Dear Editor,Plant mitochondria are essential organelles of plant cells and play crucial roles in oxidative phosphorylation and diverse metabolic processes(Wang et al.,2024).Mitochondria have an endosymbiotic origin,li...Dear Editor,Plant mitochondria are essential organelles of plant cells and play crucial roles in oxidative phosphorylation and diverse metabolic processes(Wang et al.,2024).Mitochondria have an endosymbiotic origin,likely from a proteobacterial lineage that branched off before the divergence of known alphaproteobacterial groups(Martijn et al.,2018),and contain their own genetic materials,known as plant mitochondrial genomes(PMGs).PMGs exhibit unique features that may result from mechanisms different from those of nuclei and plastids,such as DNA repair(Chevigny et al.,2020),mRNA splicing(Novikova and Belfort.2017;Guo et al.,2020),transcription regulation,and foreign sequence integration.Recent advances in genome editing technologies have facilitated targeted modifications of PMGs,enabling the functional characterization of mitochondrial genes and the generation of desirable phenotypes(Forner et al.,2023;Xu et al.,2024).Accurate annotations of PMGs are a prerequisite for basic and applied research on mitochondria,such as studies of PMG evolution or targeted breeding of new crop varieties by PMG engineering.展开更多
In this study,we searched for dispersed repeats(DRs)in the rice(Oryza sativa)genome using the iterative procedure(IP)method.The results revealed that the O.sativa genome contained 79 DR families,comprising 992739 DNA ...In this study,we searched for dispersed repeats(DRs)in the rice(Oryza sativa)genome using the iterative procedure(IP)method.The results revealed that the O.sativa genome contained 79 DR families,comprising 992739 DNA repeats,of which 496762 and 495977 were identified on the forward and reverse DNA strands,respectively.The detected DRs were,on average,374 bp in length and occupied 66.4%of the O.sativa genome.Totally 61%of DRs,identified by the IP method,overlapped with previously annotated dispersed repeats(ADRs)detected using the Extensive De Novo TE Annotator(EDTA)pipeline.展开更多
Biomedical big data,characterized by its massive scale,multi-dimensionality,and heterogeneity,offers novel perspectives for disease research,elucidates biological principles,and simultaneously prompts changes in relat...Biomedical big data,characterized by its massive scale,multi-dimensionality,and heterogeneity,offers novel perspectives for disease research,elucidates biological principles,and simultaneously prompts changes in related research methodologies.Biomedical ontology,as a shared formal conceptual system,not only offers standardized terms for multi-source biomedical data but also provides a solid data foundation and framework for biomedical research.In this review,we summarize enrichment analysis and deep learning for biomedical ontology based on its structure and semantic annotation properties,highlighting how technological advancements are enabling the more comprehensive use of ontology information.Enrichment analysis represents an important application of ontology to elucidate the potential biological significance for a particular molecular list.Deep learning,on the other hand,represents an increasingly powerful analytical tool that can be more widely combined with ontology for analysis and prediction.With the continuous evolution of big data technologies,the integration of these technologies with biomedical ontologies is opening up exciting new possibilities for advancing biomedical research.展开更多
Ericaceae is a diverse family of flowering plants distributed nearly worldwide,and it includes 126 genera and more than 4,000 species.In the present study,we developed The Ericaceae Genome Resource(TEGR,http://www.teg...Ericaceae is a diverse family of flowering plants distributed nearly worldwide,and it includes 126 genera and more than 4,000 species.In the present study,we developed The Ericaceae Genome Resource(TEGR,http://www.tegr.com.cn)as a comprehensive,user-friendly,web-based functional genomic database that is based on 16 published genomes from 16 Ericaceae species.The TEGR database contains information on many important functional genes,including 763 auxin genes,2,407 flowering genes,20,432 resistance genes,617 anthocyanin-related genes,and 470 N^(6)-methyladenosine(m^(6)A)modification genes.We identified a total of 599,174 specific guide sequences for CRISPR in the TEGR database.The gene duplication events,synteny analysis,and orthologous analysis of the16 Ericaceae species were performed using the TEGR database.The TEGR database contains 614,821 functional genes annotated through the GO,Nr,Pfam,TrEMBL,and Swiss-Prot databases.The TEGR database provides the Primer Design,Hmmsearch,Synteny,BLAST,and JBrowse tools for helping users perform comprehensive comparative genome analyses.All the high-quality reference genome sequences,genomic features,gene annotations,and bioinformatics results can be downloaded from the TEGR database.In the future,we will continue to improve the TEGR database with the latest data sets when they become available and to provide a useful resource that facilitates comparative genomic studies.展开更多
Glaucoma is an eye disease characterized by pathologically elevated intraocular pressure,optic nerve atrophy,and visual field defects,which can lead to irreversible vision loss.In recent years,the rapid development of...Glaucoma is an eye disease characterized by pathologically elevated intraocular pressure,optic nerve atrophy,and visual field defects,which can lead to irreversible vision loss.In recent years,the rapid development of artificial intelligence(AI)technology has provided new approaches for the early diagnosis and management of glaucoma.By classifying and annotating glaucoma-related images,AI models can learn and recognize the specific pathological features of glaucoma,thereby achieving automated imaging analysis and classification.Research on glaucoma imaging classification and annotation mainly involves color fundus photography(CFP),optical coherence tomography(OCT),anterior segment optical coherence tomography(AS-OCT),and ultrasound biomicroscopy(UBM)images.CFP is primarily used for the annotation of the optic cup and disc,while OCT is used for measuring and annotating the thickness of the retinal nerve fiber layer,and AS-OCT and UBM focus on the annotation of the anterior chamber angle structure and the measurement of anterior segment structural parameters.To standardize the classification and annotation of glaucoma images,enhance the quality and consistency of annotated data,and promote the clinical application of intelligent ophthalmology,this guideline has been developed.This guideline systematically elaborates on the principles,methods,processes,and quality control requirements for the classification and annotation of glaucoma images,providing standardized guidance for the classification and annotation of glaucoma images.展开更多
The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannot...The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.展开更多
During the process of organizing our original data,we unfortunately identified two error in the figures within our published article.In Fig.1,the online version incorrectly labels the SNI+NAC group as the sham+NAC gro...During the process of organizing our original data,we unfortunately identified two error in the figures within our published article.In Fig.1,the online version incorrectly labels the SNI+NAC group as the sham+NAC group.We have revised the grouping annotations in Fig.1 and have labeled the DHE staining in the figure to present the experimental design more clearly.展开更多
Natural products(NPs)have long held a significant position in various fields such as medicine,food,agriculture,and materials.The chemical space covered by NPs is extensive but often underexplored.Therefore,high-throug...Natural products(NPs)have long held a significant position in various fields such as medicine,food,agriculture,and materials.The chemical space covered by NPs is extensive but often underexplored.Therefore,high-throughput and efficient methodologies for the annotation and discovery of NPs are desired to address the complexity and diversity of NP-based systems.Mass spectrometry(MS)has emerged as a powerful platform for the annotation and discovery of NPs.MS databases provide vital support for the structural characterization of NPs by integrating extensive mass spectral data and sample information.Additionally,the released annotation methodologies,based on a variety of informatics tools,continuously improve the ability to annotate the structure and properties of compounds.This review examines the current mainstream databases and annotation methodologies,focusing on their advantages and limitations.Prospects for future technological advancements are then discussed in terms of novel applications and research objectives.Through a systematic overview,this review aims to provide valuable insights and a reference for MS-based NPs annotation,thereby promoting the discovery of novel natural entities.展开更多
Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hinde...Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hindered the comprehensive exploration of its unique phylogenetic position and therapeutic potential,thereby limiting our understanding of its genomic structure and metabolic capabilities.In this study,we present the first chromosome-level,telomere-to-telomere(T2T)genome assembly of S.moellendorffii,constructed utilizing PacBio HiFi,Oxford Nanopore(ONT),and Hi-C technologies.The assembled genome,spanning 112.83 Mb across 10 chromosomes with a contig N50 of 11.11 Mb,exhibited exceptional completeness(BUSCO score:95.7%)and accuracy(QV=48.11).Comparative genomic analysis identified 3515 gene families unique to S.moellendorffii,with significant enrichment in secondary metabolismpathways,including those related to flavonoid biosynthesis.Phylogenetic analysis revealed that S.moellendorffii diverged from Isoetes approximately 339.6 million years ago(MYA),representing a key evolutionary transition in early vascular plants.By integrating tissue-specific transcriptome and metabolome analyses,we uncovered the molecular basis of biflavone biosynthesis,identifying key enzymes and regulatory networks that govern the production of these bioactive compounds.We observed a correlation between the tissue-specific accumulation patterns of six major biflavones,including amentoflavone and ginkgetin,and the expression of their biosynthetic genes.This high-quality genome assembly,coupled with multi-omics analyses,offers unprecedented insights into the evolution of early vascular plants and elucidates the molecular mechanisms behind their specialized metabolism.展开更多
The quality of traditional Chinese medicine(TCM)prescriptions(TCMPs)is critical to clinical efficacy;however,evaluating their consistency and identifying sources of variability remain challenging.This study proposes a...The quality of traditional Chinese medicine(TCM)prescriptions(TCMPs)is critical to clinical efficacy;however,evaluating their consistency and identifying sources of variability remain challenging.This study proposes an integrated strategy to assess the quality of 100 widely sold TCMPs.A"one-for-all"chromatographic method was employed to analyze 645 sample batches.This large-scale data collection enabled statistical evaluations,such as hierarchical cluster analysis(HCA)and similarity heatmap,to identify quality inconsistencies.The introduction of a TCM-specific mass spectrometry(MS)database allowed for rapid,automated annotation of chemicals across 100 prescriptions and facilitated the tracing of raw material sources.Results indicate that 19%of prescriptions exhibited chemical inconsistencies,which are associated with high market value,low pricing,and substantial price disparities.The MS database allowed rapid annotation of 761 and 673 compounds in positive and negative modes,respec-tively,in 100 TCMPs,with 73 prescriptions reported for the first time.The tracing efforts succeeded in identifying>40%of the raw material sources for 51 prescriptions.P93(Yinianjin(YNJ))is a case in which the chromatographic profiles from three manufacturers displayed inconsistencies.Analysis using the database traced divergent peaks to Rhei Radix et Rhizoma(RRER).Verification with self-prepared samples confirmed that manufacturers utilized three distinct botanical sources.This integrated strategy provides a scalable framework for quality control in TCMPs.展开更多
Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding.However,the lack of comprehensive functional genomic annotations in animals limits the effectiveness of mos...Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding.However,the lack of comprehensive functional genomic annotations in animals limits the effectiveness of most variant function assessment methods.In this study,we gather 1030 raw epigenomic datasets from 10 animal species and systematically annotate 7 types of key regulatory regions,creating a comprehensive functional annotation map of animal genomic variants.Our findings demonstrate that integrating variants with regulatory annotations can identify tissues and cell types underlying economic traits,underscoring the utility of these annotations in functional variant discovery.Using our functional annotations,we rank the functional potential of genetic variants and classify over 127 million candidate variants into 5 functional confidence categories,with high-confidence variants significantly enriched in eQTLs and trait-associated SNPs.Incorporating these variants into genomic prediction models can improve estimated breeding value accuracy,demonstrating their practical utility in breeding programs.To facilitate the use of our results,we develop the Integrated Functional Mutation(IFmut:http://www.ifmutants.com:8212)platform,enabling researchers to explore regulatory annotations and assess the functional potential of animal variants efficiently.Our study provides a robust framework for functional genomic annotations in farm animals,enhancing variant function assessment and breeding precision.展开更多
It is believed that in ancient China,there were only works on graphology,phonology and critical interpretation,but no works on grammar.In works of grammar history published in modern times,they just dwell briefly on a...It is believed that in ancient China,there were only works on graphology,phonology and critical interpretation,but no works on grammar.In works of grammar history published in modern times,they just dwell briefly on ancient grammar,and they consider that there were only some explanations of form words,a few books of form words,but no syntactic analyses.However,in fact,in ancient classical works there were abundant materials of grammatical analyses.Ancient scholars worked out quite a few grammar rules,some of which were profound and coincidental with modern grammar theories.In the present research of ancient Chinese grammar,grammatical analyses made by ancient scholars should be summed up and inherited.展开更多
Dealing with issues such as too simple image features and word noise inference in product image sentence anmotation, a product image sentence annotation model focusing on image feature learning and key words summariza...Dealing with issues such as too simple image features and word noise inference in product image sentence anmotation, a product image sentence annotation model focusing on image feature learning and key words summarization is described. Three kernel descriptors such as gradient, shape, and color are extracted, respectively. Feature late-fusion is executed in turn by the multiple kernel learning model to obtain more discriminant image features. Absolute rank and relative rank of the tag-rank model are used to boost the key words＇ weights. A new word integration algorithm named word sequence blocks building （WSBB） is designed to create N-gram word sequences. Sentences are generated according to the N-gram word sequences and predefined templates. Experimental results show that both the BLEU-1 scores and BLEU-2 scores of the sentences are superior to those of the state-of-art baselines.展开更多
Du Yu’s Annotation of Classics and Elucidations in "Spring and Autumn Annals" is considered as a milestone for the studies of Spring and Autumn Annals, In Du’s book, the Preface to the Spring and Autumn An...Du Yu’s Annotation of Classics and Elucidations in "Spring and Autumn Annals" is considered as a milestone for the studies of Spring and Autumn Annals, In Du’s book, the Preface to the Spring and Autumn Annals is a theoretical summary and revision for the previous studies on the Spring and Autumn Annals and the Tso Chuan. Its combination of classics and elucidations makes Tso Chuan a real elucidating study on Spring and Autumn Annals. Du expounds his philosophy and political ideas in this book.展开更多
In order to implement the real-time detection of abnormality of elder and devices in an empty nest home,multi-modal joint sensors are used to collect discrete action sequences of behavior,and the improved hierarchical...In order to implement the real-time detection of abnormality of elder and devices in an empty nest home,multi-modal joint sensors are used to collect discrete action sequences of behavior,and the improved hierarchical hidden Markov model is adopted to Abstract these discrete action sequences captured by multi-modal joint sensors into an occupant’s high-level behavior—event,then structure representation models of occupant normality are modeled from large amounts of spatio-temporal data. These models are used as classifiers of normality to detect an occupant’s abnormal behavior.In order to express context information needed by reasoning and detection,multi-media ontology （MMO） is designed to annotate and reason about the media information in the smart monitoring system.A pessimistic emotion model （PEM） is improved to analyze multi-interleaving events of multi-active devices in the home.Experiments demonstrate that the PEM can enhance the accuracy and reliability for detecting active devices when these devices are in blind regions or are occlusive. The above approach has good performance in detecting abnormalities involving occupants and devices in a real-time way.展开更多
基金supported by the CAMS Innovation Fund for Medical Sciences(CIFMS)(2021-I2M-1-022)the National Science&Technology Fundamental Resources Investigation Program of China(2018FY100705)the Provincial Special Project for Construction of Innovation Demonstration Area at Chenzhou City under National Sustainable Development Plan(2023sfq04).
文摘Dear Editor,Plant mitochondria are essential organelles of plant cells and play crucial roles in oxidative phosphorylation and diverse metabolic processes(Wang et al.,2024).Mitochondria have an endosymbiotic origin,likely from a proteobacterial lineage that branched off before the divergence of known alphaproteobacterial groups(Martijn et al.,2018),and contain their own genetic materials,known as plant mitochondrial genomes(PMGs).PMGs exhibit unique features that may result from mechanisms different from those of nuclei and plastids,such as DNA repair(Chevigny et al.,2020),mRNA splicing(Novikova and Belfort.2017;Guo et al.,2020),transcription regulation,and foreign sequence integration.Recent advances in genome editing technologies have facilitated targeted modifications of PMGs,enabling the functional characterization of mitochondrial genes and the generation of desirable phenotypes(Forner et al.,2023;Xu et al.,2024).Accurate annotations of PMGs are a prerequisite for basic and applied research on mitochondria,such as studies of PMG evolution or targeted breeding of new crop varieties by PMG engineering.
基金supported by the Russian Science Foundation,Russia(Grant No.24-24-00031).
文摘In this study,we searched for dispersed repeats(DRs)in the rice(Oryza sativa)genome using the iterative procedure(IP)method.The results revealed that the O.sativa genome contained 79 DR families,comprising 992739 DNA repeats,of which 496762 and 495977 were identified on the forward and reverse DNA strands,respectively.The detected DRs were,on average,374 bp in length and occupied 66.4%of the O.sativa genome.Totally 61%of DRs,identified by the IP method,overlapped with previously annotated dispersed repeats(ADRs)detected using the Extensive De Novo TE Annotator(EDTA)pipeline.
基金supported by the National Natural Science Foundation of China(61902095).
文摘Biomedical big data,characterized by its massive scale,multi-dimensionality,and heterogeneity,offers novel perspectives for disease research,elucidates biological principles,and simultaneously prompts changes in related research methodologies.Biomedical ontology,as a shared formal conceptual system,not only offers standardized terms for multi-source biomedical data but also provides a solid data foundation and framework for biomedical research.In this review,we summarize enrichment analysis and deep learning for biomedical ontology based on its structure and semantic annotation properties,highlighting how technological advancements are enabling the more comprehensive use of ontology information.Enrichment analysis represents an important application of ontology to elucidate the potential biological significance for a particular molecular list.Deep learning,on the other hand,represents an increasingly powerful analytical tool that can be more widely combined with ontology for analysis and prediction.With the continuous evolution of big data technologies,the integration of these technologies with biomedical ontologies is opening up exciting new possibilities for advancing biomedical research.
基金supported by the National Natural Science Foundation of China(32260097)the National Guidance of Local Science and Technology Development Fund of China([2023]009)。
文摘Ericaceae is a diverse family of flowering plants distributed nearly worldwide,and it includes 126 genera and more than 4,000 species.In the present study,we developed The Ericaceae Genome Resource(TEGR,http://www.tegr.com.cn)as a comprehensive,user-friendly,web-based functional genomic database that is based on 16 published genomes from 16 Ericaceae species.The TEGR database contains information on many important functional genes,including 763 auxin genes,2,407 flowering genes,20,432 resistance genes,617 anthocyanin-related genes,and 470 N^(6)-methyladenosine(m^(6)A)modification genes.We identified a total of 599,174 specific guide sequences for CRISPR in the TEGR database.The gene duplication events,synteny analysis,and orthologous analysis of the16 Ericaceae species were performed using the TEGR database.The TEGR database contains 614,821 functional genes annotated through the GO,Nr,Pfam,TrEMBL,and Swiss-Prot databases.The TEGR database provides the Primer Design,Hmmsearch,Synteny,BLAST,and JBrowse tools for helping users perform comprehensive comparative genome analyses.All the high-quality reference genome sequences,genomic features,gene annotations,and bioinformatics results can be downloaded from the TEGR database.In the future,we will continue to improve the TEGR database with the latest data sets when they become available and to provide a useful resource that facilitates comparative genomic studies.
基金Supported by Guangdong Basic and Applied Basic Research Foundation(No.2025A1515011627)San Ming Project of Medicine in Shenzhen(No.SZSM202311012).
文摘Glaucoma is an eye disease characterized by pathologically elevated intraocular pressure,optic nerve atrophy,and visual field defects,which can lead to irreversible vision loss.In recent years,the rapid development of artificial intelligence(AI)technology has provided new approaches for the early diagnosis and management of glaucoma.By classifying and annotating glaucoma-related images,AI models can learn and recognize the specific pathological features of glaucoma,thereby achieving automated imaging analysis and classification.Research on glaucoma imaging classification and annotation mainly involves color fundus photography(CFP),optical coherence tomography(OCT),anterior segment optical coherence tomography(AS-OCT),and ultrasound biomicroscopy(UBM)images.CFP is primarily used for the annotation of the optic cup and disc,while OCT is used for measuring and annotating the thickness of the retinal nerve fiber layer,and AS-OCT and UBM focus on the annotation of the anterior chamber angle structure and the measurement of anterior segment structural parameters.To standardize the classification and annotation of glaucoma images,enhance the quality and consistency of annotated data,and promote the clinical application of intelligent ophthalmology,this guideline has been developed.This guideline systematically elaborates on the principles,methods,processes,and quality control requirements for the classification and annotation of glaucoma images,providing standardized guidance for the classification and annotation of glaucoma images.
基金the Natural Science Foundation of Shandong Province(ZR2020QC022)the Science and Technology Basic Resources Investigation Program of China(No.2019FY100900)+2 种基金the Major Program for Basic Research Project of Yunnan Province(202401BC070001)Yunnan Revitalization Talent Support Program:Yunling Scholar Project to Tingshuang Yithe open research project of“Cross Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences.
文摘The plastid genome(plastome)represents an indispensable molecular resource for studying plant phylogeny and evolution.Although plastome size is much smaller than that of nuclear genomes,accurately and efficientlyannotating and utilizing plastome sequences remain challenging.Therefore,a streamlined phylogenomic pipeline spanning plastome annotation,phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome.Here,we develop PlastidHub,a novel web application employing innovative tools to analyze plastome sequences.In comparison with existing tools,key novel functionalities in PlastidHub include:(1)standardization of quadripartite structure;(2)improvement of annotation flexibility and consistency;(3)quantitative assessment of annotation completeness;(4)diverse extraction modes for canonical and specialized sequences;(5)intelligent screening of molecular markers for biodiversity studies;(6)genelevel visual comparison of structural variations and annotation completeness.PlastidHub features cloud-based web applications that do not require users to install,update,or maintain tools;detailed help documents including user guides,test examples,a static pop-up prompt box,and dynamic pop-up warning prompts when entering unreasonable parameter values;batch processing capabilities for all tools;intermediate results for secondary use;and easy-to-operate task flows between fileupload and download.A key feature of PlastidHub is its interrelated task-based user interface design.Give that PlastidHub is easy to use without specialized computational skills or resources,this new platform should be widely used among botanists and evolutionary biologists,improving and expediting research employing the plastome.PlastidHub is available at https://www.plastidhub.cn.
文摘During the process of organizing our original data,we unfortunately identified two error in the figures within our published article.In Fig.1,the online version incorrectly labels the SNI+NAC group as the sham+NAC group.We have revised the grouping annotations in Fig.1 and have labeled the DHE staining in the figure to present the experimental design more clearly.
基金supported by the National Natural Science Foundation of China(Nos.82274064,82374026,and 82204591)。
文摘Natural products(NPs)have long held a significant position in various fields such as medicine,food,agriculture,and materials.The chemical space covered by NPs is extensive but often underexplored.Therefore,high-throughput and efficient methodologies for the annotation and discovery of NPs are desired to address the complexity and diversity of NP-based systems.Mass spectrometry(MS)has emerged as a powerful platform for the annotation and discovery of NPs.MS databases provide vital support for the structural characterization of NPs by integrating extensive mass spectral data and sample information.Additionally,the released annotation methodologies,based on a variety of informatics tools,continuously improve the ability to annotate the structure and properties of compounds.This review examines the current mainstream databases and annotation methodologies,focusing on their advantages and limitations.Prospects for future technological advancements are then discussed in terms of novel applications and research objectives.Through a systematic overview,this review aims to provide valuable insights and a reference for MS-based NPs annotation,thereby promoting the discovery of novel natural entities.
基金funded by the National Natural Science Foundation of China(Grant No.81903921)the Key project at central government level:The ability establishment of sustainable use for valuable Chinese medicine resources(2060302)the Distinguished Young Scholars of Hubei University of Chinese Medicine(Grant No.2022ZZXJ002).
文摘Selaginella moellendorffii Hieron.,a lycophyte of significant medicinal and evolutionary importance,is recognized as one of the earliest vascular plants.However,the absence of a high-quality reference genome has hindered the comprehensive exploration of its unique phylogenetic position and therapeutic potential,thereby limiting our understanding of its genomic structure and metabolic capabilities.In this study,we present the first chromosome-level,telomere-to-telomere(T2T)genome assembly of S.moellendorffii,constructed utilizing PacBio HiFi,Oxford Nanopore(ONT),and Hi-C technologies.The assembled genome,spanning 112.83 Mb across 10 chromosomes with a contig N50 of 11.11 Mb,exhibited exceptional completeness(BUSCO score:95.7%)and accuracy(QV=48.11).Comparative genomic analysis identified 3515 gene families unique to S.moellendorffii,with significant enrichment in secondary metabolismpathways,including those related to flavonoid biosynthesis.Phylogenetic analysis revealed that S.moellendorffii diverged from Isoetes approximately 339.6 million years ago(MYA),representing a key evolutionary transition in early vascular plants.By integrating tissue-specific transcriptome and metabolome analyses,we uncovered the molecular basis of biflavone biosynthesis,identifying key enzymes and regulatory networks that govern the production of these bioactive compounds.We observed a correlation between the tissue-specific accumulation patterns of six major biflavones,including amentoflavone and ginkgetin,and the expression of their biosynthetic genes.This high-quality genome assembly,coupled with multi-omics analyses,offers unprecedented insights into the evolution of early vascular plants and elucidates the molecular mechanisms behind their specialized metabolism.
基金the Guangxi Science and Technology Major Project/Program,China(Grant Nos.:GUIKEAA22096029,GUIKEAA23023035)State Key Laboratory of Drug Regulatory Science Project,National Institutes for Food and Drug Control(NIFDC),China(Grant No.:2024SKLDRS0101)+1 种基金Shanghai Institute of Material Medical(SIMM)-National EngineeringResearch Center of TCM Standardization Technology Independent Research Program,Chinathe staff members of the Large-scale MS System at the National Facility for Protein Science in Shanghai(NFPs),Zhangjiang Lab,China for providing technical support.
文摘The quality of traditional Chinese medicine(TCM)prescriptions(TCMPs)is critical to clinical efficacy;however,evaluating their consistency and identifying sources of variability remain challenging.This study proposes an integrated strategy to assess the quality of 100 widely sold TCMPs.A"one-for-all"chromatographic method was employed to analyze 645 sample batches.This large-scale data collection enabled statistical evaluations,such as hierarchical cluster analysis(HCA)and similarity heatmap,to identify quality inconsistencies.The introduction of a TCM-specific mass spectrometry(MS)database allowed for rapid,automated annotation of chemicals across 100 prescriptions and facilitated the tracing of raw material sources.Results indicate that 19%of prescriptions exhibited chemical inconsistencies,which are associated with high market value,low pricing,and substantial price disparities.The MS database allowed rapid annotation of 761 and 673 compounds in positive and negative modes,respec-tively,in 100 TCMPs,with 73 prescriptions reported for the first time.The tracing efforts succeeded in identifying>40%of the raw material sources for 51 prescriptions.P93(Yinianjin(YNJ))is a case in which the chromatographic profiles from three manufacturers displayed inconsistencies.Analysis using the database traced divergent peaks to Rhei Radix et Rhizoma(RRER).Verification with self-prepared samples confirmed that manufacturers utilized three distinct botanical sources.This integrated strategy provides a scalable framework for quality control in TCMPs.
基金supported by the National Natural Science Foundation of China(32341051)the grant from Department of Agriculture and Rural Affairs of Hubei Province(HBZY2023B006-02)+2 种基金the National Funding(2023ZD04050)the National Natural Science Foundation of China Outstanding Youth(32125035)the National Key R&D Young Scientists Project(2022YFD1302000).
文摘Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding.However,the lack of comprehensive functional genomic annotations in animals limits the effectiveness of most variant function assessment methods.In this study,we gather 1030 raw epigenomic datasets from 10 animal species and systematically annotate 7 types of key regulatory regions,creating a comprehensive functional annotation map of animal genomic variants.Our findings demonstrate that integrating variants with regulatory annotations can identify tissues and cell types underlying economic traits,underscoring the utility of these annotations in functional variant discovery.Using our functional annotations,we rank the functional potential of genetic variants and classify over 127 million candidate variants into 5 functional confidence categories,with high-confidence variants significantly enriched in eQTLs and trait-associated SNPs.Incorporating these variants into genomic prediction models can improve estimated breeding value accuracy,demonstrating their practical utility in breeding programs.To facilitate the use of our results,we develop the Integrated Functional Mutation(IFmut:http://www.ifmutants.com:8212)platform,enabling researchers to explore regulatory annotations and assess the functional potential of animal variants efficiently.Our study provides a robust framework for functional genomic annotations in farm animals,enhancing variant function assessment and breeding precision.
文摘It is believed that in ancient China,there were only works on graphology,phonology and critical interpretation,but no works on grammar.In works of grammar history published in modern times,they just dwell briefly on ancient grammar,and they consider that there were only some explanations of form words,a few books of form words,but no syntactic analyses.However,in fact,in ancient classical works there were abundant materials of grammatical analyses.Ancient scholars worked out quite a few grammar rules,some of which were profound and coincidental with modern grammar theories.In the present research of ancient Chinese grammar,grammatical analyses made by ancient scholars should be summed up and inherited.
基金The National Natural Science Foundation of China(No.61133012)the Humanity and Social Science Foundation of the Ministry of Education(No.12YJCZH274)+1 种基金the Humanity and Social Science Foundation of Jiangxi Province(No.XW1502,TQ1503)the Science and Technology Project of Jiangxi Science and Technology Department(No.20121BBG70050,20142BBG70011)
文摘Dealing with issues such as too simple image features and word noise inference in product image sentence anmotation, a product image sentence annotation model focusing on image feature learning and key words summarization is described. Three kernel descriptors such as gradient, shape, and color are extracted, respectively. Feature late-fusion is executed in turn by the multiple kernel learning model to obtain more discriminant image features. Absolute rank and relative rank of the tag-rank model are used to boost the key words＇ weights. A new word integration algorithm named word sequence blocks building （WSBB） is designed to create N-gram word sequences. Sentences are generated according to the N-gram word sequences and predefined templates. Experimental results show that both the BLEU-1 scores and BLEU-2 scores of the sentences are superior to those of the state-of-art baselines.
文摘Du Yu’s Annotation of Classics and Elucidations in "Spring and Autumn Annals" is considered as a milestone for the studies of Spring and Autumn Annals, In Du’s book, the Preface to the Spring and Autumn Annals is a theoretical summary and revision for the previous studies on the Spring and Autumn Annals and the Tso Chuan. Its combination of classics and elucidations makes Tso Chuan a real elucidating study on Spring and Autumn Annals. Du expounds his philosophy and political ideas in this book.
基金The National Natural Science Foundation of China(No.60773110)the Youth Education Fund of Hunan Province(No.07B014)
文摘In order to implement the real-time detection of abnormality of elder and devices in an empty nest home,multi-modal joint sensors are used to collect discrete action sequences of behavior,and the improved hierarchical hidden Markov model is adopted to Abstract these discrete action sequences captured by multi-modal joint sensors into an occupant’s high-level behavior—event,then structure representation models of occupant normality are modeled from large amounts of spatio-temporal data. These models are used as classifiers of normality to detect an occupant’s abnormal behavior.In order to express context information needed by reasoning and detection,multi-media ontology （MMO） is designed to annotate and reason about the media information in the smart monitoring system.A pessimistic emotion model （PEM） is improved to analyze multi-interleaving events of multi-active devices in the home.Experiments demonstrate that the PEM can enhance the accuracy and reliability for detecting active devices when these devices are in blind regions or are occlusive. The above approach has good performance in detecting abnormalities involving occupants and devices in a real-time way.
