The liver performs several vital functions such as metabolism,toxin removal,and glucose storage through the coordination of various cell types.With the recent breakthrough of the single-cell/single-nucleus RNAseq(sc/s...The liver performs several vital functions such as metabolism,toxin removal,and glucose storage through the coordination of various cell types.With the recent breakthrough of the single-cell/single-nucleus RNAseq(sc/snRNA-seq)techniques,there is a great opportunity to establish a reference cell map of the liver at single-cell resolution with transcriptome-wise features.In this study,we build a unified liver cell atlas uniLIVER(http://lifeome.net/database/uniliver)by integrative analysis of a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets.Moreover,we introduce LiverCT,a machine learning based method for mapping any query dataset to the liver reference map by introducing the definition of“variant”cellular states analogous to the sequence variants in genomic analysis.Applying LiverCT on liver cancer datasets,we find that the“deviated”states of T cells are highly correlated with the stress pathway activities in hepatocellular carcinoma,and the enrichments of tumor cells with the hepatocyte-cholangiocyte“intermediate”states significantly indicate poor prognosis.Besides,we find that the tumor cells of different patients have different zonation tendencies and this zonation tendency is also significantly associated with the prognosis.This reference atlas mapping framework can also be extended to any other tissues.展开更多
Objective During 2003-2005, an outbreak of meningitis due to Neisseria meningitidis serogroup C occurred in China. With the aim to find strain clues result in the final epidemics, the ancestral strain 053442, a clinic...Objective During 2003-2005, an outbreak of meningitis due to Neisseria meningitidis serogroup C occurred in China. With the aim to find strain clues result in the final epidemics, the ancestral strain 053442, a clinical isolate, and a carrier strain 053426 with different gene type were analyzed. Methods Clinical strain 053442 and carrier strain 053426 were cultured on GC agar plates under the same condition. Two-dimensional electrophoresis was performed using the pH 3–10 nonlinear IPG strips of 24 cm length, and all the protein spots were identified by matrix-assisted laser desorption/ionization time of flight spectrometry. Results 502 and 380 protein spots were identified in 053426 and 053442 respectively, relating to 266 and 202 different genes covering a wide range of cellular functions. The express volume and number of proteins involved in energy metabolism, protein synthesis and amino acid biosynthesis in 053426 were higher than in 053442. Virulence factor Opa, Opc and a series of proteins involved in pilus assembly and retraction were identified in 053442, which appear to be of primary importance in colonization and invasion of human cells. Compared to 053442, virulence protein species were less in 053426, with lower express volumes too. No Opa and Opc were detected in 053426. Conclusion The different protein expression profiles of the clinical strain 053442 and carrier strain 053426 in the present study provide some clues of the different pathogenicity of the two strains, which may account for result in the final epidemics.展开更多
This paper first analyzes the features of two classes of numerical methods for global analysis of nonlinear dynamical systems, which regard state space respectively as continuous and discrete ones. On basis of this un...This paper first analyzes the features of two classes of numerical methods for global analysis of nonlinear dynamical systems, which regard state space respectively as continuous and discrete ones. On basis of this understanding it then points out that the previously proposed method of point mapping under cell reference (PMUCR), has laid a frame work for the development of a two scaled numerical method suitable for the global analysis of high dimensional nonlinear systems, which may take the advantages of both classes of single scaled methods but will release the difficulties induced by the disadvantages of them. The basic ideas and main steps of implementation of the two scaled method, namely extended PMUCR, are elaborated. Finally, two examples are presented to demonstrate the capabilities of the proposed method.展开更多
基金funded by the National Key Research and Development Program of China(No.2021YFF1200901)the National Natural Science Foundation of China(Nos.61721003,62133006,and 92268104)。
文摘The liver performs several vital functions such as metabolism,toxin removal,and glucose storage through the coordination of various cell types.With the recent breakthrough of the single-cell/single-nucleus RNAseq(sc/snRNA-seq)techniques,there is a great opportunity to establish a reference cell map of the liver at single-cell resolution with transcriptome-wise features.In this study,we build a unified liver cell atlas uniLIVER(http://lifeome.net/database/uniliver)by integrative analysis of a large-scale sc/snRNA-seq data collection of normal human liver with 331,125 cells and 79 samples from 6 datasets.Moreover,we introduce LiverCT,a machine learning based method for mapping any query dataset to the liver reference map by introducing the definition of“variant”cellular states analogous to the sequence variants in genomic analysis.Applying LiverCT on liver cancer datasets,we find that the“deviated”states of T cells are highly correlated with the stress pathway activities in hepatocellular carcinoma,and the enrichments of tumor cells with the hepatocyte-cholangiocyte“intermediate”states significantly indicate poor prognosis.Besides,we find that the tumor cells of different patients have different zonation tendencies and this zonation tendency is also significantly associated with the prognosis.This reference atlas mapping framework can also be extended to any other tissues.
基金supported by a grant (the Key Technologies R&D Program 2005BA711A09) from the Ministry of Science and Technology, of China
文摘Objective During 2003-2005, an outbreak of meningitis due to Neisseria meningitidis serogroup C occurred in China. With the aim to find strain clues result in the final epidemics, the ancestral strain 053442, a clinical isolate, and a carrier strain 053426 with different gene type were analyzed. Methods Clinical strain 053442 and carrier strain 053426 were cultured on GC agar plates under the same condition. Two-dimensional electrophoresis was performed using the pH 3–10 nonlinear IPG strips of 24 cm length, and all the protein spots were identified by matrix-assisted laser desorption/ionization time of flight spectrometry. Results 502 and 380 protein spots were identified in 053426 and 053442 respectively, relating to 266 and 202 different genes covering a wide range of cellular functions. The express volume and number of proteins involved in energy metabolism, protein synthesis and amino acid biosynthesis in 053426 were higher than in 053442. Virulence factor Opa, Opc and a series of proteins involved in pilus assembly and retraction were identified in 053442, which appear to be of primary importance in colonization and invasion of human cells. Compared to 053442, virulence protein species were less in 053426, with lower express volumes too. No Opa and Opc were detected in 053426. Conclusion The different protein expression profiles of the clinical strain 053442 and carrier strain 053426 in the present study provide some clues of the different pathogenicity of the two strains, which may account for result in the final epidemics.
基金supported by the National Natural Science Foundation of China (NSFC) (10872155)
文摘This paper first analyzes the features of two classes of numerical methods for global analysis of nonlinear dynamical systems, which regard state space respectively as continuous and discrete ones. On basis of this understanding it then points out that the previously proposed method of point mapping under cell reference (PMUCR), has laid a frame work for the development of a two scaled numerical method suitable for the global analysis of high dimensional nonlinear systems, which may take the advantages of both classes of single scaled methods but will release the difficulties induced by the disadvantages of them. The basic ideas and main steps of implementation of the two scaled method, namely extended PMUCR, are elaborated. Finally, two examples are presented to demonstrate the capabilities of the proposed method.
