Traditional villages represent a concentrated expression of the preservation and transmission of traditional culture within the context of rural revitalization,conveying important social,historical,and cultural values...Traditional villages represent a concentrated expression of the preservation and transmission of traditional culture within the context of rural revitalization,conveying important social,historical,and cultural values.Based on the perspective of spatial genes,this study selected 67 typical traditional villages in the Wuling Mountain Area in Southwest China as the case study.Between 2021 and 2024,by identifying and extracting spatial genes through the semi-structured interviews,Laddering Technique,and Landscape Pattern Index,and applying the geo-detector,the study explored the morphological characteristics and influencing mechanisms of traditional Tujia villages from the perspective of spatial genes of ecological-production-living.The findings are as follows:1)the spatial genes of traditional Tujia villages in the Wuling Mountain Area exhibit distinct patterns.Ecological genes,categorized by natural environment and layout,demonstrate a transition from clustered to dispersed patterns from the southern to northern regions.Production genes,categorized by location and cultivation patterns,show concentrated agricultural lands in the south and fragmented in the north.Living genes,divided into house plans,facades,and public buildings,reveal a higher prevalence of courtyards,stilted houses,and public buildings in northern areas.2)The spatial genes have evolved through the combined influence of four key factors:natural environment,socioeconomic development,policy systems,and ethnic culture.3)The integration of multi-source data and the application of both qualitative and quantitative approaches provide a comprehensive framework for analyzing traditional village form and their influencing mechanisms.This methodology offers valuable insights for developing sustainable strategies for the conservation of traditional Tujia traditional villages in this region.展开更多
Recent advancements in spatial transcriptomics(ST)technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues,p...Recent advancements in spatial transcriptomics(ST)technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues,providing critical insights into spatial gene expression patterns,tissue organization,and gene functionality.However,existing methods for clustering spatially variable genes(SVGs)into co-expression modules often fail to detect rare or unique spatial expression patterns.To address this,we present spatial transcriptomics iterative hierarchical clustering(stIHC),a novel method for clustering SVGs into co-expression modules,representing groups of genes with shared spatial expression patterns.Through three simulations and applications to ST datasets from technologies such as 10x Visium,10x Xenium,and Spatial Transcriptomics,stIHC outperforms clustering approaches used by popular SVG detection methods,including SPARK,SPARK-X,MERINGUE,and SpatialDE.Gene ontology enrichment analysis confirms that genes within each module share consistent biological functions,supporting the functional relevance of spatial co-expression.Robust across technologies with varying gene numbers and spatial resolution,stIHC provides a powerful tool for decoding the spatial organization of gene expression and the functional structure of complex tissues.展开更多
The liver serves as a central organ regulating numerous complex metabolic processes[1,2].Hepatic lobule metabolic zonation supports distinct hepatocyte functions through spatially dependent gene expression that is gov...The liver serves as a central organ regulating numerous complex metabolic processes[1,2].Hepatic lobule metabolic zonation supports distinct hepatocyte functions through spatially dependent gene expression that is governed by intricate signaling networks and interactions with diverse non-parenchymal cells[3–5].Notably,liver sinusoidal endothelial cells(LSECs)provide critical regulatory functions during hepatic regeneration and pathological adaptation[6].However,current hepatic pathology research is limited by inadequate models that poorly replicate human disease phenotypes and pharmacological responses.展开更多
基金Under the auspices of Natural Science Foundation General Project of Hainan Province(No.722MS066)Chongqing Municipal Education Science Planning Project(No.K25ZZ2070096)。
文摘Traditional villages represent a concentrated expression of the preservation and transmission of traditional culture within the context of rural revitalization,conveying important social,historical,and cultural values.Based on the perspective of spatial genes,this study selected 67 typical traditional villages in the Wuling Mountain Area in Southwest China as the case study.Between 2021 and 2024,by identifying and extracting spatial genes through the semi-structured interviews,Laddering Technique,and Landscape Pattern Index,and applying the geo-detector,the study explored the morphological characteristics and influencing mechanisms of traditional Tujia villages from the perspective of spatial genes of ecological-production-living.The findings are as follows:1)the spatial genes of traditional Tujia villages in the Wuling Mountain Area exhibit distinct patterns.Ecological genes,categorized by natural environment and layout,demonstrate a transition from clustered to dispersed patterns from the southern to northern regions.Production genes,categorized by location and cultivation patterns,show concentrated agricultural lands in the south and fragmented in the north.Living genes,divided into house plans,facades,and public buildings,reveal a higher prevalence of courtyards,stilted houses,and public buildings in northern areas.2)The spatial genes have evolved through the combined influence of four key factors:natural environment,socioeconomic development,policy systems,and ethnic culture.3)The integration of multi-source data and the application of both qualitative and quantitative approaches provide a comprehensive framework for analyzing traditional village form and their influencing mechanisms.This methodology offers valuable insights for developing sustainable strategies for the conservation of traditional Tujia traditional villages in this region.
基金Science Foundation Ireland,Grant/Award Numbers:18/CRT/6214,18/CRT/6214(S4)。
文摘Recent advancements in spatial transcriptomics(ST)technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues,providing critical insights into spatial gene expression patterns,tissue organization,and gene functionality.However,existing methods for clustering spatially variable genes(SVGs)into co-expression modules often fail to detect rare or unique spatial expression patterns.To address this,we present spatial transcriptomics iterative hierarchical clustering(stIHC),a novel method for clustering SVGs into co-expression modules,representing groups of genes with shared spatial expression patterns.Through three simulations and applications to ST datasets from technologies such as 10x Visium,10x Xenium,and Spatial Transcriptomics,stIHC outperforms clustering approaches used by popular SVG detection methods,including SPARK,SPARK-X,MERINGUE,and SpatialDE.Gene ontology enrichment analysis confirms that genes within each module share consistent biological functions,supporting the functional relevance of spatial co-expression.Robust across technologies with varying gene numbers and spatial resolution,stIHC provides a powerful tool for decoding the spatial organization of gene expression and the functional structure of complex tissues.
基金supported in part by the National Key Research and Development Program of China(2022YFA1103400 and 2022YFC2406704)the National Natural Science Foundation of China(32371477,82090051,and 92168207).
文摘The liver serves as a central organ regulating numerous complex metabolic processes[1,2].Hepatic lobule metabolic zonation supports distinct hepatocyte functions through spatially dependent gene expression that is governed by intricate signaling networks and interactions with diverse non-parenchymal cells[3–5].Notably,liver sinusoidal endothelial cells(LSECs)provide critical regulatory functions during hepatic regeneration and pathological adaptation[6].However,current hepatic pathology research is limited by inadequate models that poorly replicate human disease phenotypes and pharmacological responses.
