Deep Multi-Constraint Soft Clustering Analysis for Single-Cell RNA-Seq Data via Zero-Inflated Autoencoder Embedding.

Clustering cells into subgroups plays a critical role in single cell-based analyses, which facilitates to reveal cell heterogeneity and diversity. Due to the ever-increasing scRNA-seq data and low RNA capture rate, it has become challenging to cluster high-dimensional and sparse scRNA-seq data. In this study, we propose a single-cell Multi-Constraint deep soft K-means Clustering(scMCKC) framework. Based on zero-inflated negative binomial (ZINB) model-based autoencoder, scMCKC constructs a novel cell-level compactness constraint by considering association between similar cell, to emphasize the compactness between clusters. Besides, scMCKC utilizes pairwise constraint encoded by prior information to guide clustering. Meanwhile, a weighted soft K-means algorithm is leveraged to determine the cell populations, which assigns the label based on affinity between data and clustering center. Experiments on eleven scRNA-seq datasets demonstrate that scMCKC is superior to the state-of-the-art methods and notably improves cluster performance. Moreover, we validate the robustness on human kidney dataset, which demonstrates that scMCKC exhibits comprehensively excellent performance on clustering analysis. The ablation study on eleven datasets proves that the novel cell-level compactness constraint is conductive to the clustering results.

Acinic cell carcinoma of parotid gland.

Acinic cell carcinoma (ACC) is a rare malignant tumor of the salivary glands that accounts for 6%-10% of all salivary gland malignancies. It has a propensity to considerably recur, metastasize to the lung or cervical lymph nodes. In addition, ACC can potentially be fatal. The parotid gland is where ACC most frequently begins. The purpose of this paper was to describe an unusual case of parotid gland ACC in a 58-year-old Vietnamese adult female. Before surgery, a fine-needle aspiration biopsy revealed the existence of tumor cells with acinar differentiation. Following that, she underwent successful surgery without complications. The existence of ACC was verified by the postoperative final histologic results.

Adenoid cystic carcinoma of the parotid gland.

Adenoid cystic carcinoma (ACC) is a slowly progressing malignant tumor of the salivary glands that mostly affects minor salivary glands. ACC of parotid gland is exceptionally rare. In this article, we aimed to provide a case report of parotid gland ACC in a 55-year-old female that was misdiagnosed as benign mixed tumor. The patient was successfully treated by surgery without any complications. We recommend that ACC of parotid gland should be considered in differential diagnosis of benign mixed tumor since there still existed overlapped imaging characteristics.

Detection of the Potential Inactivation of Tetrodotoxin by Lactic Acid Bacterial Exopolysaccharide.

Screening for compounds that can neutralize the toxicity of tetrodotoxin (TTX) or reduce its negative effects is necessary. Our study tested the TTX detoxification capacity of exopolysaccharide (EPS) extracted from lactic acid bacteria. EPS of Leuconostoc mesenteroides N3 isolated from the Vung Tau sea (Vietnam), Lactobacillus plantarum PN05, and Lactobacillus rhamnosus PN04 were used in the study. To more completely evaluate the importance of EPS in detoxification, EPS samples of Leuconostoc mesenteroides N3, Lactobacillus plantarum PN05 and Lactobacillus rhamnosus PN04 were also tested. The majority of EPS of these bacteria contained glucose; this was observed using thin layer chromatography (TLC) and high-performance liquid chromatography (HPLC) analysis. As observed with FTIR analysis, only EPS of Lactobacillus plantarum PN05 contained methyl groups. The results indicated that detoxification of TTX in mice could be obtained at an optimal dose of 248 µg EPS from Leuconostoc mesenteroides incubated with 54 µg cuprous oxide for 40 min or 148 µg EPS Lactobacillus rhamnosus incubated with 55 µg cuprous oxide for 40 min, while EPS from Lactobacillus plantarum showed TTX detoxification capacity without cuprous oxide combination. Consequently, EPS from Lactobacillus plantarum PN05 can be used in TTX prevention. This is the first report on the importance of lactic acid bacteria in TTX detoxification.

Identifying Functional Modules in Co-Regulatory Networks Through Overlapping Spectral Clustering.

At the co-regulatory network level, functional modules comprising microRNAs (miRNAs), transcription factors (TFs), and common target genes (mRNAs) are found to be widespread in diverse organisms from bacteria to human, suggesting that co-regulatory functional modules (CRMs) serve as basic building blocks of transcription networks. Identification of CRMs would contribute to explore the miRNAs and TFs regulatory mechanism to specific cancer. However, few studies considered the functional modules which contain TFs and overlapping parts now. In this paper, we propose a novel computational framework called overlapping spectral clustering (OSC) to systematically detect overlapping CRMs using miRNA/mRNA/TF expression profiles. First, empirical Bayes theories are used to improve building more exact relation matrix instead of simple Pearson correlation analysis. In order to ensure the adaptivity of the whole framework, the eigenvalue decomposition (Eigengap) is employed to determine the module number automatically. Then considering key regulators which may involve in more function modules, we propose a novel overlapping detection approach to observe whether the edges between modules can be overlapped by other modules. Comparing with existing methods on breast cancer and ovary cancer data sets from The Cancer Genome Atlas, we showed that the CRMs identified by OSC are more functionally enriched. 80% TFs and 90% miRNAs in CRMs are related to corresponding diseases. And the overlapping parts between CRMs were also analyzed and verified by standard databases and previous literatures.