According to Edward T.Hall,communication is the core of culture,and the use of space or distance plays a key role as a significant cultural factor in the interpersonal relationship.However,as a hidden dimension,it is ...According to Edward T.Hall,communication is the core of culture,and the use of space or distance plays a key role as a significant cultural factor in the interpersonal relationship.However,as a hidden dimension,it is often out of people’s awareness.This paper aims to explore how Chinese teachers and students respond to each other and their surroundings in the use of space.In addition,considering that China falls into a typical high-context culture,this paper expects to make out the impacts of high-context culture on the use,perception,and sense of the space in the interaction.The study of classroom space will,to a degree,contribute to establishing the relationship of mutual trust and harmony,which is helpful to the teaching and learning.展开更多
Drawing parallels between linguistic constructs and cellular biology,Large Language Models(LLMs)have achieved success in diverse downstream applications for single-cell data analysis.However,to date,it still lacks met...Drawing parallels between linguistic constructs and cellular biology,Large Language Models(LLMs)have achieved success in diverse downstream applications for single-cell data analysis.However,to date,it still lacks methods to take advantage of LLMs to infer Ligand-Receptor(LR)-mediated cell-cell communications for spatially resolved transcriptomic data.Here,we propose SpaCCC to facilitate the inference of spatially resolved cell-cell communications,which relies on our fine-tuned single-cell LLM and functional gene interaction network to embed ligand and receptor genes into a unified latent space.The LR pairs with a significant closer distance in latent space are taken to be more likely to interact with each other.After that,the molecular diffusion and permutation test strategies are respectively employed to calculate the communication strength and filter out communications with low specificities.The benchmarked performance of SpaCCC is evaluated on real single-cell spatial transcriptomic datasets with superiority over other methods.SpaCCC also infers known LR pairs concealed by existing aggregative methods and then identifies communication patterns for specific cell types and their signaling pathways.Furthermore,SpaCCC provides various cell-cell communication visualization results at both single-cell and cell type resolution.In summary,SpaCCC provides a sophisticated and practical tool allowing researchers to decipher spatially resolved cell-cell communications and related communication patterns and signaling pathways based on spatial transcriptome data.展开更多
文摘According to Edward T.Hall,communication is the core of culture,and the use of space or distance plays a key role as a significant cultural factor in the interpersonal relationship.However,as a hidden dimension,it is often out of people’s awareness.This paper aims to explore how Chinese teachers and students respond to each other and their surroundings in the use of space.In addition,considering that China falls into a typical high-context culture,this paper expects to make out the impacts of high-context culture on the use,perception,and sense of the space in the interaction.The study of classroom space will,to a degree,contribute to establishing the relationship of mutual trust and harmony,which is helpful to the teaching and learning.
基金supported by the National Natural Science Foundation of China-Science and Technology Development Fund(No.62361166662)the National Key R&D Program of China(Nos.2023YFC3503400 and 2022YFC3400400)+4 种基金the Key R&D Program of Hunan Province(Nos.2023GK2004,2023SK2059,and 2023SK2060)the Top 10 Technical Key Project in Hunan Province(No.2023GK1010)the Key Technologies R&D Program of Guangdong Province(No.2023B1111030004 to FFH)the Funds of State Key Laboratory of Chemo/Biosensing and Chemometrics,the National Supercomputing Center in Changsha(http://nscc.hnu.edu.cn/)Peng Cheng Lab.Graduate Research Innovation Project of Hunan Province(No.QL20230101).
文摘Drawing parallels between linguistic constructs and cellular biology,Large Language Models(LLMs)have achieved success in diverse downstream applications for single-cell data analysis.However,to date,it still lacks methods to take advantage of LLMs to infer Ligand-Receptor(LR)-mediated cell-cell communications for spatially resolved transcriptomic data.Here,we propose SpaCCC to facilitate the inference of spatially resolved cell-cell communications,which relies on our fine-tuned single-cell LLM and functional gene interaction network to embed ligand and receptor genes into a unified latent space.The LR pairs with a significant closer distance in latent space are taken to be more likely to interact with each other.After that,the molecular diffusion and permutation test strategies are respectively employed to calculate the communication strength and filter out communications with low specificities.The benchmarked performance of SpaCCC is evaluated on real single-cell spatial transcriptomic datasets with superiority over other methods.SpaCCC also infers known LR pairs concealed by existing aggregative methods and then identifies communication patterns for specific cell types and their signaling pathways.Furthermore,SpaCCC provides various cell-cell communication visualization results at both single-cell and cell type resolution.In summary,SpaCCC provides a sophisticated and practical tool allowing researchers to decipher spatially resolved cell-cell communications and related communication patterns and signaling pathways based on spatial transcriptome data.
