Dimensionality Reduction of Single-Cell RNA Sequencing Data by Combining Entropy and Denoising AutoEncoder.

ABSTRACT Single-cell RNA sequencing (scRNA-seq) can present cellular heterogeneity at higher resolution when measuring the gene expression in an individual cell. However, there are still some computational problems in scRNA-seq data, including high dimensionality, high sparseness, and high noise. To solve them, dimensionality reduction is essential as it reduces dimensions and also removes most of the zeros and noise. Therefore, we propose a hybrid dimensionality reduction algorithm for scRNA-seq data by integrating binning-based entropy and a denoising autoencoder, named ScEDA. In ScEDA, a novel binning-based entropy estimation method is performed to select efficient genes, while removing noise. For each gene, binning-based entropy is designed to describe the differences in its expression across all cells, that is, the distribution of expression of each gene in all cells. Genes are regarded as inefficient and removed when they achieve low binning-based entropy. Moreover, by combining Kullback-Leibler (KL) divergence with the autoencoder, the objective function is reconstructed to maximize the similarity in distribution between input data and reconstructed data. Furthermore, by adding Poisson-distributed noise to the original input data, the denoising autoencoder is used to improve robustness. Compared with three other clustering methods, ScEDA provides superior average performance on 16 real scRNA-seq datasets, with obvious enhancement in large-scale datasets.

Mutational Screening of Skeletal Genes in 14 Chinese Children with Osteogenesis Imperfecta Using Targeted Sequencing.

Background: As a heterogeneous hereditary connective tissue disorder, osteogenesis imperfecta (OI) is clinically characterized by increased fracture susceptibility. Analysis of genetic pathogenic variants in patients with OI provides a basis for genetic counseling and prenatal diagnosis. Methods: In this study, 14 diagnosed OI patients from sporadic Chinese families were enrolled to be screened for potential mutations from these patients by next-generation sequencing technology. Results: 34 different variants were identified. 18 variants were from 4 OI-related genes including COL1A1, COL1A2, P3H1, and WNT1, and 10 variants are novel. Most OI patients (11 out of 14, 78%) harbor variants in type I collagen genes. Conclusions: Our results support previously established estimates of the distribution and prevalence of OI mutations and highlight both phenotype and genetic heterogeneity among and within families. We report several novel variants of OI, which expands the clinical spectrum of OI. In summary, our data provides disease-causing genes information for genetic counseling towards OI patients and families and also provides a reference for clinicians in the diagnosis of OI, also in prenatal diagnosis of this disease.

Rotational osteotomy with single incision and elastic fixation for congenital radioulnar synostosis in children: a retrospective cohort study.

Background: Derotational osteotomy remains the most commonly performed procedure in patients with congenital radioulnar synostosis (CRUS). Bone fixation is mostly performed using K-wires or plates. Many scars, loss of correction and neurovascular complications in the form were the most common complications across the studies. This report introduces a novel, minimally-invasive surgical approach, and reviews our experience. Methods: Twenty-seven children with CRUS were treated using the new technique, including bilateral forearms in 12 cases and unilateral forearm in 15 cases. A transverse osteotomy was performed at the ulnar and radial fusion site, the forearm was derotated osteotomy to the target position, intramedullary nailing was performed, and the elbow was flexed 90 degrees with a long-arm cast after surgery. One week after surgery, the forearm swelling disappeared, the long-arm cast was replaced, the elbow flexed at 90 degrees, and the forearm fixed in the maximum supination position for 4 weeks. Pre- and post-operative positions of the forearm were recorded; the pre- and post-operative activities of daily living (ADL) item scores were recorded for each patient. Results: All patients were followed up postoperatively for a mean duration of 20.7 months. The mean initial pronation deformity was 59.7±12.20 (40 to 100) degrees. The mean correction achieved was 51.2±14.50 degrees, resulting in a mean final position of 8.59±8.10 degrees of supination. The fixed angles of forearm pronation after surgery were corrected to 0-20°, with a mean of 8.33º [standard deviation (SD) 7.98°), and the difference was statistically significant compared with that before surgery (P<0.01). The patients' pre- and post-operative ADL item scores were 3.6 and 4.5, respectively, which was a 0.9-point change and was statistically significant (P<0.01). After surgery, 26 patients obtained good healing, and only one patient had delayed union, which was healed with forearm immobilization for a further month. Conclusions: Rotational osteotomy with single incision and elastic fixation for CRUS in children is a simple operation, and provides advantages including small trauma, fewer postoperative complications, and good efficacy.

Exosome-loaded extracellular matrix-mimic hydrogel with anti-inflammatory property Facilitates/promotes growth plate injury repair.

Growth plate cartilage has limited self-repair ability, leading to poor bone bridge formation post-injury and ultimately limb growth defects in children. The current corrective surgeries are highly invasive, and outcomes can be unpredictable. Following growth plate injury, the direct loss of extracellular matrix (ECM) coupled with further ECM depletion due to the inhibitory effects of inflammation on the cartilage matrix protein greatly hinder chondrocyte regeneration. We designed an exosome (Exo) derived from bone marrow mesenchymal stem cells (BMSCs) loaded ECM-mimic hydrogel to promote cartilage repair by directly supplementing ECM and anti-inflammatory properties. Aldehyde-functionalized chondroitin sulfate (OCS) was introduced into gelatin methacryloyl (GM) to form GMOCS hydrogel. Our results uncovered that GMOCS hydrogel could significantly promote the synthesis of ECM due to the doping of OCS. In addition, the GMOCS-Exos hydrogel could further promote the anabolism of chondrocytes by inhibiting inflammation and ultimately promote growth plate injury repair through ECM remodeling.