Deep genome skimming(DGS)has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses.However,its reliability with low DNA quality and quantity typical of archival spe...Deep genome skimming(DGS)has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses.However,its reliability with low DNA quality and quantity typical of archival specimens,such as herbarium material,remains largely unexplored.We used Rhododendron as a case study to evaluate best practices for DGS in phylogenetic analyses at both deep and shallow scales.We first investigated locus recovery variation with sequencing depth,before evaluating the phylogenetic utility of different sets of loci,including Angiosperms353,target nuclear exons,and extended exon-flanking regions.We found DGS effectively recovered nuclear genes from herbarium specimens,with~15coverage performing similarly to deeper sequencing.The recovery of target exon and flanking regions was improved by using supercontigs as a reference,offering a potential solution to limited sequencing depth.The high-integrity nuclear sequences recovered robust phylogenetic relationships within Rhododendron.Notably,exon-flanking regions showed significant potential for resolving relationships at shallow scales.Genes recovered with taxon-specific references had less missing data than those recovered by Angiosperms353 and generated higher-resolution phylogenetic trees.This study demonstrates the utility of DGS data for obtaining numerous nuclear genes from herbarium specimens for phylogenetic studies,and makes recommendations for best practices regarding sequencing coverage,locus selection,and bioinformatic approaches.展开更多
The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main...The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main lineages,especially deep phylogenies,remain largely unresolved.In this study,we used genome-skimming,plastome assembly,and single-copy orthologs(SCOs)from 66 Salix accessions,along with publicly available plastome and sequence read archive(SRA)datasets to obtain a robust backbone phylogeny of Salix,clarify relationships between its main lineages,and gain a more precise understanding of the origin and diversification of this species-rich genus.The plastome and SCO datasets resolved Salix into two robust clades,with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies.Our results support the classification of Salix into five subgenera:Salix,Urbaniana,Triandrae,Longifoliae and Vetrix.We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade,while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene.These changes coincided with contemporaneous tectonic and climate change events.Our results provide a foundation for future systematic and evolutionary studies of Salix.Additionally,we showed that genome skimming data is an efficient,rapid,and reliable approach for obtaining extensive genomic data for phylogenomic studies,enabling the comprehensive elucidation of Salix relationships.展开更多
In order to make the slag from desulphurization and slag skimming(SDSS)to be comprehensively recycled and utilized,a combined process of beneficiation and building materials preparation was proposed to recover iron fr...In order to make the slag from desulphurization and slag skimming(SDSS)to be comprehensively recycled and utilized,a combined process of beneficiation and building materials preparation was proposed to recover iron from SDSS,meanwhile to apply the remaining slag tailings as cement admixture.From this process,three iron-rich products were recovered in stages by clean gravity-magnetic separation,slag tailings were left.Slag powder was prepared by ultrafine grinding of slag tailings.The stability,setting time and cement mortar strength of the slag tailings cements(STC)which were mixed with Portland cement and slag powder were studied respectively.The results showed that a proper overall performance still could be obtained at the slag powder content of 30%.Chemical composition analysis,X-ray diffraction(XRD)analysis,metallographic microscope and scanning electron microscope(SEM)analysis were employed to assess the characteristics of the SDSS and the products obtained from the whole process.The results indicated that the three iron-rich products could be used as a raw material for steelmaking and ironmaking and the relatively large amount of calcium silicate(C_(2)S)and tricalcium silicate(C_(3)S)in the slag tailings make the addition of slag powder into the Portland cement feasible.展开更多
Celtis is a Cannabaceae genus of 60e70 species of trees,or rarely shrubs,commonly known as hackberries.This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mam...Celtis is a Cannabaceae genus of 60e70 species of trees,or rarely shrubs,commonly known as hackberries.This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals.Although previous studies have identified its phylogenetic position,interspecific relationships within Celtis remain unclear.In this study,we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources.The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp,with a typical angiosperm quadripartite structure,and encoded a total of 132 genes with 20 duplicated in the IRs.Comparative analyses showed that plastome content and structure were relatively conserved.Whole plastomes showed no signs of gene loss,translocations,inversions,or genome rearrangement.Six plastid hotspot regions(trnH-psbA,psbA-trnK,trnG-trnR,psbC-trnS,cemA-petA and rps8-rpl14),4097 polymorphic nuclear SSRs,as well as 62 low or single-copy gene fragments were identified within Celtis.Moreover,the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C.biondii as sister to the((((C.koraiensis,C.sinensis),C.tetrandra),C.julianae),C.cerasifera)clade.These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny,population genetics,and conservation biology.展开更多
This paper has proposed a new modelling and simulating technique for the echo of the semi-active radar seeker against the sea skimming target. The echo modelling is based on the electromagnetic scattering mechanisms. ...This paper has proposed a new modelling and simulating technique for the echo of the semi-active radar seeker against the sea skimming target. The echo modelling is based on the electromagnetic scattering mechanisms. A modified Four-path model based on the radar detection scene is used to describe the multipath scattering between the target and rough sea surface. A Facet-based Small Slope Approximation (FBSSA) method is employed to calculate the scattering from the sea surface. The Physical Optics (PO) and the Equivalent Edge Current (EEC) Method is used to calculate the target scattering. In the echo simulations. The results present the original echo and the echo processed by the signal processing procedures, where the clutter and multipath effect can be observed.展开更多
This paper deals with some aspects of the air entrainment process along the chute of spillway and study of pressure fluctuations. The experimental study has been carried out using stepped spillway model located in the...This paper deals with some aspects of the air entrainment process along the chute of spillway and study of pressure fluctuations. The experimental study has been carried out using stepped spillway model located in the campus of Government College of Engineering, Amravati (India). It is observed that air concentration is increasing with discharge as well as with number of step. Air concentration is increasing along the length of spillway. It is also observed that the bottom mean air concentration increases with step height in the upstream reach of stepped spillway, which is prone to cavitation. The pressure profiles exhibit a wavy pattern down the stepped chute and pressure on each step increases with ratio of critical depth to step height (yc/h).展开更多
As a widely used flood energy dissipator, the stepped spillway can significantly dissipate the kinetic or hydraulic energy due to the air-entrainment in skimming flow over the steps. The free-surface aeration involves...As a widely used flood energy dissipator, the stepped spillway can significantly dissipate the kinetic or hydraulic energy due to the air-entrainment in skimming flow over the steps. The free-surface aeration involves the sharp deformation of the free surface and the complex turbulent shear flows. In this study, the volume of fluid （VOF）, mixture, and Eulerian methods are utilized to simulate the air-entrainment by coupling with the Reynolds-averaged Navier-Stokes/large eddy simulation （RANS/LES） turbulence models. The free surface deformation, air volume fraction, pressure, and velocity are compared for the three different numerical methods. Only the Eulerian＋RANS method fails to capture the free-surface aeration. The air volume fraction predicted by the VOF＋LES method best matches the experimental measurement, while the mixture＋LES method predicts the inception point of the air entrainment more accurately.展开更多
This paper illustrates the similarity and dissimilarity between two basic reading skills- skimming and scanning from different ways.It advises readers to understand and make full use of them in their everyday reading....This paper illustrates the similarity and dissimilarity between two basic reading skills- skimming and scanning from different ways.It advises readers to understand and make full use of them in their everyday reading.They will make reading easier and help improve reading comprehension to a certain extent.展开更多
The genus Clematis(Ranunculaceae)comprises over 300 species with remarkable morphological and ecological diversity worldwide.Despite its horticultural,medicinal,and ecological importance,a well-resolved phylogeny and ...The genus Clematis(Ranunculaceae)comprises over 300 species with remarkable morphological and ecological diversity worldwide.Despite its horticultural,medicinal,and ecological importance,a well-resolved phylogeny and coherent infrageneric classification are still lacking.Here,we reconstruct a robust phylogeny for Clematis using a phylogenomic approach and revise its infrageneric taxonomy.We incorporated 198 samples representing 151 species,two subspecies,and 12 varieties,covering all subgenera and most sections worldwide,obtained from both fresh and herbarium material.Nuclear single nucleotide polymorphisms(SNPs)and complete plastid genomes were assembled for phylogenetic analyses.We also prepared a nuclear ribosomal ITS(nrITS)dataset comprising 171 species,two subspecies,and 12 varieties(217 samples)to include as many species as possible for phylogenetic inference.Phylogenies based on plastid genomes and nrITS exhibited limited resolution and modest support,highlighting challenges in resolving certain relationships.Nuclear SNP analyses yielded a robust phylogenetic tree with 22 well-supported clades corresponding to 22 sections,with most previously recognized subgenera and sections not recovered as monophyletic.Ancestral state reconstruction of 12 key morphological characters revealed multiple independent origins of character states.This study presents the first comprehensive sectional classification for Clematis based on robust phylogenomic evidence,redefines morphological characteristics for each section,and resolves long-standing taxonomic ambiguities.Our results establish a framework for future studies on the evolution,ecology,and horticultural potential of this globally significant genus.展开更多
Numerical simulation of stepped channel flow was conducted using turbulence models based on the VOF technique. Stepped channel flow is a complicated air-water two-phase flow with free surface, which can be divided int...Numerical simulation of stepped channel flow was conducted using turbulence models based on the VOF technique. Stepped channel flow is a complicated air-water two-phase flow with free surface, which can be divided into three flow regimes： skimming flow, nappe flow and transition flow. The characteristics of skimming flow over mild stepped channel was investigated, including friction factors, air concentration profiles velocity field, clear-water and bulked depths, static pressure, etc. Smooth channel flow was also simulated to compare the hydraulic characteristics of the stepped channel flow with the smooth one. Comparisons between the computed and the measured were made. Furthermore, comparison of the computed air concentration with Straub and Anderson＇s data was also performed. The Fluent 6.1 software was employed to conduct this numerical simulation work.展开更多
基金the National Key Research and Development Program of China(2023YFA0915800)the Science and Technology Basic Resources Investigation Program(2021FY100200)+3 种基金the Key Basic Research program of Yunnan Province,China(202101BC070003)the Large-scale Scientific Facilities of the Chinese Academy of Sciences(2017-LSFGBOWS-02)the Chinese Academy of Sciences President's International Fellowship Initiative(2025PD0021)We are grateful to curator of KUN to access the herbarium specimens,and Jiayun Zou,Zhirong Zhang,Jing Yang,Hongtao Li and Chunxia Zeng,for their help with sample collection,laboratory work and data analysis.Molecular experiments and data analysis were performed at the Laboratory of Molecular Biology and iFlora High-Performance Computing Center of Germplasm Bank of Wild Species,Kunming Institute of Botany,CAS.
文摘Deep genome skimming(DGS)has emerged as a promising approach to recover orthologous nuclear genes for large-scale phylogenomic analyses.However,its reliability with low DNA quality and quantity typical of archival specimens,such as herbarium material,remains largely unexplored.We used Rhododendron as a case study to evaluate best practices for DGS in phylogenetic analyses at both deep and shallow scales.We first investigated locus recovery variation with sequencing depth,before evaluating the phylogenetic utility of different sets of loci,including Angiosperms353,target nuclear exons,and extended exon-flanking regions.We found DGS effectively recovered nuclear genes from herbarium specimens,with~15coverage performing similarly to deeper sequencing.The recovery of target exon and flanking regions was improved by using supercontigs as a reference,offering a potential solution to limited sequencing depth.The high-integrity nuclear sequences recovered robust phylogenetic relationships within Rhododendron.Notably,exon-flanking regions showed significant potential for resolving relationships at shallow scales.Genes recovered with taxon-specific references had less missing data than those recovered by Angiosperms353 and generated higher-resolution phylogenetic trees.This study demonstrates the utility of DGS data for obtaining numerous nuclear genes from herbarium specimens for phylogenetic studies,and makes recommendations for best practices regarding sequencing coverage,locus selection,and bioinformatic approaches.
基金supported by NSFC(32070226,32360065)the Key Projects of the Joint Fund of the National Natural Science Foundation of China(U23A20149)+3 种基金the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2024QZKK0200)Yunnan Fundamental Research Projects(202101AS070032)the CAS“Light ofWest China”Program(xbzg-zdsys-202110)the Yunnan Innovation Team Project(202305AS350004,with LD/NY/SB/CJG/CJH as the core member).
文摘The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value.However,taxonomy and systematics of Salix is extremely difficult and relationships between main lineages,especially deep phylogenies,remain largely unresolved.In this study,we used genome-skimming,plastome assembly,and single-copy orthologs(SCOs)from 66 Salix accessions,along with publicly available plastome and sequence read archive(SRA)datasets to obtain a robust backbone phylogeny of Salix,clarify relationships between its main lineages,and gain a more precise understanding of the origin and diversification of this species-rich genus.The plastome and SCO datasets resolved Salix into two robust clades,with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies.Our results support the classification of Salix into five subgenera:Salix,Urbaniana,Triandrae,Longifoliae and Vetrix.We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade,while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene.These changes coincided with contemporaneous tectonic and climate change events.Our results provide a foundation for future systematic and evolutionary studies of Salix.Additionally,we showed that genome skimming data is an efficient,rapid,and reliable approach for obtaining extensive genomic data for phylogenomic studies,enabling the comprehensive elucidation of Salix relationships.
基金The authors gratefully acknowledge the National Key Research and Development Program of China(No.2018YFC1901902)the Liao Ning Revitalization Talents Program(No.XLYC1907162).
文摘In order to make the slag from desulphurization and slag skimming(SDSS)to be comprehensively recycled and utilized,a combined process of beneficiation and building materials preparation was proposed to recover iron from SDSS,meanwhile to apply the remaining slag tailings as cement admixture.From this process,three iron-rich products were recovered in stages by clean gravity-magnetic separation,slag tailings were left.Slag powder was prepared by ultrafine grinding of slag tailings.The stability,setting time and cement mortar strength of the slag tailings cements(STC)which were mixed with Portland cement and slag powder were studied respectively.The results showed that a proper overall performance still could be obtained at the slag powder content of 30%.Chemical composition analysis,X-ray diffraction(XRD)analysis,metallographic microscope and scanning electron microscope(SEM)analysis were employed to assess the characteristics of the SDSS and the products obtained from the whole process.The results indicated that the three iron-rich products could be used as a raw material for steelmaking and ironmaking and the relatively large amount of calcium silicate(C_(2)S)and tricalcium silicate(C_(3)S)in the slag tailings make the addition of slag powder into the Portland cement feasible.
基金supported by the National Natural Science Foundation of China(Grant Nos.31900188,31970225)Natural Science Foundation of Zhejiang Province(Grant No.LY19C030007).
文摘Celtis is a Cannabaceae genus of 60e70 species of trees,or rarely shrubs,commonly known as hackberries.This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals.Although previous studies have identified its phylogenetic position,interspecific relationships within Celtis remain unclear.In this study,we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources.The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp,with a typical angiosperm quadripartite structure,and encoded a total of 132 genes with 20 duplicated in the IRs.Comparative analyses showed that plastome content and structure were relatively conserved.Whole plastomes showed no signs of gene loss,translocations,inversions,or genome rearrangement.Six plastid hotspot regions(trnH-psbA,psbA-trnK,trnG-trnR,psbC-trnS,cemA-petA and rps8-rpl14),4097 polymorphic nuclear SSRs,as well as 62 low or single-copy gene fragments were identified within Celtis.Moreover,the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C.biondii as sister to the((((C.koraiensis,C.sinensis),C.tetrandra),C.julianae),C.cerasifera)clade.These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny,population genetics,and conservation biology.
文摘This paper has proposed a new modelling and simulating technique for the echo of the semi-active radar seeker against the sea skimming target. The echo modelling is based on the electromagnetic scattering mechanisms. A modified Four-path model based on the radar detection scene is used to describe the multipath scattering between the target and rough sea surface. A Facet-based Small Slope Approximation (FBSSA) method is employed to calculate the scattering from the sea surface. The Physical Optics (PO) and the Equivalent Edge Current (EEC) Method is used to calculate the target scattering. In the echo simulations. The results present the original echo and the echo processed by the signal processing procedures, where the clutter and multipath effect can be observed.
文摘This paper deals with some aspects of the air entrainment process along the chute of spillway and study of pressure fluctuations. The experimental study has been carried out using stepped spillway model located in the campus of Government College of Engineering, Amravati (India). It is observed that air concentration is increasing with discharge as well as with number of step. Air concentration is increasing along the length of spillway. It is also observed that the bottom mean air concentration increases with step height in the upstream reach of stepped spillway, which is prone to cavitation. The pressure profiles exhibit a wavy pattern down the stepped chute and pressure on each step increases with ratio of critical depth to step height (yc/h).
基金supported by the Guangdong Special Research Fund of Public Welfare and Capacity Building(2015A020216008)the Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund(the second phase)
文摘As a widely used flood energy dissipator, the stepped spillway can significantly dissipate the kinetic or hydraulic energy due to the air-entrainment in skimming flow over the steps. The free-surface aeration involves the sharp deformation of the free surface and the complex turbulent shear flows. In this study, the volume of fluid （VOF）, mixture, and Eulerian methods are utilized to simulate the air-entrainment by coupling with the Reynolds-averaged Navier-Stokes/large eddy simulation （RANS/LES） turbulence models. The free surface deformation, air volume fraction, pressure, and velocity are compared for the three different numerical methods. Only the Eulerian＋RANS method fails to capture the free-surface aeration. The air volume fraction predicted by the VOF＋LES method best matches the experimental measurement, while the mixture＋LES method predicts the inception point of the air entrainment more accurately.
文摘This paper illustrates the similarity and dissimilarity between two basic reading skills- skimming and scanning from different ways.It advises readers to understand and make full use of them in their everyday reading.They will make reading easier and help improve reading comprehension to a certain extent.
基金funded by the National Natural Science Foundation of China(grant no.31670207).
文摘The genus Clematis(Ranunculaceae)comprises over 300 species with remarkable morphological and ecological diversity worldwide.Despite its horticultural,medicinal,and ecological importance,a well-resolved phylogeny and coherent infrageneric classification are still lacking.Here,we reconstruct a robust phylogeny for Clematis using a phylogenomic approach and revise its infrageneric taxonomy.We incorporated 198 samples representing 151 species,two subspecies,and 12 varieties,covering all subgenera and most sections worldwide,obtained from both fresh and herbarium material.Nuclear single nucleotide polymorphisms(SNPs)and complete plastid genomes were assembled for phylogenetic analyses.We also prepared a nuclear ribosomal ITS(nrITS)dataset comprising 171 species,two subspecies,and 12 varieties(217 samples)to include as many species as possible for phylogenetic inference.Phylogenies based on plastid genomes and nrITS exhibited limited resolution and modest support,highlighting challenges in resolving certain relationships.Nuclear SNP analyses yielded a robust phylogenetic tree with 22 well-supported clades corresponding to 22 sections,with most previously recognized subgenera and sections not recovered as monophyletic.Ancestral state reconstruction of 12 key morphological characters revealed multiple independent origins of character states.This study presents the first comprehensive sectional classification for Clematis based on robust phylogenomic evidence,redefines morphological characteristics for each section,and resolves long-standing taxonomic ambiguities.Our results establish a framework for future studies on the evolution,ecology,and horticultural potential of this globally significant genus.
文摘Numerical simulation of stepped channel flow was conducted using turbulence models based on the VOF technique. Stepped channel flow is a complicated air-water two-phase flow with free surface, which can be divided into three flow regimes： skimming flow, nappe flow and transition flow. The characteristics of skimming flow over mild stepped channel was investigated, including friction factors, air concentration profiles velocity field, clear-water and bulked depths, static pressure, etc. Smooth channel flow was also simulated to compare the hydraulic characteristics of the stepped channel flow with the smooth one. Comparisons between the computed and the measured were made. Furthermore, comparison of the computed air concentration with Straub and Anderson＇s data was also performed. The Fluent 6.1 software was employed to conduct this numerical simulation work.
