RESUMO
During early embryonic development, cell fate commitment represents a critical transition or "tipping point" of embryonic differentiation, at which there is a drastic and qualitative shift of the cell populations. In this study, we presented a computational approach, scGET, to explore the gene-gene associations based on single-cell RNA sequencing (scRNA-seq) data for critical transition prediction. Specifically, by transforming the gene expression data to the local network entropy, the single-cell graph entropy (SGE) value quantitatively characterizes the stability and criticality of gene regulatory networks among cell populations and thus can be employed to detect the critical signal of cell fate or lineage commitment at the single-cell level. Being applied to five scRNA-seq datasets of embryonic differentiation, scGET accurately predicts all the impending cell fate transitions. After identifying the "dark genes" that are non-differentially expressed genes but sensitive to the SGE value, the underlying signaling mechanisms were revealed, suggesting that the synergy of dark genes and their downstream targets may play a key role in various cell development processes.The application in all five datasets demonstrates the effectiveness of scGET in analyzing scRNA-seq data from a network perspective and its potential to track the dynamics of cell differentiation. The source code of scGET is accessible at https://github.com/zhongjiayuna/scGET_Project.
RESUMO
<p><b>OBJECTIVE</b>To explore the relationship between the time after thrombosis and the efficacy of combined ultrasound and microbubble treatment for rescuing the ischemic tissues.</p><p><b>METHODS</b>Rat models of thrombosis in the right common iliac artery were established and received combined ultrasound and microbubble treatment at 3, 6 and 12 h after thrombosis. The recanalization rate of the right common iliac artery was assessed using both 2-dimensional and Doppler ultrasound. The plateau acoustic intensity (AI) was quantified for estimating the skeletal microvascular blood volume, and skeletal muscle injury markers including myoglobin (Mb) and creatinine kinase (CK) were measured using ELISA. Postmortem TUNEL staining was used to detect the apoptotic rate of skeletal muscle cells in the hind limb of the rats.</p><p><b>RESULTS</b>Compared with those in 3 h group, the recanalization rate and AI were significantly lower, and the levels of Mb and CK and the apoptotic rate of the skeletal muscle cells were significantly higher in both 6 h group and 12 h group ( < 0.05). Compared with those in 6 h group, the rats receiving treatment at 12 h after thrombosis showed significantly lowered AI and increased Mb, CK and apoptotic rate of the skeletal muscle cells ( < 0.05).</p><p><b>CONCLUSIONS</b>The efficacy of combined ultrasound and microbubble treatment for rescuing ischemic tissues tends to be attenuated as the time after thrombosis prolongs in rats.</p>