eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species.

SUMMARY: We developed the eccDB database to integrate available resources for extrachromosomal circular DNA (eccDNA) data. eccDB is a comprehensive repository for storing, browsing, searching, and analyzing eccDNAs from multispecies. The database provides regulatory and epigenetic information on eccDNAs, with a focus on analyzing intrachromosomal and interchromosomal interactions to predict their transcriptional regulatory functions. Moreover, eccDB identifies eccDNAs from unknown DNA sequences and analyzes the functional and evolutionary relationships of eccDNAs among different species. Overall, eccDB offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher the molecular regulatory mechanisms of eccDNAs. AVAILABILITY AND IMPLEMENTATION: eccDB is freely available at http://www.xiejjlab.bio/eccDB.

Construction of the Six-lncRNA Prognosis Signature as a Novel Biomarker in Esophageal Squamous Cell Carcinoma.

Esophageal squamous cell carcinoma (ESCC) is a common malignant gastrointestinal tumor threatening global human health. For patients diagnosed with ESCC, determining the prognosis is a huge challenge. Due to their important role in tumor progression, long non-coding RNAs (lncRNAs) may be putative molecular candidates in the survival prediction of ESCC patients. Here, we obtained three datasets of ESCC lncRNA expression profiles (GSE53624, GSE53622, and GSE53625) from the Gene Expression Omnibus (GEO) database. The method of statistics and machine learning including survival analysis and LASSO regression analysis were applied. We identified a six-lncRNA signature composed of AL445524.1, AC109439.2, LINC01273, AC015922.3, LINC00547, and PSPC1-AS2. Kaplan-Meier and Cox analyses were conducted, and the prognostic ability and predictive independence of the lncRNA signature were found in three ESCC datasets. In the entire set, time-dependent ROC curve analysis showed that the prediction accuracy of the lncRNA signature was remarkably greater than that of TNM stage. ROC and stratified analysis indicated that the combination of six-lncRNA signature with the TNM stage has the highest accuracy in subgrouping ESCC patients. Furthermore, experiments subsequently confirmed that one of the lncRNAs LINC01273 may play an oncogenic role in ESCC. This study suggested the six-lncRNA signature could be a valuable survival predictor for patients with ESCC and have potential to be an auxiliary biomarker of TNM stage to subdivide ESCC patients more accurately, which has important clinical significance.

Preparation and characterization of printed magnesium scaffolds for bone tissue engineering / 中国组织工程研究

BACKGROUND:The traditional methods for preparing magnesium scaffolds include casting,powder metallurgy and laser processing technology.But these methods have some defects in pore connectivity,structure complexity,and personalization.Therefore,it is of great importance to explore a new method for the preparation of porous magnesium scaffolds.OBJECTIVE:To investigate the preparation and characterization of porous magnesium scaffolds fabricated by three-dimensional (3D) printing technology.METHODS:A magnesium porous scaffold was prepared by 3D printing.The high-stability magnesium paste (consisting of magnesium powder,2-hydroxyethyl cellulose,polyethylene glycol,glycerol trioleate,ammonia,deionized water and absolute ethanol) was extruded from the pneumatic extrusion printing system to construct the scaffold,which was then sintered under protective atmosphere.The scaffold microstructure was observed by scanning electron microscope.The phase composition of scaffold was observed by X-ray diffraction.The porosity was measured by drainage method.The compressive strength was measured by universal testing machine.The degradation was studied by immersing the scaffold in saline for 30 days,and the degradation rate and the pH value of soak solution were measured at regular intervals.RESULTS AND CONCLUSION:(1) The magnesium scaffold was piled up by cylindrical filaments,and both the sizes of filaments and the pores were (450±50) μm.Also,there were many micropores in the filaments that formed the secondary pores.The porosity of the scaffold was (65.0±2.5)％ and the compressive strength was (0.87±0.15) MPa.The principal phase of the scaffold was magnesium.(2) The degradation of the scaffold continued with the soaking time,and the degradation rate showed a steady trend,which was (10±0.2) mm per year in average.The pH value of the soak solution increased in the first 5 days,and then the pH value was kept at 10.5±0.2.To conclude,3D printing technology provides a new method for porous magnesium scaffold preparation and application in bone tissue engineering.