However,little is known about whether the light environment can be sufficiently improved by changing the population distribution to inhibit culm lodging.Therefore,in this study,we used the wheat cultivar“Xinong 979”to establish a low-density homogeneous distribution treatment(LD),high-density homogeneous distribution treatment(HD),and high-density heterogeneous distribution treatment(HD-h)to study the regulatory effects and mechanism responsible for differences in the lodging resistance of wheat culms under different population distributions.Compared with LD,HD significantly reduced the light transmittance in the middle and basal layers of the canopy,the net photosynthetic rate in the middle and lower leaves of plants,the accumulation of lignin in the culm,and the breaking resistance of the culm,and thus the lodging index values increased significantly,with lodging rates of 67.5%in 2020–2021 and 59.3%in 2021–2022.Under HD-h,the light transmittance and other indicators in the middle and basal canopy layers were significantly higher than those under HD,and the lodging index decreased to the point that no lodging occurred.Compared with LD,the activities of phenylalanine ammonia-Lyase(PAL),4-coumarate:coenzyme A ligase(4CL),catechol-O-methyltransferase(COMT),and cinnamyl-alcohol dehydrogenase(CAD)in the lignin synthesis pathway were significantly reduced in the culms under HD during the critical period for culm formation,and the relative expression levels of TaPAL,Ta4CL,TaCOMT,and TaCAD were significantly downregulated.However,the activities of lignin synthesis-related enzymes and their gene expression levels were significantly increased under HD-h compared with HD.A partial least squares path modeling analysis found significant positive effects between the canopy light environment,the photosynthetic capacity of the middle and lower leaves of plants,lignin synthesis and accumulation,and lodging resistance in the culms.Thus,under conventional high-density planting,the risk of wheat lodging was significantly higher.Accordingly,the canopy light environment can be optimized by changing the heterogeneity of the population distribution to improve the photosynthetic capacity of the middle and lower leaves of plants,promote lignin accumulation in the culm,and enhance lodging resistance in wheat.These findings provide a basis for understanding the mechanism responsible for the lower mechanical strength of the culm under high-yield wheat cultivation,and a theoretical basis and for developing technical measures to enhance lodging resistance. 展开更多
关键词 canopy light environment LIGNIN LODGING population distribution WHEAT
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Land-population-industry based village evolution and its influencing factors in the upper Tuojiang River
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作者 ZHAN Yunjun JI Yuxin +2 位作者 HUANG Jiejun MA Changying MA Chuanqi 《Journal of Mountain Science》 SCIE CSCD 2024年第8期2790-2809,共20页
With economic development and urbanization in China,the rural settlements have experienced great change.To explore the evolution process of rural settlements in terms of land,population and industry can reveal the dev... With economic development and urbanization in China,the rural settlements have experienced great change.To explore the evolution process of rural settlements in terms of land,population and industry can reveal the development law of rural spatial distribution,population structure and industrial economy in different stages and regions.Studying the development status and evolution characteristics of villages in the upper Tuojiang River basin in Southwest China in the past 20 years are of significant value.The upper Tuojiang River basin includes the main types of terrain found in the Southwest region:mountainous,plains,and hills,exhibiting a certain typicality of geographical characteristics.This study took towns and townships at the town-level scale as the basic unit of research,and constructed an evaluation system for village evolution based on'land,population,and industry'.It employed Criteria Importance Through Inter-Criteria Correlation(CRITIC)analysis to examine the characteristics of village evolution in the area from 2000 to 2020,and used geographic detector analysis to identify the leading factors affecting village evolution.The results show that:(1)From 2000 to 2010,villages in the upper Tuojiang River basin experienced significant changes,and the pace of these transformations slowed from 2010 to 2020.(2)From a comprehensive perspective,from 2000 to 2020,villages in hilly areas show a decline,while villages in plain areas near the city center show a positive urbanization development.(3)Road accessibility and distance from the city center are the main factors that explain the spatial differentiation of village evolution degree in the study area.This study elucidates the spatiotemporal evolution characteristics of villages in the upper Tuojiang River basin and identifies the primary factors contributing to their changes,which will provide a reference for investigating the development of rural areas in different terrains of Southwest China. 展开更多
关键词 Village evolution LAND population Industry Geographic detector
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Evaluation and Projection of Population Exposure to Temperature Extremes over the Beijing−Tianjin−Hebei Region Using a High-Resolution Regional Climate Model RegCM4 Ensemble
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作者 Peihua QIN Zhenghui XIE +1 位作者 Rui HAN Buchun LIU 《Advances in Atmospheric Sciences》 SCIE CAS CSCD 2024年第6期1132-1146,共15页
Temperature extremes over rapidly urbanizing regions with high population densities have been scrutinized due to their severe impacts on human safety and economics.First of all,the performance of the regional climate ... Temperature extremes over rapidly urbanizing regions with high population densities have been scrutinized due to their severe impacts on human safety and economics.First of all,the performance of the regional climate model RegCM4 with a hydrostatic or non-hydrostatic dynamic core in simulating seasonal temperature and temperature extremes was evaluated over the historical period of 1991–99 at a 12-km spatial resolution over China and a 3-km resolution over the Beijing−Tianjin−Hebei(JJJ)region,a typical urban agglomeration of China.Simulations of spatial distributions of temperature extremes over the JJJ region using RegCM4 with hydrostatic and non-hydrostatic cores showed high spatial correlations of more than 0.8 with the observations.Under a warming climate,temperature extremes of annual maximum daily temperature(TXx)and summer days(SU)in China and the JJJ region showed obvious increases by the end of the 21st century while there was a general reduction in frost days(FD).The ensemble of RegCM4 with different land surface components was used to examine population exposure to temperature extremes over the JJJ region.Population exposure to temperature extremes was found to decrease in 2091−99 relative to 1991−99 over the majority of the JJJ region due to the joint impacts of increases in temperature extremes over the JJJ and population decreases over the JJJ region,except for downtown areas.Furthermore,changes in population exposure to temperature extremes were mainly dominated by future population changes.Finally,we quantified changes in exposure to temperature extremes with temperature increase over the JJJ region.This study helps to provide relevant policies to respond future climate risks over the JJJ region. 展开更多
关键词 CMIP6 convection-permitting population exposure RegCM4 temperature extremes
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Photosynthetic response to a winter heatwave in leading and trailing edge populations of the intertidal red alga Corallina offi-cinalis(Rhodophyta)
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作者 Regina Kolzenburg Federica Ragazzola +3 位作者 Laura Tamburello Katy R.Nicastro Christopher D.McQuaid Gerardo I.Zardi 《Acta Oceanologica Sinica》 SCIE CAS CSCD 2024年第7期70-77,共8页
Marine heatwaves(MHWs)caused by anthropogenic climate change are becoming a key driver of change at the ecosystem level.Thermal conditions experienced by marine organisms across their distribution,particularly towards... Marine heatwaves(MHWs)caused by anthropogenic climate change are becoming a key driver of change at the ecosystem level.Thermal conditions experienced by marine organisms across their distribution,particularly towards the equator,are likely to approach their physiological limits,resulting in extensive mortality and subsequent changes at the population level.Populations at the margins of their species’distribution are thought to be more sensitive to climate-induced environmental pressures than central populations,but our understanding of variability in fitness-related physiological traits in trailing versus leading-edge populations is limited.In a laboratory simulation study,we tested whether two leading(Iceland)and two trailing(Spain)peripheral populations of the intertidal macroalga Corallina officinalis display different levels of maximum potential quantum efficiency(Fv/Fm)resilience to current and future winter MHWs scenarios.Our study revealed that ongoing and future local winter MHWs will not negatively affect leading-edge populations of C.officinalis,which exhibited stable photosynthetic efficiency throughout the study.Trailing edge populations showed a positive though non-significant trend in photosynthetic efficiency throughout winter MHWs exposure.Poleward and equatorward populations did not produce significantly different results,with winter MHWs having no negative affect on Fv/Fm of either population.Additionally,we found no long-term regional or population-level influence of a winter MHWs on this species’photosynthetic efficiency.Thus,we found no statistically significant difference in thermal stress responses between leading and trailing populations.Nonetheless,C.officinalis showed a trend towards higher stress responses in southern than northern populations.Because responses rest on a variety of local population traits,they are difficult to predict based solely on thermal pressures. 展开更多
关键词 marginal population coralline algae climate change ECOPHYSIOLOGY photophysiology MACROALGAE FV/FM
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Migration Networks Pattern of China’s Floating Population from the Perspective of Complex Network
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作者 LIU Wangbao CHEN Ranran 《Chinese Geographical Science》 SCIE CSCD 2024年第2期327-341,共15页
Since China’s reform and opening-up,the growing disparity between urban and rural areas and regions has led to massive migration.With China’s Rural Revitalization Strategy and the industrial transfer from the easter... Since China’s reform and opening-up,the growing disparity between urban and rural areas and regions has led to massive migration.With China’s Rural Revitalization Strategy and the industrial transfer from the eastern coastal areas to the inland,the migration direction and pattern of the floating population have undergone certain changes.Using the 2017 China Migrants Dynamic Survey(CMDS),excluding Hong Kong,Macao,and Taiwan regions of China,organized by China’s National Health Commission,the relationship matrix of the floating population is constructed according to the inflow place of the interviewees and their outflow place(the location of the registered residence)in the questionnaire survey.We then apply the complex network model to analyze the migration direction and network pattern of China’s floating population from the city scale.The migration network shows an obvious hierarchical agglomeration.The first-,second-,third-and fourth-tier distribution cities are municipalities directly under the central government,provincial capital cities,major cities in the central and western regions and ordinary cities in all provinces,respectively.The migration trend is from the central and western regions to the eastern coastal areas.The migration network has‘small world’characteristics,forming nine communities.It shows that most node cities in the same community are closely linked and geographically close,indicating that the migration network of floating population is still affected by geographical proximity.Narrowing the urban-rural and regional differences will promote the rational distribution this population.It is necessary to strengthen the reform of the registered residence system,so that the floating population can enjoy urban public services comparable to other populations,and allow migrants to live and work in peace. 展开更多
关键词 complex network floating population migration network spatial pattern community structure
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Theoretical investigations of population trapping phenomena in atomic four-color,three-step photoionization scheme
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作者 卢肖勇 孙亚鹏 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第3期333-340,共8页
The four-color three-step selective photoionization process of atom is very important in laser isotope separation technology.The population trapping phenomena and their influences are studied theoretically in monochro... The four-color three-step selective photoionization process of atom is very important in laser isotope separation technology.The population trapping phenomena and their influences are studied theoretically in monochromatic and non-monochromatic laser fields based on the density matrix theory in this work.Time evolutions of the photoionization properties of the four-color,three-step process are given.The population trapping effects occur intensely in monochromatic excitation,while it gradually turns weak as the laser bandwidth increases.The effects of bandwidth,Rabi frequency,time delay,and frequency detuning on the population trapping effect are investigated in monochromatic and non-monochromatic laser fields.The effects of laser process parameters and atomic parameters on the effective selective photoionization are also discussed.The ionization probability and selectivity factors,as evaluation indexes,are difficult to improve synchronously by adjusting systematic parameters.Besides,the existence of metastable state may play a negative role when its population is low enough. 展开更多
关键词 population trapping metastable state selective photoionization laser bandwidth
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Chromosome-level genome and population genomics of the intermediate horseshoe bat(Rhinolophus affinis)reveal the molecular basis of virus tolerance in Rhinolophus and echolocation call frequency variation
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作者 Le Zhao Jiaqing Yuan +8 位作者 Guiqiang Wang Haohao Jing Chen Huang Lulu Xu Xiao Xu Ting Sun Wu Chen Xiuguang Mao Gang Li 《Zoological Research》 SCIE CSCD 2024年第5期1147-1160,共14页
Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,... Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,and unique immune system.Advances in evolutionary biology,supported by high-quality reference genomes and comprehensive whole-genome data,have significantly enhanced our understanding of species origins,speciation mechanisms,adaptive evolutionary processes,and phenotypic diversity.However,genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data,with only a single published genome of R.ferrumequinum currently available.In this study,we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat(R.affinis).Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae.Notably,we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway,DNA repair,and apoptosis,which displayed signs of rapid evolution.In addition,we observed an expansion of the major histocompatibility complex class II(MHC-II)region and a higher copy number of the HLA-DQB2 gene in horseshoe bats compared to other chiropteran species.Based on whole-genome resequencing and population genomic analyses,we identified multiple candidate loci(e.g.,GLI3)associated with variations in echolocation call frequency across R.affinis subspecies.This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research. 展开更多
关键词 Reference-quality genome Comparative genomics population genomics Positive selection Bats
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Multi-environment BSA-seq using large F3 populations is able to achieve reliable QTL mapping with high power and resolution: An experimental demonstration in rice
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作者 Yan Zheng Ei Ei Khine +9 位作者 Khin Mar Thi Ei Ei Nyein Likun Huang Lihui Lin Xiaofang Xie Min Htay Wai Lin Khin Than Oo Myat Myat Moe San San Aye Weiren Wu 《The Crop Journal》 SCIE CSCD 2024年第2期549-557,共9页
Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq ... Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability. 展开更多
关键词 BSA-seq QTL mapping Large F3 population Multi-environment experiment Cross-validation
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The effect of Common Cuckoo parasitism on the annual productivity of a host population
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作者 Alfred Trnka 《Avian Research》 SCIE CSCD 2024年第2期287-291,共5页
Avian interspecific brood parasitism is an excellent system for studying coevolutionary processes in nature because brood parasites directly affect host reproductive success.Most research on avian brood parasitism has... Avian interspecific brood parasitism is an excellent system for studying coevolutionary processes in nature because brood parasites directly affect host reproductive success.Most research on avian brood parasitism has,therefore,focused primarily on specific host anti-parasite behaviours and parasite counter-adaptations.However,the population-level consequences of brood parasitism for host species are poorly understood.This study investigated the effect of Common Cuckoo(Cuculus canorus)parasitism on the productivity of a local population of the Great Reed Warbler(Acrocephalus arundinaceus)host in south-western Slovakia.A total of 495 females nesting at the studied site successfully fledged 1321 of their own young and 63 young of the Common Cuckoo over the course of 15 years(2008-2022),and the annual rate of successful parasitism ranged from 18% to 44% over this period.As predicted,higher rates of successful cuckoo parasitism significantly reduced the annual productivity of the local Great Reed Warbler population,and its contribution to decreased host reproductive success was at about the same rate as overall nest failure caused by predation and other environmental factors.Such a heavily parasitized population was probably maintained by immigrants from other populations and density-dependent selection,which is also consistent with source-sink dynamics.However,further long-term studies monitoring parasitized populations are required to confirm these findings. 展开更多
关键词 Acrocephalus arundinaceus Cuculus canorus Great Reed Warbler population growth Reproductive success
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Resurvey After 20 Years:Updating the Distribution,Population,and Potential Threats of the Chinting Alpine Toad
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作者 Yuezheng FAN Qingfeng CHEN +7 位作者 Yuwen CHENG Kaicheng TANG Ling SUN Yonghao HUANG Lan ZHAO Dong LIANG Xiaoyi WANG Junhua HU 《Asian Herpetological Research》 SCIE CSCD 2024年第2期73-81,共9页
Considering the increased anthropogenic impacts,species with a limited range and low detectability often lack fundamental information and conservation actions,placing them at a high risk of endangerment.The Chinting a... Considering the increased anthropogenic impacts,species with a limited range and low detectability often lack fundamental information and conservation actions,placing them at a high risk of endangerment.The Chinting alpine toad Scutiger chintingensis is a rare mountain amphibian endemic to the eastern margin of the Qinghai-Xizang Plateau in China.Within its whole distribution range,only three known populations(Wolong,Emei,and Wawu)exist and no recent population status report has been documented for this species over the past two decades.From 2020 to 2023,we investigated the species distribution,and assessed the risk factors for the main populations.We recorded this species in all distribution areas,and updated a new distribution site with a lower elevation limit.The relative population density was 0.024±0.012 ind./m^(2)on Mount Emei,whereas only 0.008±0.017 ind./m^(2)on Mount Wawu.No significant difference was observed in the number of individuals between the two populations;however,the relative population density was significantly different.Sewage and waste discharge resulting from the construction of scenic areas,as well as disturbances from tourism,were the primary anthropogenic factors that influenced the survival of this species.Our results provide the updated information on the distribution and population status of the Chinting alpine toad,and suggest that unrecorded populations,as well as a wider elevation range,may exist for this species.Our findings emphasise the importance of timely updates of species distribution and population information and offer a basis for the future conservation of endangered amphibians. 展开更多
关键词 DISTRIBUTION endemic amphibian population size Scutiger chintingensis threat factor
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Standardization of meibomian gland dysfunction in an Egyptian population sample using a non-contact meibography technique
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作者 Ahmed Mohamed Karara Zeinab El-Sanabary +2 位作者 Mostafa Ali El-Helw Tamer Ahmed Macky Mohamad Amr Salah Eddin Abdelhakim 《International Journal of Ophthalmology(English edition)》 SCIE CAS 2024年第1期61-65,共5页
AIM:To develop normative data for meibomian gland dysfunction(MGD)parameters,using non-contact meibography technique of Sirius Costruzione Strumenti Oftalmici(CSO)machine,in an Egyptian population sample.METHODS:Obser... AIM:To develop normative data for meibomian gland dysfunction(MGD)parameters,using non-contact meibography technique of Sirius Costruzione Strumenti Oftalmici(CSO)machine,in an Egyptian population sample.METHODS:Observational,cross-sectional,analytic study,in which 104 Egyptian volunteers were included.Both upper lids were examined,using“Sirius CSO”machine.Each eyelid was given a degree of meibomian gland loss(MGL),which was calculated by the software of the machine.RESULTS:Mean percentage MGL in right upper lid was of 30.9%±12.6%,and that of left upper lid was 32.6%±11.8%.Thirty-four volunteers(32.7%)had first-degree MGL in their right upper lid,and 67.3%had second-degree loss.One volunteer(1%)had zero-degree MGL in left upper lid,28(26.9%)had first-degree loss,and 75(72.1%)had second-degree loss.Degree of MGL in right upper eyelid was not related to age,but degree of MGL in left upper eyelid increased with age.There was statistically significant difference between both genders for degree of MGL in right eye(P=0.036)and in left eye(P=0.027).CONCLUSION:Noncontact meibography is a useful non-invasive tool for diagnosing MGL.MGL is diagnosed in 100%of apparently normal individuals;26.9%-32.7%of which have first-degree MGL,and 67.3%-72.1%have second-degree MGL. 展开更多
关键词 Egyptian population meibomian gland dysfunction non-contact meibography STANDARDIZATION upper lid
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Increased population exposures to extreme precipitation in Central Asia under 1.5℃ and 2℃ global warming scenarios
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作者 Wei Wei Shan Zou +4 位作者 Weili Duan Yaning Chen Shuai Li Takahiro Sayama Jianyu Zhu 《Geography and Sustainability》 CSCD 2024年第3期343-356,共14页
The increase in extreme precipitation(EP)may pose a serious threat to the health and safety of population in arid and semi-arid regions.The current research on the impact of EP on population in Central Asia(CA)is insu... The increase in extreme precipitation(EP)may pose a serious threat to the health and safety of population in arid and semi-arid regions.The current research on the impact of EP on population in Central Asia(CA)is insufficient and there is an urgent need for a comprehensive assessment.Hence,we opted for precipitation and temperature data under two Shared Socioeconomic Pathways(SSP2-4.5 and SSP5-8.5)from ten Global Climate Models(GCMs),which were obtained from the NASA Earth Exchange Global Daily Downscaled Projections(NEX-GDDP-CMIP6).By integrating population data in 2020 and 2050(SSP2 and SSP5),we investigated the future changes in EP and population exposure in CA under 1.5℃and 2℃global warming scenarios(GWSs).Our analysis indicates that EP in CA is projected to increase with global warming.Under the SSP5-8.5,the maximum daily precipitation(Rx1day)exhibits an average response rate to global warming of 3.58%/K(1.99-4.06%/K).With rising temperatures,an increasing number of areas and populations in CA will be impacted by EP,especially in the Fergana valley.Approximately 25%of the population(land area)in CA is exposed to Rx1day with increases of more than 8.31%(9.32%)under 1.5℃GWS and 14.18%(13.25%)under 2℃GWS.Controlling temperature rise can be effective in reducing population exposures to EP.For instance,limiting the temperature increase to 1.5℃instead of 2℃results in a 2.79%(1.75%-4.59%)reduction in population exposure to Rx1day.Finally,we found that climate change serves as the predominant factor influencing the population exposure to EP,while the role of population redistribution,although relatively minor,should not be disregarded.Particularly for prolonged drought,the role of population redistribution manifests negatively. 展开更多
关键词 Extreme precipitation Global warming population exposure Central Asia
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An Enhanced Multiview Transformer for Population Density Estimation Using Cellular Mobility Data in Smart City
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作者 Yu Zhou Bosong Lin +1 位作者 Siqi Hu Dandan Yu 《Computers, Materials & Continua》 SCIE EI 2024年第4期161-182,共22页
This paper addresses the problem of predicting population density leveraging cellular station data.As wireless communication devices are commonly used,cellular station data has become integral for estimating populatio... This paper addresses the problem of predicting population density leveraging cellular station data.As wireless communication devices are commonly used,cellular station data has become integral for estimating population figures and studying their movement,thereby implying significant contributions to urban planning.However,existing research grapples with issues pertinent to preprocessing base station data and the modeling of population prediction.To address this,we propose methodologies for preprocessing cellular station data to eliminate any irregular or redundant data.The preprocessing reveals a distinct cyclical characteristic and high-frequency variation in population shift.Further,we devise a multi-view enhancement model grounded on the Transformer(MVformer),targeting the improvement of the accuracy of extended time-series population predictions.Comparative experiments,conducted on the above-mentioned population dataset using four alternate Transformer-based models,indicate that our proposedMVformer model enhances prediction accuracy by approximately 30%for both univariate and multivariate time-series prediction assignments.The performance of this model in tasks pertaining to population prediction exhibits commendable results. 展开更多
关键词 population density estimation smart city TRANSFORMER multiview learning
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A Population Dynamics Approach to the Distribution of Space Debris in Low Earth Orbit
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作者 John Jurkiewicz Peter Hinow 《Communications on Applied Mathematics and Computation》 EI 2024年第1期340-353,共14页
The presence of the debris in the Earth’s orbit poses a significant risk to human activity in outer space.This debris population continues to grow due to ground launches,the loss of external parts from space ships,an... The presence of the debris in the Earth’s orbit poses a significant risk to human activity in outer space.This debris population continues to grow due to ground launches,the loss of external parts from space ships,and uncontrollable collisions between objects.A computationally feasible continuum model for the growth of the debris population and its spatial distribution is therefore critical.Here we propose a diffusion-collision model for the evolution of the debris density in the low-Earth orbit and its dependence on the ground-launch policy.We parametrize this model and test it against data from publicly available object catalogs to examine timescales for the uncontrolled growth.Finally,we consider sensible launch policies and cleanup strategies and how they reduce the future risk of collisions with active satellites or space ships. 展开更多
关键词 population dynamics Space debris Kessler syndrome DIFFUSION Low-Earth orbit
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Dependence of Rydberg-atom-based sensor performance on different Rydberg atom populations in one atomic-vapor cell
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作者 武博 姚佳伟 +2 位作者 吴逢川 安强 付云起 《Chinese Physics B》 SCIE EI CAS CSCD 2024年第2期365-370,共6页
The atomic-vapor cell is a vital component for Rydberg atomic microwave sensors,and impacts on overall capability of Rydberg sensors.However,the conventional analysis approach on effect of vapor-cell length contains t... The atomic-vapor cell is a vital component for Rydberg atomic microwave sensors,and impacts on overall capability of Rydberg sensors.However,the conventional analysis approach on effect of vapor-cell length contains two implicit assumptions,that is,the same atomic population density and buffer gas pressure,which make it unable to accurately capture actual response about effect of Rydberg-atom-based sensor performance on different Rydberg atom populations.Here,utilizing a stepped cesium atomic-vapor cell with five different dimensions at the same atomic population density and buffer gas pressure,the height and full width at half maximum of electromagnetically induced transparency(EIT)signal,and the sensitivity of the atomic superheterodyne sensor are comprehensively investigated under conditions of the same Rabi frequencies(saturated laser power).It is identified that EIT signal height is proportional to the cell length,full width at half maximum and sensitivity grow with the increment of cell length to a certain extent.Employing the coherent integration signal theory and atomic linear expansion coefficient method,theoretical analysis of the EIT height and sensitivity are further investigated.The results could shed new light on understanding and design of ultrahigh-sensitivity Rydberg atomic microwave sensors and find promising applications in quantum measurement,communication,and imaging. 展开更多
关键词 Rydberg atom population Rydberg-atom-based receiver stepped atomic-vapor cell
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