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Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

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Journal of Animal Science and Biotechnology 2024年第1期15卷 88-107页

作者： Guangliang Gao Hongmei Zhang Jiangping Ni Xianzhi Zhao Keshan Zhang Jian Wang Xiangdong Kong Qigui Wang Chongqing Academy of Animal Science Rongchang DistrictChongqing 402460China Livestock and Poultry Multi‑Omics Key Laboratory of Ministry of Agriculture and rural Affairs College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130China Chongqing engineering Research Center of Goose Genetic Improvement Rongchang DistrictChongqing 402460China department of Cardiovascular Ultrasound and Non‑Invasive Cardiology Sichuan Academy of Medical Sciences and Sichuan Provincial People’s HospitalUniversity of Electronic Science and Technology of ChinaChengdu611731China Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province University of Electronic Science and Technology of ChinaChengdu611731China JiguangGene Biotechnology Co. Ltd.Nanjing210032China Jiangsu Agri-Animal Vocational College Taizhou225300China Poultry Science Institute Chongqing Academy of Animal ScienceNo.51 Changzhou AvenueRongchang DistrictChongqing 402460P.R.China

Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic *** a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic *** To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq *** constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose ***,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among ***-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition *** instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique ***,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild *** study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple orga

关键词： Gene-CDS haplotype Goose GWAS Pan-genome Presence-absence variation Selection signal

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Uphill or downhill?Cropland use change and its drivers from the perspective of slope spectrum

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Journal of Mountain Science 2024年第2期21卷 484-499页

作者： PAN Sipei LIANG Jiale CHEN Wanxu PENG Yelin College of Land Management Nanjing Agricultural UniversityNanjing 210095China National&Local Joint engineering Research Center for rural Land Resources Use and Consolidation Nanjing 210095China Jiangsu Provincial Key Laboratory of Geographic Information Technology School of Geography and Ocean ScienceNanjing UniversityNanjing 210023China Key Laboratory of Natural Resources Monitoring and Supervision in Southern Hilly Region Ministry of Natural ResourcesChangsha 410118China Yunnan Key Laboratory of Plateau Geographic Processes and Environmental Changes Faculty of GeographyYunnan Normal UniversityKunming 650500China Hubei Key Laboratory of Regional Ecology and Environmental Change School of Geography and Information EngineeringChina University of GeosciencesWuhan 430074China

The continuous decrease of low-slope cropland resources caused by construction land crowding poses huge threat to regional sustainable development and food *** spectrum analysis of topographic and geomorphic features is considered as a digital terrain analysis method which reflects the macro-topographic features by using micro-topographic ***,pieces of studies have extended the concept of slope spectrum in the field of geoscience to construction land to explore its expansion law,while research on the slope trend of cropland from that perspective remains *** address the gap,in virtue of spatial analysis and geographically weighted regression(GWR)model,the cropland use change in the Yangtze River Basin(YRB)from 2000 to 2020 was analyzed and the driving factors were explored from the perspective of slope *** showed that the slope spectrum curves of cropland area-frequency in the YRB showed a first upward then a downward *** change curve of the slope spectrum of cropland in each province(municipality)exhibited various distribution *** analysis of morphological parameters of cropland slope spectrum revealed that the further down the YRB,the stronger the flattening characteristics,the more obvious the *** province experienced the greatest downhill cropland climbing(CLC)was Shannxi,while province experienced the highest uphill CLC was *** most common cropland use change type in the YRB was horizontal expansion *** factors affecting average cropland climbing index(ACCI)were quite stable in different periods,while population density(POP)changed from negative to positive during the study *** research is of practical significance for the rational utilization of cropland at the watershed scale.

关键词： Cropland climbing Land use change Slope spectrum Driving factors geographically weighted regression Yangtze River Basin

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Factors affecting land dissection density in geomorphological regions of China

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Journal of Mountain Science 2024年第4期21卷 1372-1387页

作者： SUN Xiaolin ZHAO Yinjun PENG Peihao CHENG Weiming WEI Yongping YANG Ronghao LI Jiaxu College of Earth sciences Chengdu University of TechnologyChengdu 610059China School of Civil engineering Guangxi Polytechnic of ConstructionNanning 530001China Key Laboratory of Environment Change and Resources Use in Beibu Gulf Ministry of EducationNanning Normal UniversityNanning 530001China Key Laboratory of Earth Surface Process and Intelligent Simulation(Guangxi) Nanning Normal UniversityNanning 530001China State Key Laboratory of Resources and Environmental Information System Institute of Geographic Sciences and Natural Resources ResearchCASBeijing 100101China School of Earth and Environmental sciences The University of QueenslandBrisbane 4702Australia School of Geography and Planning Nanning Normal UniversityNanning 530001China

Land dissection density(LDD)provides morphological evidence regarding prior intense soil erosion and quantifies the distribution of land dissections.A comprehensive understanding of the potential factors influencing the spatial pattern and value of the LDD is vital in geological disasters,soil erosion,and other related *** dissection phenomena in China affects large areas with different morphological,pedological,and climatic *** studies have focused on the potential factors influencing the LDD at a watershed ***,these results are insufficient to reflect the status quo of dissection development and its primary influencing factors on a national ***’s spatial patterns and the dominant factors at a regional scale in millions of square kilometers remain to be *** study used the geomorphon-based method and the geographical detector model to quantify the spatial pattern of LDD over China and identify the dominant factors affecting this pattern in China’s six first-order geomorphological regions(GR1~GR6).The results yield the following findings:(1)LDD in China ranges from 0~4.55 km/km^(2),which is larger in central and eastern regions than in other regions of China;(2)dominant factors and their dominant risk subcategories vary with each geomorphological region’s primary internal and external forces;(3)the influence of natural factors is more significant on the large regional scale in millions of square kilometers compared to anthropogenic factors;relief degree of land surface(RDLS)is dominant in GR1,GR2,and GR5;the slope is dominant in GR6,soil type is dominant in GR3 and GR4,and lithology plays a critical role in the dominant interactions of GR3,GR4,and GR6;(4)the interactions between factors on LDD’s spatial pattern have a more significant effect than individual factors.

关键词： Land dissection density Influencing factors Regional scale Spatial pattern geographical detector model Geomorphon-based method China

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Optimizing Spatial Pattern Analysis in Serial Remote Sensing Images through Empirical Mode Decomposition and Ant Colony Optimization

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Journal of Harbin Institute of Technology(New Series) 2024年第4期31卷 52-60页

作者： J Srinivasan S Uma Saleem Raja Abdul Samad Jayabrabu Ramakrishnan department of Computer Applications Madanapalle Institute of Technology&Science(MITS)Madanapalle 517325Andhra PradeshIndia department of Information Technology Panimalar Engineering CollegeChennai 600123India Information Technology department College of Computing and Information SciencesUniversity of Technology and Applied Sciences-Shinas 324Sultanate of Oman department of Information Technology and Security College of Computer Science and Information TechnologyJazan UniversityJazan 45142Kingdom of Saudi Arabia

Serial remote sensing images offer a valuable means of tracking the evolutionary changes and growth of a specific geographical area over *** the original images may provide limited insights,they harbor considerable potential for identifying clusters and *** aggregation of these serial remote sensing images(SRSI)becomes increasingly viable as distinct patterns emerge in diverse scenarios,such as suburbanization,the expansion of native flora,and agricultural *** a novel approach,we propose an innovative method for extracting sequential patterns by combining Ant Colony Optimization(ACD)and Empirical Mode Decomposition(EMD).This integration of the newly developed EMD and ACO techniques proves remarkably effective in identifying the most significant characteristic features within serial remote sensing images,guided by specific *** findings highlight a substantial improvement in the efficiency of sequential pattern mining through the application of this unique hybrid method,seamlessly integrating EMD and ACO for feature *** study exposes the potential of our innovative methodology,particularly in the realms of urbanization,native vegetation expansion,and agricultural activities.

关键词： spatial pattern analysis EMD ACO

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Genetic diversity of RNA viruses infecting invertebrate pests of rice

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Science China(Life sciences) 2024年第1期67卷 175-187页

作者： Haoran Wang Shufen Chao Qing Yan Shu Zhang Guoqing Chen Chonghui Mao Yang Hu Fengquan Yu Shuo Wang Liang Lv Baojun Yang Jiachun He Songbai Zhang Liangsheng Zhang Peter Simmonds Guozhong Feng State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 311400China State Key Laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Institute of Plant Protection&Soil Fertilizer Hubei Academy of Agricultural SciencesWuhan 430064China Institute of Plant Protection Guizhou Academy of Agricultural SciencesGuiyang 550000China Institute of Plant Protection Liaoning Academy of Agricultural SciencesShenyang 110161China Sanya Agricultural Technology Extension and Service Centre Sanya 572000China College of Agriculture Yangtze UniversityJingzhou 434000China Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry UniversityFuzhou 350002China Genomics and Genetic engineering Laboratory of Ornamental Plants College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310012China Nuffield department of Medicine Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxford OX13SYUnited Kingdom

Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop ***,information on viruses infecting invertebrate pests of crops is *** this report,we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice *** identified 296 new RNA viruses and 13 known RNA *** viruses clustered within 31 families,with many highly divergent viruses constituting potentially new families and *** the identified viruses,13 RNA viruses clustered within the Fiersviridae family of bacteriophages,and 48 RNA viruses clustered within families and genera of *** detected known rice viruses in novel invertebrate hosts at high ***,some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus *** potential insect pathogenic RNA viruses were detected in invertebrate *** analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral ***-species transmission of RNA viruses was detected between invertebrate *** identified viral genomes showed extensive variation for invertebrate viral families or ***,the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species,the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

关键词： invertebrate species metatranscriptome viral diversity viral transmission viral genomes

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小浪底水库运用以来黄河下游时空冲淤规律与模拟

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Journal of geographical sciences 2024年第3期34卷 591-609页

作者：沈逸吴保生王彦君覃超郑珊 State Key Laboratory of Hydroscience and engineering Tsinghua UniversityBeijing100084China Key Laboratory of Hydrosphere sciences of the Ministry of Water Resources Tsinghua UniversityBeijing100084China department of Hydraulic engineering Tsinghua UniversityBeijing100084China Key Laboratory of River Regulation and Flood Control of Ministry of Water Resources Yangtze River Scientific Research InstituteWuhan430010China State Key Laboratory of Water Resources and Hydropower engineering Science Wuhan UniversityWuhan430072China

This study focuses on the Lower Yellow River(LYR),which has experienced continuous erosion since the operation of Xiaolangdi Reservoir in 1999,and its spatiotemporal variation process is *** on the single-step mode of the Delayed Response Model(DRM),we proposed a calculation method for simulating the accumulated erosion and deposition volume in the *** coefficient of determination R^(2)between the calculated and measured values from 2000 to 2020 is ***,the LYR is undergoing continuous erosion,however the erosion rate is gradually slowing down,and the difference between the equilibrium and calculated values of accumulated erosion and deposition volume gradually decreases,which means riverbed erosion has a tendency towards ***,we derive a formula to simulate the spatial distribution of the main channel accumulated erosion volume per unit river length in the LYR based on the non-equilibrium suspended sediment transport *** coefficient of determination R^(2)between the fitted values and measured values from 2003 to 2015 is approximately 0.98-0.99,with a relative error of approximately 6.2%.The findings in this research suggest that under the current background of decreasing sediment inflow and continuous erosion in the LYR,it takes approximately 3.0 years for the riverbed to achieve half of the erosion and deposition adjustment and approximately 13.0 years to achieve 95%of the ***,the spatial distribution of accumulated main channel erosion volume in the LYR tends to become uniform with the continuous development of *** results could provide a valuable reference for analysing the complex spatiotemporal variation process in the LYR.

关键词： Lower Yellow River erosion and deposition adjustment Delayed Response Model non-equilibrium sediment transport equation

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Influenza and pneumococcal vaccination coverage and associated factors in patients hospitalized with acute exacerbations of COPD in China:Findings from real-world data

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Chinese Medical Journal 2024年第10期137卷 1179-1189页

作者： Ruoxi He Xiaoxia Ren Ke Huang Jieping Lei Hongtao Niu Wei Li Fen Dong Baicun Li Ye Wang Ting Yang Chen Wang School of Population Medicine and Public Health Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China department of Respiratory Medicine National Key Clinical SpecialtyBranch of National Clinical Research Center for Respiratory DiseaseXiangya HospitalCentral South UniversityChangshaHunan 410008China department of Pulmonary and Critical Care Medicine Center of Respiratory MedicineChina-Japan Friendship HospitalBeijing 100029China Institute of Respiratory Medicine Chinese Academy of Medical SciencesBeijing 100029China National Center for Respiratory Medicine Beijing 100029China National Clinical Research Center for Respiratory Diseases Beijing 100029China department of Clinical Research and Data Management Center of Respiratory MedicineChina-Japan Friendship HospitalBeijing 100029China

Background:Influenza and pneumococcal vaccination are a priority in patients with chronic obstructive pulmonary disease(COPD).However,limited information is available on vaccination coverage among patients with acute exacerbations of COPD(AECOPD)in *** study aimed to determine the rates and associated factors of influenza and pneumococcal vaccination in patients hospitalized with ***:Baseline data from a national,multicenter,hospital-based study that included adult inpatients with AECOPD between 2017 and 2021 were *** outcomes of interest were the influenza vaccination in the past year and the pneumococcal vaccination in the past 5 *** ensure national representativeness,rates were weighted according to the distribution of hospital levels and types enrolled in this *** Poisson regression based on mixed-effects models were used to determine the associated *** independent variables included the region and hospital features where the participants were located,sociodemographic characteristics(age,sex,rural/urban residence,education,etc.),and clinical indicators(COPD disease history,lung function parameters,comorbidities,etc.).The treatment profiles of the vaccinated and unvaccinated participants were ***:Of 6949 eligible participants,the weighted rates of influenza/pneumococcal,influenza,and pneumococcal vaccination were 2.72%(95%confidence interval[CI]:2.34%-3.10%),2.09%(95%CI:1.76%-2.43%),and 1.25%(95%CI:0.99%-1.51%),*** multivariable models,age≥60 years(60-69 years,odds ratio[OR]:1.90,95%CI:1.11-3.25;≥80 years,OR:2.00,95%CI:1.06-3.78),geographical regions(Northern China relative to Eastern China,OR:5.09,95%CI:1.96-13.21),urban residence(OR:1.69,95%CI:1.07-2.66),a higher education level(junior high school,OR:1.77,95%CI:1.21-2.58;senior high school or above,OR:2.61,95%CI:1.69-4.03),former smoking(OR:1.79,95%CI:1.15-2.79),and regular inhaled medication treatment(OR:3.28,95%CI:2.29-4.70)were

关键词： Chronic obstructive pulmonary disease Influenza Pneumococcal Vaccine AECOPD

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Outage Probability Analysis for D2D-Enabled Heterogeneous Cellular Networks with Exclusion Zone:A Stochastic Geometry Approach

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工程与科学中的计算机建模(英文) 2024年第1期138卷 639-661页

作者： Yulei Wang Li Feng Shumin Yao Hong Liang Haoxu Shi Yuqiang Chen School of Computer Science and engineering Macao University of Science and TechnologyTaipaMacaoChina department of Broadband Communication Peng Cheng LaboratoryShenzhenChina School of Artificial Intelligence Dongguan PolytechnicDongguanChina

Interference management is one of the most important issues in the device-to-device(D2D)-enabled heterogeneous cellular networks(HetCNets)due to the coexistence of massive cellular and D2D devices in which D2D devices reuse the cellular *** alleviate the interference,an efficient interference management way is to set exclusion zones around the cellular *** this paper,we adopt a stochastic geometry approach to analyze the outage probabilities of cellular and D2D users in the D2D-enabled *** main difficulties contain three aspects:1)how to model the location randomness of base stations,cellular and D2D users in practical networks;2)how to capture the randomness and interrelation of cellular and D2D transmissions due to the existence of random exclusion zones;3)how to characterize the different types of interference and their impacts on the outage probabilities of cellular and D2D *** then run extensive Monte-Carlo simulations which manifest that our theoretical model is very accurate.

关键词： Device-to-device(D2D)-enabled heterogeneous cellular networks(HetCNets) exclusion zone stochastic geometry(SG) Matérn hard-core process(MHCP)

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Effect of temperature on mudstone disintegration process revealed with image analysis

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Journal of Mountain Science 2022年第7期19卷 2126-2135页

作者： YAN Luo-bin Srdjan PETROVIC HUANG Cheng XIE Chun-xia ZONG Hui-ming Milica KASANIN-GRUBIN School of geographical sciences Southwest UniversityChongqing400715China Danxia Landscape Research Institute Shaoguan512330China Institute of Chemistry Technology and MetallurgyDepartment of Catalysis and Chemical Engineering and Center for Environmental Chemistry and EngineeringUniversity of BelgradeBelgrade11000Serbia School of geographical and Planning Sun Yat-sen UniversityGuangzhou410275China

Quantifying rock weathering processes,especially in ways of nondisturbance and on-site investigation,is one of the most critical tasks in predicting rocks erosion rates and understanding the sediment *** proposed a more reproducible approach to test how image analysis can quantify the changes in the size and shape of fragments during the weathering *** artificial models were designed to select suitable metrics among over 20 *** validate the efficiency of image analysis,we analyzed rocks from badlands in Nanxiong Basin,Southeast China,under three different ranges of temperature differences(TD)during cyclic wetting and drying(WD).Our results show that TDs can accelerate the disintegration rate,and even if there is only a 20℃ difference in the range of TDs,an apparent difference in fragment size was ***,the shape of fragments became more round as the increasing number of cyclic treatments,and for samples that went through the same number of treatments,the larger the temperature difference,the more round the shape *** that serves as another evidence for landscape evolution response to climatic warming.

关键词： Mechanical weathering Temperature effect Quantifying weathering rates Fragment size Fragment shape

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What control the spatial patterns and predictions of runoff response over the contiguous USA?

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Journal of geographical sciences 2024年第7期34卷 1297-1322页

作者： JIANG Shanhu DU Shuping REN Liliang GONG Xinglong YAN Denghua YUAN Shanshui LIU Yi YANG Xiaoli XU Chongyu The National Key Laboratory of Water Disaster Prevention Hohai UniversityNanjing210098China College of Hydrology and Water Resources Hohai UniversityNanjing210098China School of Water Conservancy&Civil engineering Northeast Agricultural UniversityHarbin150030China department of Water Resources China Institute of Water Resources and Hydropower ResearchBeijing100038China department of Geosciences University of OsloOsloNorway

Understanding the nonlinear relationship between hydrological response and key factors and the cause behind this relationship is vital for water resource management and earth system *** this study,we undertook several steps to explore the ***,we partitioned runoff response change(RRC)into multiple components associated with climate and catchment properties,and examined the spatial patterns and smoothness indicated by the Moran's Index of RRC across the contiguous United States(CONUS).Subsequently,we employed a machine learning model to predict RRC using catchment attribute predictors encompassing climate,topography,hydrology,soil,land use/cover,and ***,we identified the primary factors influencing RRC and quantified how these key factors control RRC by employing the accumulated local effect,which allows for the representation of not only dominant but also secondary ***,we explored the relationship between ecoregion patterns,climate gradients,and the distribution of RRC across *** findings indicate that:(1)RRC demonstrating significant connections between catchments tends to be well predicted by catchment attributes in space;(2)climate,hydrology,and topography emerge as the top three key attributes nonlinearly influencing the RRC patterns,with their second-order effects determining the heterogeneous patterns of RRC;and(3)local Moran's I signifies a collaborative relationship between the patterns of RRC and their spatial smoothness,climate space,and ecoregions.

关键词： hydrological response prediction machine learning accumulated local effect Moran’s Index large-sample study

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