This letter demonstrates an experimental approach to measuring the angular-momentum-resolved population of excited states in laser-produced argon ions.By measuring the spectra of free induction decay emissions corresp...This letter demonstrates an experimental approach to measuring the angular-momentum-resolved population of excited states in laser-produced argon ions.By measuring the spectra of free induction decay emissions corresponding to the resonant transitions between Rydberg states,the relative population of the Rydberg states is obtained with known Einstein A-coefficients.This study deepens the mechanistic understanding of coherent dynamics in laser-driven ionic excited states,and establishes experimental benchmarks essential for validating and refining advanced quantum kinetic models in strong-field physics.展开更多
Recent advances in spatially resolved transcriptomics(SRT)have provided new opportunities for characterizing spatial structures of various tissues.Graph-based geometric deep learning has gained widespread adoption for...Recent advances in spatially resolved transcriptomics(SRT)have provided new opportunities for characterizing spatial structures of various tissues.Graph-based geometric deep learning has gained widespread adoption for spatial domain identification tasks.Currently,most methods define adjacency relation between cells or spots by their spatial distance in SRT data,which overlooks key biological interactions like gene expression similarities,and leads to inaccuracies in spatial domain identification.To tackle this challenge,we propose a novel method,SpaGRA(https://github.com/sunxue-yy/SpaGRA),for automatic multi-relationship construction based on graph augmentation.SpaGRA uses spatial distance as prior knowledge and dynamically adjusts edge weights with multi-head graph attention networks(GATs).This helps SpaGRA to uncover diverse node relationships and enhance message passing in geometric contrastive learning.Additionally,SpaGRA uses these multi-view relationships to construct negative samples,addressing sampling bias posed by random selection.Experimental results show that SpaGRA presents superior domain identification performance on multiple datasets generated from different protocols.Using SpaGRA,we analyze the functional regions in the mouse hypothalamus,identify key genes related to heart development in mouse embryos,and observe cancer-associated fibroblasts enveloping cancer cells in the latest Visium HD data.Overall,SpaGRA can effectively characterize spatial structures across diverse SRT datasets.展开更多
Silicene,a silicon analog of graphene,holds promise for next-generation electronics due to its tunable bandgap and larger spin-orbit coupling.Despite extensive efforts to synthesize and characterize silicene on metal ...Silicene,a silicon analog of graphene,holds promise for next-generation electronics due to its tunable bandgap and larger spin-orbit coupling.Despite extensive efforts to synthesize and characterize silicene on metal substrates,bondresolved imaging of its atomic structure has remained elusive.Here,we report the fabrication and bond-resolved characterization of silicene on Au(111)substrate.Three silicene phases tuned by surface reconstruction and annealing temperatures are achieved.Using CO-terminated scanning tunneling microscopy(STM)tips,we resolve these silicene phases with atomic precision,determining their bond lengths,local strain,and geometric configurations.Furthermore,we correlate these structural features with their electronic properties,revealing the effect of strain and substrate interactions on the electronic properties of silicene.This work establishes silicene's intrinsic bonding topology and resolves longstanding controversies in silicene research.展开更多
Fluid-structure-particle interactions in three spatial dimensions happen in many environmental and engineering flows.This paper presents the parallel algorithms for the hybrid diffuse and sharp interface immersed boun...Fluid-structure-particle interactions in three spatial dimensions happen in many environmental and engineering flows.This paper presents the parallel algorithms for the hybrid diffuse and sharp interface immersed boundary(IB)method developed in our previous work.For the moving structure modeled using the sharp interface IB method,a recursive box method is developed for efficiently classifying the background grid nodes.For the particles modeled using the diffuse interface IB method,a‘master-slave’approach is adopted.For the particle-particle interaction(PPI)and particle-structure interaction(PSI),a fast algorithm for classifying the active and inactive Lagrangian points,which discretize the particle surface,is developed for the‘dry’contact approach.The results show that the proposed recursive box method can reduce the classifying time from 52seconds to 0.3 seconds.Acceptable parallel efficiency is obtained for cases with different particle concentrations.Furthermore,the lubrication model is utilized when a particle approaches a wall,enabling an accurate simulation of the rebounding phenomena in the benchmark particle-wall collision problem.At last,the capability of the proposed computational framework is demonstrated by simulating particle-laden turbulent channel flows with rough walls.展开更多
The construction of a new beamline,BL10U1,was completed at the Shanghai synchrotron radiation facility in 2020.This multipurpose beamline was designed to provide X-ray scattering techniques such as ultra-small-angle X...The construction of a new beamline,BL10U1,was completed at the Shanghai synchrotron radiation facility in 2020.This multipurpose beamline was designed to provide X-ray scattering techniques such as ultra-small-angle X-ray scattering(USAXS),small-angle X-ray scattering(SAXS),wide-angle X-ray scattering,and microfocus SAXS(μSAXS)for a broad user community.To realize fast time-resolved USAXS experiments,the beamline adopted an in-vacuum undulator with a total length of 1.6 m as the photon source.An in-house cryogenic-cooled double multilayer monochromator was installed to deliver a photon flux of approximately 10^(13) photons/s at a photon energy of 10 keV.The three-year successful operation of this beamline demonstrated that the monochromator operated smoothly,as expected.BL10U1 has three end stations in succession:USAXS end station,μSAXS end station,and end station for industrial applications.The minimum scattering vector q~0.0042 nm^(-1) at 10 keV can be achieved at the USAXS end station equipped with a 28 m-long and 1.8 m-diameter vacuum flight tube.At theμSAXS end station,a beam spot of less than 10×8μm was achieved for micro-SAXS experiments.In contrast,in situ experimental instruments up to 5 m high and 8 m wide can be mounted at the industrial application end station,which offers industrial scientists the opportunity to use their large industrial equipment.BL10U1 opens up a new capability to investigate phenomena such as non-equilibrium and dynamic processes of materials with a wide length scale from angstroms to micrometers with millisecond time resolution.In this paper,we also report beamline design considerations and commissioning results.展开更多
Pulmonary fibrosis (PF) is a chronic progressive end-stage lung disease. However, the mechanisms underlying the progression of this disease remain elusive. Presently, clinically employed drugs are scarce for the treat...Pulmonary fibrosis (PF) is a chronic progressive end-stage lung disease. However, the mechanisms underlying the progression of this disease remain elusive. Presently, clinically employed drugs are scarce for the treatment of PF. Hence, there is an urgent need for developing novel drugs to address such diseases. Our study found for the first time that a natural source of Prismatomeris connata Y. Z. Ruan (Huang Gen, HG) ethyl acetate extract (HG-2) had a significant anti-PF effect by inhibiting the expression of the transforming growth factor beta 1/suppressor of mothers against decapentaplegic (TGF-β1/Smad) pathway. Network pharmacological analysis suggested that HG-2 had effects on tyrosine kinase phosphorylation, cellular response to reactive oxygen species, and extracellular matrix (ECM) disassembly. Moreover, mass spectrometry imaging (MSI) was used to visualize the heterogeneous distribution of endogenous metabolites in lung tissue and reveal the anti-PF metabolic mechanism of HG-2, which was related to arginine biosynthesis and alanine, asparate and glutamate metabolism, the downregulation of arachidonic acid metabolism, and the upregulation of glycerophospholipid metabolism. In conclusion, we elaborated on the relationship between metabolite distribution and the progression of PF, constructed the regulatory metabolic network of HG-2, and discovered the multi-target therapeutic effect of HG-2, which might be conducive to the development of new drugs for PF.展开更多
Hedgehogs,small nocturnal mammals of the Erinaceinae subfamily,play a crucial role in maintaining ecological balance(Hernandez,2008;Taucher et al.,2020).Atelerix albiventris(A.albiventris),a species native to West and...Hedgehogs,small nocturnal mammals of the Erinaceinae subfamily,play a crucial role in maintaining ecological balance(Hernandez,2008;Taucher et al.,2020).Atelerix albiventris(A.albiventris),a species native to West and Central Africa,is the smallest of the African hedgehogs.A.albiventris has undergone domestication and is utilized in biomedical research and offered in the exotic pet trade(Santana et al.,2010).In recent years,hedgehog population numbers have shown a declining trend due to human-induced disturbance(Johnson et al.,2015).展开更多
Human cancer is one of the leading causes of death worldwide.Tumor heterogeneity and complex microenvironment are major challenges for anti-cancer treatment.A better understanding of the tumor heterogeneity might cont...Human cancer is one of the leading causes of death worldwide.Tumor heterogeneity and complex microenvironment are major challenges for anti-cancer treatment.A better understanding of the tumor heterogeneity might contribute to more precise diagnosis and treatment.Recent advances in single-cell RNA-sequencing(scRNA-seq)have provided valuable insights into cell fate determination and development in cancer,but the main limitation is that cellular spatial information is lost.Fortunately,spatially resolved transcriptomics technologies have enabled gene expression profiling with spatial coordinates in tissues,which opens up new avenues for deciphering the cancer spatial structure and accelerating oncological research.展开更多
DEAR EDITOR,Big cats,such as Amur tigers(Panthera tigris altaica)and Amur leopards(P.pardus orientalis),are apex predator and have evolved specialized traits for hunting and carnivory(Moya et al.,2022),thus playing a ...DEAR EDITOR,Big cats,such as Amur tigers(Panthera tigris altaica)and Amur leopards(P.pardus orientalis),are apex predator and have evolved specialized traits for hunting and carnivory(Moya et al.,2022),thus playing a crucial role in maintaining biodiversity and ecosystem integrity by regulating prey-predator dynamics.However,human-induced pressures,habitat fragmentation,and environmental alterations have restricted these species in small and isolated populations.Currently,all extant big cats are categorized as endangered or threatened according to their conservation status.Amur tigers and Amur leopards share overlapping geographic ranges,habitats,and certain prey species in the forests of Northeast Asia(Jiang et al.,2015).To reduce interspecies conflict,these carnivores exhibit differentiated dietary and temporal niches.Amur tigers predominantly prey on large ungulates,while Amur leopards hunt small to medium-sized animals(Sugimoto et al.,2016).Additionally,they occupy different temporal niches,with tigers being active at night and leopards more active during the day.Despite spatial and temporal niche partitioning,interspecific competition between these two species is inevitable.Tigers,benefiting from their greater size,have a competitive advantage over leopards,which can manifest in occasional leopard predation by tigers and declines in leopard populations with increasing tiger density(Jiang et al.,2015).Tigers also displace leopards from marginal habitats in nature reserves where they coexist.展开更多
Tumors are spatially heterogeneous tissues that comprise numerous cell types with intricate structures.By interacting with the microenvironment,tumor cells undergo dynamic changes in gene expression and metabolism,res...Tumors are spatially heterogeneous tissues that comprise numerous cell types with intricate structures.By interacting with the microenvironment,tumor cells undergo dynamic changes in gene expression and metabolism,resulting in spatiotemporal variations in their capacity for proliferation and metastasis.In recent years,the rapid development of histological techniques has enabled efficient and high-throughput biomolecule analysis.By preserving location information while obtaining a large number of gene and molecular data,spatially resolved metabolomics(SRM)and spatially resolved transcriptomics(SRT)approaches can offer new ideas and reliable tools for the in-depth study of tumors.This review provides a comprehensive introduction and summary of the fundamental principles and research methods used for SRM and SRT techniques,as well as a review of their applications in cancer-related fields.展开更多
The photodissociation dynamics of 2-iodotoluene following excitation at 266 nm have been investigated employing femtosecond time-resolved mass spectrometry. The photofragments are detected by multiphoton ionization us...The photodissociation dynamics of 2-iodotoluene following excitation at 266 nm have been investigated employing femtosecond time-resolved mass spectrometry. The photofragments are detected by multiphoton ionization using an intense laser field centered at 800 nm. A dissociation time of 3804-50 fs was measured from the rising time of the co-fragments of toluene radical （C7H7） and iodine atom （I）, which is attributed to the averaged time needed for the C-I bond breaking for the simultaneously excited nσ and ππ＊ states by 266 nm pump light. In addition, a probe light centered at 298.23 nm corresponding to resonance wavelength of ground-state iodine atom is used to selectively ionize ground-state iodine atoms generated from the dissociation of initially populated hσ＊ and ππ＊ states. And a rise time of 4004-50 fs is extracted from the fitting of time-dependent I＋ transient, which is in agreement with the dissociation time obtained by multiphoton ionization with 800 nm, suggesting that the main dissociative products are ground-state iodine atoms.展开更多
The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the s...The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the scientific community has been able to visualize life at an unprecedented resolution.Most recently,the Spatially Resolved Transcriptomics(SRT)technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life,including the origin of different cellular populations developed from totipotent cells and human diseases.In this review,we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools,as well as the representative SRT applications.With the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects,we can foresee the bright future of such new tools in understanding life at the most profound analytical level.展开更多
Background: Probable benign paroxysmal positional vertigo, spontaneously resolved (pBPPVsr), is a variant of benign paroxysmal positional vertigo (BPPV) in which there is no observable nystagmus and no vertigo with an...Background: Probable benign paroxysmal positional vertigo, spontaneously resolved (pBPPVsr), is a variant of benign paroxysmal positional vertigo (BPPV) in which there is no observable nystagmus and no vertigo with any positional maneuver. Objectives: To calculate the incidence pBPPVsr, compare the characteristics of the patients with pBPPVsr and BPPV not spontaneously resolved and describe the spontaneous resolution in the natural course of BPPV. Methods: Multicenter prospective descriptive study. During a one-year period, all patients with suspected BPPV that presented to the Neurotology Units of five participating centers were recruited. The incidence of pBPPVsr was calculated as a percentage of the total number of patients with BPPV. The prevalence of several variables was compared between pBPPVsr and BPPV not spontaneously resolved. The timing of spontaneous resolution was estimated using Kaplan-Meier curves. Results: 457 patients met the inclusion criteria. The incidence of pBPPVsr was 33.5%. It was significantly higher in males, in patients with normal bone mass and in patients who were not taking sulpiride. A rate of 18% of spontaneous resolution after the first month and 51% after the first year was found. This percentage did not change in a significant way after this moment. The curves for males, patients under 50 and patients with normal blood pressure decreased significantly faster. Conclusions: In our serie, BPPV spontaneously resolved in half of the patients with BPPV during the first year. This seemed to occur more commonly in males and could have been hindered by sulpiride intake, osteoporosis, advanced age and high blood pressure.展开更多
In situ time-resolved spectroscopy is an effective method to monitor the catalysis reaction in real time and reveal the catalytic mechanistic pathway.The dynamic evolution of coordination and electronic structures of ...In situ time-resolved spectroscopy is an effective method to monitor the catalysis reaction in real time and reveal the catalytic mechanistic pathway.The dynamic evolution of coordination and electronic structures of catalytic active sites during the CO2 reduction reaction is still a "black box," impeding the design of high-efficiency catalysts.In a recent report published in J.Am.Chem.Soc.,by multiple in situ time-resolved spectroscopy.展开更多
The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and ha...The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing,Oxford Nanopore 50-kb ultra-long,and high-throughput chromatin conformation capture technologies.The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps,while a total of 633.0 Mb genomic sequences were generated.The origination analysis identified 338.5Mb genomic sequences originating from citron(53.5%),147.4Mb frommandarin(23.3%),and 147.1Mb frompummelo(23.2%).The genome included 30528 protein-coding genes,and most of the assembled sequences were found to be repetitive sequences.Several significantly expanded gene families were associated with plant-pathogen interactions,plant hormone signal transduction,and the biosynthesis of major active components,such as terpenoids and f lavor compounds.Most HLB-tolerant genes were expanded in the lemon genome,such as 2-oxoglutarate(2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1,cell wall-related genes,and lignin synthesis genes.Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon.Our results provide insight into lemon genome evolution,active component biosynthesis,and genes associated with HLB tolerance.展开更多
Cultivated strawberry(Fragaria×ananassa),a perennial herb belonging to the family Rosaceae,is a complex octoploid with high heterozygosity at most loci.However,there is no research on the haplotype of the octoplo...Cultivated strawberry(Fragaria×ananassa),a perennial herb belonging to the family Rosaceae,is a complex octoploid with high heterozygosity at most loci.However,there is no research on the haplotype of the octoploid strawberry genome.Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar,“Yanli”,using single molecule real-time sequencing and high-throughput chromosome conformation capture technology.The“Yanli”genome was 823 Mb in size,with a long terminal repeat assembly index of 14.99.The genome was phased into two haplotypes,Hap1(825 Mb with contig N50 of 26.70 Mb)and Hap2(808 Mb with contig N50 of 27.51 Mb).Using the combination of Hap1 and Hap2,we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry.We identified a∼10 Mb inversion and translocation on chromosome 2-1.104957 and 102356 protein-coding genes were annotated in Hap1 and Hap2,respectively.Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F.×ananassa genome.In summary,we obtained a high-quality haplotype-resolved genome assembly of F.×ananassa,which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.展开更多
Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a hap...Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.展开更多
Size-resolved aerosol samples were collected by MOUDI in four seasons in 2007 in Beijing. The PM10 and PM1.8mass concentrations were 166.0 ± 120.5 and 91.6 ± 69.7 μg/m^3, respectively,throughout the measure...Size-resolved aerosol samples were collected by MOUDI in four seasons in 2007 in Beijing. The PM10 and PM1.8mass concentrations were 166.0 ± 120.5 and 91.6 ± 69.7 μg/m^3, respectively,throughout the measurement, with seasonal variation： nearly two times higher in autumn than in summer and spring. Serious fine particle pollution occurred in winter with the PM1.8/PM10 ratio of 0.63, which was higher than other seasons. The size distribution of PM showed obvious seasonal and diurnal variation, with a smaller fine mode peak in spring and in the daytime. OM（organic matter = 1.6 × OC（organic carbon）） and SIA（secondary inorganic aerosol） were major components of fine particles, while OM, SIA and Ca^2＋were major components in coarse particles. Moreover, secondary components, mainly SOA（secondary organic aerosol） and SIA,accounted for 46%-96% of each size bin in fine particles, which meant that secondary pollution existed all year. Sulfates and nitrates, primarily in the form of（NH4）2SO4, NH4NO3, Ca SO4, Na2SO4 and K2SO4, calculated by the model ISORROPIA II, were major components of the solid phase in fine particles. The PM concentration and size distribution were similar in the four seasons on non-haze days, while large differences occurred on haze days, which indicated seasonal variation of PM concentration and size distribution were dominated by haze days. The SIA concentrations and fractions of nearly all size bins were higher on haze days than on non-haze days, which was attributed to heterogeneous aqueous reactions on haze days in the four seasons.展开更多
Against tumor-dependent metabolic vulnerability is an attractive strategy for tumor-targeted therapy.However,metabolic inhibitors are limited by the drug resistance of cancerous cells due to their metabolic plasticity...Against tumor-dependent metabolic vulnerability is an attractive strategy for tumor-targeted therapy.However,metabolic inhibitors are limited by the drug resistance of cancerous cells due to their metabolic plasticity and heterogeneity.Herein,choline metabolism was discovered by spatially resolved metabolomics analysis as metabolic vulnerability which is highly active in different cancer types,and a choline-modified strategy for small molecule-drug conjugates(SMDCs)design was developed to fool tumor cells into indiscriminately taking in choline-modified chemotherapy drugs for targeted cancer therapy,instead of directly inhibiting choline metabolism.As a proof-of-concept,choline-modified SMDCs were designed,screened,and investigated for their druggability in vitro and in vivo.This strategy improved tumor targeting,preserved tumor inhibition and reduced toxicity of paclitaxel,through targeted drug delivery to tumor by highly expressed choline transporters,and site-specific release by carboxylesterase.This study expands the strategy of targeting metabolic vulnerability and provides new ideas of developing SMDCs for precise cancer therapy.展开更多
After online publication of the article 1,the authors noticed the affiliation“College of Landscape Architecture and Life Science/Institute of Special Plants,Chongqing University of Arts and Sciences,Yongchuan,Chongqi...After online publication of the article 1,the authors noticed the affiliation“College of Landscape Architecture and Life Science/Institute of Special Plants,Chongqing University of Arts and Sciences,Yongchuan,Chongqing,China”for author Yiqing Liu was missing.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.12234020,12474281,12450403,and 12274461)the Science and Technology Innovation Program of Hunan Province(Grant No.2022RC1193)。
文摘This letter demonstrates an experimental approach to measuring the angular-momentum-resolved population of excited states in laser-produced argon ions.By measuring the spectra of free induction decay emissions corresponding to the resonant transitions between Rydberg states,the relative population of the Rydberg states is obtained with known Einstein A-coefficients.This study deepens the mechanistic understanding of coherent dynamics in laser-driven ionic excited states,and establishes experimental benchmarks essential for validating and refining advanced quantum kinetic models in strong-field physics.
基金supported by the National Natural Science Foundation of China(Nos.62303271,U1806202,62103397)the Natural Science Foundation of Shandong Province(ZR2023QF081)Funding for open access charge:the National Natural Science Foundation of China(Nos.62303271,U1806202).
文摘Recent advances in spatially resolved transcriptomics(SRT)have provided new opportunities for characterizing spatial structures of various tissues.Graph-based geometric deep learning has gained widespread adoption for spatial domain identification tasks.Currently,most methods define adjacency relation between cells or spots by their spatial distance in SRT data,which overlooks key biological interactions like gene expression similarities,and leads to inaccuracies in spatial domain identification.To tackle this challenge,we propose a novel method,SpaGRA(https://github.com/sunxue-yy/SpaGRA),for automatic multi-relationship construction based on graph augmentation.SpaGRA uses spatial distance as prior knowledge and dynamically adjusts edge weights with multi-head graph attention networks(GATs).This helps SpaGRA to uncover diverse node relationships and enhance message passing in geometric contrastive learning.Additionally,SpaGRA uses these multi-view relationships to construct negative samples,addressing sampling bias posed by random selection.Experimental results show that SpaGRA presents superior domain identification performance on multiple datasets generated from different protocols.Using SpaGRA,we analyze the functional regions in the mouse hypothalamus,identify key genes related to heart development in mouse embryos,and observe cancer-associated fibroblasts enveloping cancer cells in the latest Visium HD data.Overall,SpaGRA can effectively characterize spatial structures across diverse SRT datasets.
基金Project supported by the National Natural Science Foundation of China(Grant No.12474181)the Guangdong Basic and Applied Basic Research Foundation(Grant Nos.2021B0301030002 and 2024A1515010656)the Guangdong Science and Technology Project(Grant No.2021QN02X859)。
文摘Silicene,a silicon analog of graphene,holds promise for next-generation electronics due to its tunable bandgap and larger spin-orbit coupling.Despite extensive efforts to synthesize and characterize silicene on metal substrates,bondresolved imaging of its atomic structure has remained elusive.Here,we report the fabrication and bond-resolved characterization of silicene on Au(111)substrate.Three silicene phases tuned by surface reconstruction and annealing temperatures are achieved.Using CO-terminated scanning tunneling microscopy(STM)tips,we resolve these silicene phases with atomic precision,determining their bond lengths,local strain,and geometric configurations.Furthermore,we correlate these structural features with their electronic properties,revealing the effect of strain and substrate interactions on the electronic properties of silicene.This work establishes silicene's intrinsic bonding topology and resolves longstanding controversies in silicene research.
基金Project supported by the National Natural Science Foundation of China(Nos.12202456 and12172360)the Basic Science Center Program for“Multiscale Problems in Nonlinear Mechanics”of the National Natural Science Foundation of China(No.11988102)the China Postdoctoral Science Foundation(No.2021M693241)。
文摘Fluid-structure-particle interactions in three spatial dimensions happen in many environmental and engineering flows.This paper presents the parallel algorithms for the hybrid diffuse and sharp interface immersed boundary(IB)method developed in our previous work.For the moving structure modeled using the sharp interface IB method,a recursive box method is developed for efficiently classifying the background grid nodes.For the particles modeled using the diffuse interface IB method,a‘master-slave’approach is adopted.For the particle-particle interaction(PPI)and particle-structure interaction(PSI),a fast algorithm for classifying the active and inactive Lagrangian points,which discretize the particle surface,is developed for the‘dry’contact approach.The results show that the proposed recursive box method can reduce the classifying time from 52seconds to 0.3 seconds.Acceptable parallel efficiency is obtained for cases with different particle concentrations.Furthermore,the lubrication model is utilized when a particle approaches a wall,enabling an accurate simulation of the rebounding phenomena in the benchmark particle-wall collision problem.At last,the capability of the proposed computational framework is demonstrated by simulating particle-laden turbulent channel flows with rough walls.
基金This work was supported by the National Key R&D Program of China(No.2020YFA0405802)the Shanghai Large Scientific Facilities Center.
文摘The construction of a new beamline,BL10U1,was completed at the Shanghai synchrotron radiation facility in 2020.This multipurpose beamline was designed to provide X-ray scattering techniques such as ultra-small-angle X-ray scattering(USAXS),small-angle X-ray scattering(SAXS),wide-angle X-ray scattering,and microfocus SAXS(μSAXS)for a broad user community.To realize fast time-resolved USAXS experiments,the beamline adopted an in-vacuum undulator with a total length of 1.6 m as the photon source.An in-house cryogenic-cooled double multilayer monochromator was installed to deliver a photon flux of approximately 10^(13) photons/s at a photon energy of 10 keV.The three-year successful operation of this beamline demonstrated that the monochromator operated smoothly,as expected.BL10U1 has three end stations in succession:USAXS end station,μSAXS end station,and end station for industrial applications.The minimum scattering vector q~0.0042 nm^(-1) at 10 keV can be achieved at the USAXS end station equipped with a 28 m-long and 1.8 m-diameter vacuum flight tube.At theμSAXS end station,a beam spot of less than 10×8μm was achieved for micro-SAXS experiments.In contrast,in situ experimental instruments up to 5 m high and 8 m wide can be mounted at the industrial application end station,which offers industrial scientists the opportunity to use their large industrial equipment.BL10U1 opens up a new capability to investigate phenomena such as non-equilibrium and dynamic processes of materials with a wide length scale from angstroms to micrometers with millisecond time resolution.In this paper,we also report beamline design considerations and commissioning results.
基金supported by the National Natural Science Foundation of China(Grant No.:82074104)the Research Project of Clinical Toxicology Transformation from the Chinese Society of Toxicology,China(Grant No.:CST2021CT101)the Chinese Academy of Medical Science Innovation Fund for Medical Sciences,China(Grant Nos.:2017-I2M-1-011 and 2022-I2M-2-002).
文摘Pulmonary fibrosis (PF) is a chronic progressive end-stage lung disease. However, the mechanisms underlying the progression of this disease remain elusive. Presently, clinically employed drugs are scarce for the treatment of PF. Hence, there is an urgent need for developing novel drugs to address such diseases. Our study found for the first time that a natural source of Prismatomeris connata Y. Z. Ruan (Huang Gen, HG) ethyl acetate extract (HG-2) had a significant anti-PF effect by inhibiting the expression of the transforming growth factor beta 1/suppressor of mothers against decapentaplegic (TGF-β1/Smad) pathway. Network pharmacological analysis suggested that HG-2 had effects on tyrosine kinase phosphorylation, cellular response to reactive oxygen species, and extracellular matrix (ECM) disassembly. Moreover, mass spectrometry imaging (MSI) was used to visualize the heterogeneous distribution of endogenous metabolites in lung tissue and reveal the anti-PF metabolic mechanism of HG-2, which was related to arginine biosynthesis and alanine, asparate and glutamate metabolism, the downregulation of arachidonic acid metabolism, and the upregulation of glycerophospholipid metabolism. In conclusion, we elaborated on the relationship between metabolite distribution and the progression of PF, constructed the regulatory metabolic network of HG-2, and discovered the multi-target therapeutic effect of HG-2, which might be conducive to the development of new drugs for PF.
基金supported by the National Natural Science Foundation of China(32370689 and 32070601)the Natural Science Fund for Excellent Young Scholars of Shandong Province(ZR2022YQ23)。
文摘Hedgehogs,small nocturnal mammals of the Erinaceinae subfamily,play a crucial role in maintaining ecological balance(Hernandez,2008;Taucher et al.,2020).Atelerix albiventris(A.albiventris),a species native to West and Central Africa,is the smallest of the African hedgehogs.A.albiventris has undergone domestication and is utilized in biomedical research and offered in the exotic pet trade(Santana et al.,2010).In recent years,hedgehog population numbers have shown a declining trend due to human-induced disturbance(Johnson et al.,2015).
基金supported by the National Natural Science Foundation of China(62003028)supported by a Scholarship from the China Scholarship Council。
文摘Human cancer is one of the leading causes of death worldwide.Tumor heterogeneity and complex microenvironment are major challenges for anti-cancer treatment.A better understanding of the tumor heterogeneity might contribute to more precise diagnosis and treatment.Recent advances in single-cell RNA-sequencing(scRNA-seq)have provided valuable insights into cell fate determination and development in cancer,but the main limitation is that cellular spatial information is lost.Fortunately,spatially resolved transcriptomics technologies have enabled gene expression profiling with spatial coordinates in tissues,which opens up new avenues for deciphering the cancer spatial structure and accelerating oncological research.
基金supported by the Fundamental Research Funds for the Central Universities of China(2572022DQ03)National Natural Science Foundation of China(32170517)+1 种基金Guangdong Provincial Key Laboratory of Genome Read and Write(2017B030301011)supported by China National GeneBank(CNGB)。
文摘DEAR EDITOR,Big cats,such as Amur tigers(Panthera tigris altaica)and Amur leopards(P.pardus orientalis),are apex predator and have evolved specialized traits for hunting and carnivory(Moya et al.,2022),thus playing a crucial role in maintaining biodiversity and ecosystem integrity by regulating prey-predator dynamics.However,human-induced pressures,habitat fragmentation,and environmental alterations have restricted these species in small and isolated populations.Currently,all extant big cats are categorized as endangered or threatened according to their conservation status.Amur tigers and Amur leopards share overlapping geographic ranges,habitats,and certain prey species in the forests of Northeast Asia(Jiang et al.,2015).To reduce interspecies conflict,these carnivores exhibit differentiated dietary and temporal niches.Amur tigers predominantly prey on large ungulates,while Amur leopards hunt small to medium-sized animals(Sugimoto et al.,2016).Additionally,they occupy different temporal niches,with tigers being active at night and leopards more active during the day.Despite spatial and temporal niche partitioning,interspecific competition between these two species is inevitable.Tigers,benefiting from their greater size,have a competitive advantage over leopards,which can manifest in occasional leopard predation by tigers and declines in leopard populations with increasing tiger density(Jiang et al.,2015).Tigers also displace leopards from marginal habitats in nature reserves where they coexist.
基金supported by the National Natural Science Foundation of China(Grant No.:81974500)the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences,China(Grant No.:2022-I2M-2-001).
文摘Tumors are spatially heterogeneous tissues that comprise numerous cell types with intricate structures.By interacting with the microenvironment,tumor cells undergo dynamic changes in gene expression and metabolism,resulting in spatiotemporal variations in their capacity for proliferation and metastasis.In recent years,the rapid development of histological techniques has enabled efficient and high-throughput biomolecule analysis.By preserving location information while obtaining a large number of gene and molecular data,spatially resolved metabolomics(SRM)and spatially resolved transcriptomics(SRT)approaches can offer new ideas and reliable tools for the in-depth study of tumors.This review provides a comprehensive introduction and summary of the fundamental principles and research methods used for SRM and SRT techniques,as well as a review of their applications in cancer-related fields.
基金This work was supported by the National Basic Research Program of China （973 Program） （No.2013CB922200） and the National Natural Science Foundation of China （No.91121006, No.21273274, No.21173256, and No.21303255）.
文摘The photodissociation dynamics of 2-iodotoluene following excitation at 266 nm have been investigated employing femtosecond time-resolved mass spectrometry. The photofragments are detected by multiphoton ionization using an intense laser field centered at 800 nm. A dissociation time of 3804-50 fs was measured from the rising time of the co-fragments of toluene radical （C7H7） and iodine atom （I）, which is attributed to the averaged time needed for the C-I bond breaking for the simultaneously excited nσ and ππ＊ states by 266 nm pump light. In addition, a probe light centered at 298.23 nm corresponding to resonance wavelength of ground-state iodine atom is used to selectively ionize ground-state iodine atoms generated from the dissociation of initially populated hσ＊ and ππ＊ states. And a rise time of 4004-50 fs is extracted from the fitting of time-dependent I＋ transient, which is in agreement with the dissociation time obtained by multiphoton ionization with 800 nm, suggesting that the main dissociative products are ground-state iodine atoms.
基金supported by the Shenzhen Key Laboratory of Single-Cell Omics(ZDSYS20190902093613831)the Guangdong Provincial Key Laboratory of Genome Read and Write(2017B030301011)Longqi Liu was supported by the National Natural Science Foundation of China(31900466).
文摘The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the scientific community has been able to visualize life at an unprecedented resolution.Most recently,the Spatially Resolved Transcriptomics(SRT)technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life,including the origin of different cellular populations developed from totipotent cells and human diseases.In this review,we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools,as well as the representative SRT applications.With the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects,we can foresee the bright future of such new tools in understanding life at the most profound analytical level.
文摘Background: Probable benign paroxysmal positional vertigo, spontaneously resolved (pBPPVsr), is a variant of benign paroxysmal positional vertigo (BPPV) in which there is no observable nystagmus and no vertigo with any positional maneuver. Objectives: To calculate the incidence pBPPVsr, compare the characteristics of the patients with pBPPVsr and BPPV not spontaneously resolved and describe the spontaneous resolution in the natural course of BPPV. Methods: Multicenter prospective descriptive study. During a one-year period, all patients with suspected BPPV that presented to the Neurotology Units of five participating centers were recruited. The incidence of pBPPVsr was calculated as a percentage of the total number of patients with BPPV. The prevalence of several variables was compared between pBPPVsr and BPPV not spontaneously resolved. The timing of spontaneous resolution was estimated using Kaplan-Meier curves. Results: 457 patients met the inclusion criteria. The incidence of pBPPVsr was 33.5%. It was significantly higher in males, in patients with normal bone mass and in patients who were not taking sulpiride. A rate of 18% of spontaneous resolution after the first month and 51% after the first year was found. This percentage did not change in a significant way after this moment. The curves for males, patients under 50 and patients with normal blood pressure decreased significantly faster. Conclusions: In our serie, BPPV spontaneously resolved in half of the patients with BPPV during the first year. This seemed to occur more commonly in males and could have been hindered by sulpiride intake, osteoporosis, advanced age and high blood pressure.
文摘In situ time-resolved spectroscopy is an effective method to monitor the catalysis reaction in real time and reveal the catalytic mechanistic pathway.The dynamic evolution of coordination and electronic structures of catalytic active sites during the CO2 reduction reaction is still a "black box," impeding the design of high-efficiency catalysts.In a recent report published in J.Am.Chem.Soc.,by multiple in situ time-resolved spectroscopy.
基金supported by the Guangxi Major Project of Science and Technology(Guike AA18118027)the Postdoctoral Project of Hainan Yazhou Bay Seed Laboratory Program(B21Y10203)the Scientific Research and Development Fund of the College of Agriculture,Guangxi University(EE101731).
文摘The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing,Oxford Nanopore 50-kb ultra-long,and high-throughput chromatin conformation capture technologies.The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps,while a total of 633.0 Mb genomic sequences were generated.The origination analysis identified 338.5Mb genomic sequences originating from citron(53.5%),147.4Mb frommandarin(23.3%),and 147.1Mb frompummelo(23.2%).The genome included 30528 protein-coding genes,and most of the assembled sequences were found to be repetitive sequences.Several significantly expanded gene families were associated with plant-pathogen interactions,plant hormone signal transduction,and the biosynthesis of major active components,such as terpenoids and f lavor compounds.Most HLB-tolerant genes were expanded in the lemon genome,such as 2-oxoglutarate(2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1,cell wall-related genes,and lignin synthesis genes.Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon.Our results provide insight into lemon genome evolution,active component biosynthesis,and genes associated with HLB tolerance.
基金This work was financially supported by National Natural Science Foundation of China(No.32130092,No.31872072)LiaoNing Revitalization Talents Pro-gram(No.XLYC1902069).
文摘Cultivated strawberry(Fragaria×ananassa),a perennial herb belonging to the family Rosaceae,is a complex octoploid with high heterozygosity at most loci.However,there is no research on the haplotype of the octoploid strawberry genome.Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar,“Yanli”,using single molecule real-time sequencing and high-throughput chromosome conformation capture technology.The“Yanli”genome was 823 Mb in size,with a long terminal repeat assembly index of 14.99.The genome was phased into two haplotypes,Hap1(825 Mb with contig N50 of 26.70 Mb)and Hap2(808 Mb with contig N50 of 27.51 Mb).Using the combination of Hap1 and Hap2,we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry.We identified a∼10 Mb inversion and translocation on chromosome 2-1.104957 and 102356 protein-coding genes were annotated in Hap1 and Hap2,respectively.Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F.×ananassa genome.In summary,we obtained a high-quality haplotype-resolved genome assembly of F.×ananassa,which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.
基金This study was supported by the Foundation for the Introduction of Talent of Pingdingshan University(PXY-BSQD2016009)the Key Research Project of Colleges and Universities of Henan Province(182102110132,172102110111)+6 种基金the National Natural Science Foundation(31600527)the Fundamental Research Funds for the Central Universities of Beijing Forestry University(2018BLCB08)the Project for the Construction of World Class Universities of Beijing Forestry University(2019XKJS0308)the Scientific Research Foundation for National Natural Science Fund(31600527)Z.L.is funded by a postdoctoral fellowship from the Special Research Fund of Ghent University(BOFPDO2018001701)Y.V.P.acknowledges fundings from the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(grant agreement No 833522)from Ghent University(Methusalem funding,BOF.MET.2021.0005.01).
文摘Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.
基金supported by the National Natural Science Foundation of China (Nos. 41175018, 41475113)the special fund of the State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry (No. LAPC-KF-2014-01)
文摘Size-resolved aerosol samples were collected by MOUDI in four seasons in 2007 in Beijing. The PM10 and PM1.8mass concentrations were 166.0 ± 120.5 and 91.6 ± 69.7 μg/m^3, respectively,throughout the measurement, with seasonal variation： nearly two times higher in autumn than in summer and spring. Serious fine particle pollution occurred in winter with the PM1.8/PM10 ratio of 0.63, which was higher than other seasons. The size distribution of PM showed obvious seasonal and diurnal variation, with a smaller fine mode peak in spring and in the daytime. OM（organic matter = 1.6 × OC（organic carbon）） and SIA（secondary inorganic aerosol） were major components of fine particles, while OM, SIA and Ca^2＋were major components in coarse particles. Moreover, secondary components, mainly SOA（secondary organic aerosol） and SIA,accounted for 46%-96% of each size bin in fine particles, which meant that secondary pollution existed all year. Sulfates and nitrates, primarily in the form of（NH4）2SO4, NH4NO3, Ca SO4, Na2SO4 and K2SO4, calculated by the model ISORROPIA II, were major components of the solid phase in fine particles. The PM concentration and size distribution were similar in the four seasons on non-haze days, while large differences occurred on haze days, which indicated seasonal variation of PM concentration and size distribution were dominated by haze days. The SIA concentrations and fractions of nearly all size bins were higher on haze days than on non-haze days, which was attributed to heterogeneous aqueous reactions on haze days in the four seasons.
基金supported by the National Natural Science Foundation of China(Grant Nos.:81974500,81773678)the CAMS Innovation Fund for Medical Sciences(Grant No.:2022-I2M-2-001).
文摘Against tumor-dependent metabolic vulnerability is an attractive strategy for tumor-targeted therapy.However,metabolic inhibitors are limited by the drug resistance of cancerous cells due to their metabolic plasticity and heterogeneity.Herein,choline metabolism was discovered by spatially resolved metabolomics analysis as metabolic vulnerability which is highly active in different cancer types,and a choline-modified strategy for small molecule-drug conjugates(SMDCs)design was developed to fool tumor cells into indiscriminately taking in choline-modified chemotherapy drugs for targeted cancer therapy,instead of directly inhibiting choline metabolism.As a proof-of-concept,choline-modified SMDCs were designed,screened,and investigated for their druggability in vitro and in vivo.This strategy improved tumor targeting,preserved tumor inhibition and reduced toxicity of paclitaxel,through targeted drug delivery to tumor by highly expressed choline transporters,and site-specific release by carboxylesterase.This study expands the strategy of targeting metabolic vulnerability and provides new ideas of developing SMDCs for precise cancer therapy.
文摘After online publication of the article 1,the authors noticed the affiliation“College of Landscape Architecture and Life Science/Institute of Special Plants,Chongqing University of Arts and Sciences,Yongchuan,Chongqing,China”for author Yiqing Liu was missing.
