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A critical task in single-cell RNA sequencing (scRNA-Seq) data analysis is to identify cell types from heterogeneous tissues. While the majority of classification methods demonstrated high performance in scRNA-Seq annotation problems, a robust and accurate solution is desired to generate reliable outcomes for downstream analyses, for instance, marker genes identification, differentially expressed genes, and pathway analysis. It is hard to establish a universally good metric. Thus, a universally good classification method for all kinds of scenarios does not exist. In addition, reference and query data in cell classification are usually from different experimental batches, and failure to consider batch effects may result in misleading conclusions. To overcome this bottleneck, we propose a robust ensemble approach to classify cells and utilize a batch correction method between reference and query data. We simulated four scenarios that comprise simple to complex batch effect and account for varying cell-type proportions. We further tested our approach on both lung and pancreas data. We found improved prediction accuracy and robust performance across simulation scenarios and real data. The incorporation of batch effect correction between reference and query, and the ensemble approach improve cell-type prediction accuracy while maintaining robustness. We demonstrated these through simulated and real scRNA-Seq data.

Yiqi Huoxue Recipe (YHR) is commonly used in China to treat diseases such as heart failure (HF). It has been reported that YHR can treat HF and has a certain protective effect on myocardial cell damage. The purpose of this study is to determine the cardioprotective effects of YHR on HF-induced apoptosis and to clarify its mechanism of action. Oxygen glucose deprivation/recovery (OGD/R) induces H9C2 cell apoptosis model. Ligation of the left anterior descending artery (LAD) coronary artery can induce an animal model of HF. We found that YHR protected H9C2 cells from OGD/R-induced apoptosis, reduced the level of reactive oxygen species (ROS) in H9C2 cells, and increased the mitochondrial membrane potential in H9C2 cells. The results of in vivo animal experiments showed that in the HF model, YHR could reduce infarct area of heart tissue and cardiomyocyte apoptosis rate. YHR regulated the expression of key apoptotic molecules, including increasing the ratio of Bcl-2 and Bax, and reducing the expression of Kelch-like ECH-associated protein 1 (Keap1) and caspase-3. Interestingly, YHR also regulates the expression of NF-E2-related factor 2 (Nrf2) in the nucleus. In summary, YHR may provide cardioprotective effects in heart failure through inhibiting the Keap1/Nrf2/HIF-1α apoptosis pathway., Graphical Abstract