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The spatial reconstruction of single-cell RNA sequencing (scRNA-seq) data into spatial transcriptomics (ST) is a rapidly evolving field that addresses the significant challenge of aligning gene expression profiles to their spatial origins within tissues. This task is complicated by the inherent batch effects and the need for precise gene expression characterization to accurately reflect spatial information. To address these challenges, we developed SELF-Former, a transformer-based framework that utilizes multi-scale structures to learn gene representations, while designing spatial correlation constraints for the reconstruction of corresponding ST data. SELF-Former excels in recovering the spatial information of ST data and effectively mitigates batch effects between scRNA-seq and ST data. A novel aspect of SELF-Former is the introduction of a gene filtration module, which significantly enhances the spatial reconstruction task by selecting genes that are crucial for accurate spatial positioning and reconstruction. The superior performance and effectiveness of SELF-Former's modules have been validated across four benchmark datasets, establishing it as a robust and effective method for spatial reconstruction tasks. SELF-Former demonstrates its capability to extract meaningful gene expression information from scRNA-seq data and accurately map it to the spatial context of real ST data. Our method represents a significant advancement in the field, offering a reliable approach for spatial reconstruction. [ABSTRACT FROM AUTHOR]

Abstract: The crystal structure of new ternary compounds Al2R11Ge8 (R=Y, Gd, Tb, Dy, Ho, Er) was studied using X-ray powder diffraction data by Rietveld method. Scanning electron microscopy (SEM) coupled with energy dispersive X-ray spectroscopy (EDS) was used for sample composition examination. The compounds crystallized in the Ge10Ho11 structure type (space group I4/mmm). The phase was not found in the systems with R=La, Ce, Pr and Nd. The lattice thermal expansion study of the Al2Er11Ge8 compound was carried out using high-temperature powder X-ray diffraction technique from 293K to 743K, and the calculated lattice and volume thermal expansion coefficients were α a =0.88×10−5 K−1, α c =1.22×10−5 K−1, and α V =3.01×10−5 K−1, respectively. [Copyright &y& Elsevier]

Abstract: A new ternary compound La2Cu0.8Ge3 was synthesized and studied. The crystal structure of La2Cu0.8Ge3 was refined from X-ray powder diffraction data by Rietveld method. The new compound was found to have a tetragonal α-ThSi2 structure with space group I41/amd (No. 141), and a =0.42807(2)nm, c =1.45626(6)nm, Z =2 and D calc =6.931g/cm3. The thermal expansion properties of La2Cu0.8Ge3 were investigated using high-temperature powder X-ray diffraction technique in the temperature range from 321K to 753K. Results show that its unit-cell parameters increase with increasing temperature. The coefficients of average lattice thermal expansion are , and . [Copyright &y& Elsevier]

Single-cell RNA sequencing (scRNA-seq) offers opportunities to study gene expression of tens of thousands of single cells simultaneously, to investigate cell-to-cell variation, and to reconstruct cell-type-specific gene regulatory networks. Recovering dropout events in a sparse gene expression matrix for scRNA-seq data is a long-standing matrix completion problem. In this article, we introduce Bfimpute, a Bayesian factorization imputation algorithm that reconstructs two latent gene and cell matrices to impute the final gene expression matrix within each cell group, with or without the aid of cell type labels or bulk data. Bfimpute achieves better accuracy than ten other publicly notable scRNA-seq imputation methods on simulated and real scRNA-seq data, as measured by several different evaluation metrics. Bfimpute can also flexibly integrate any gene- or cell-related information that users provide to increase performance., Competing Interests: The authors declare no competing interests., (© 2021 The Author(s).)

Background: Cavernous transformation of the portal vein rarely occurs after a choledochal cyst surgery., Case Characteristics: A 7-year-old boy with a history of a choledochal cyst surgery was admitted with recurrent oral and nasal bleeding over next two years. After excluding coagulopathies and hematopathies, we treated him with percutaneous transhepatic angioplasty., Outcome: The flow of the portal vein recovered immediately after balloon dilation. The patient's symptoms were relieved, and no recurrence or complications occurred., Message: Stenosis and cavernous transformation of portal vein can be successfully managed by percutaneous transhepatic angioplasty.

Autologous implantation of bone mesenchymal stem cells (BMSCs) has achieved promising clinical efficacy for the treatment of early-stage osteonecrosis of the femoral head (ONFH). However, the underlying mechanisms are not completely elucidated. Here, we investigated the effect of BMSCs on the early ONFH in vitro and in vivo. In co-cultured system, primary BMSCs enhanced the activity and inhibited the apoptosis of primary OB. The concentrations of VEGF and BMP-2 in the co-cultured medium were significantly higher than those without co-culture. Importantly, BMSCs implantation increased OB, capillaries and VEGF and BMP-2 expressions of the necrotic areas of femoral head in the ONFH rabbits. In conclusion, our results indicated that BMSCs treated the early ONFH possibly through increasing OB and capillaries, as well as VEGF and BMP-2 expression in the femoral head. These results provided possible mechanisms for the treatment of early-stage ONFH with BMSCs transplantation.

As an inflammatory obliterative cholangiopathy of neonates, biliary atresia (BA) affects both intrahepatic and extrahepatic bile ducts. Its etiology has remained largely unknown. Gene expression profiling was conduced for extrahepatic bile duct tissues (including porta hepatis & common bile duct) to identify novel targets for further studies of BA. Among these tissues, porta hepatis was regarded as fibrosis group while common bile duct as self-control group. The analysis of gene expression profile in these tissues was performed with Affymetrix human microarray. Quantitative RT-PCR (qRT-PCR) was performed to confirm these results. The differential expressions of genes were identified through fold-change filtering. Gene Ontology (GO) and pathway analyses were performed using standard enrichment computation method. It was found that a total of 140 genes were differentially expressed between porta hepatis and common bile duct tissues, 19 genes up-regulated and 121 genes down-regulated. Moreover, GO analysis found that cell adhesion molecules, extracellular matrix formation, protein digestion & absorption functions may be involved in the pathogenesis of porta hepatis fibrosis. Lastly the qRT-PCR data confirmed that IL7 and CLDN2 were significantly up-regulated and both might be involved in the etiology of BA, the expression level of VCAM1 was positively correlated with severity of liver fibrosis in the BA infants. Our results demonstrated that the expressions of these aberrant genes responding to fibrosis in porta hepatis of patients with BA. Further studies of these genes may provide useful insights into the pathological mechanisms of BA.