Co-expression and interaction network analysis reveals dysregulated neutrophil and T-cell activation as the core mechanism associated with septic shock.

Septic shock as a subset of sepsis, has a much higher mortality, while the mechanism is still elusive. This study was aimed at identifying core mechanisms associated with septic shock and its high mortality by investigating transcriptome data. We screened 72 septic-shock-associated genes (SSAGs) with differential expression between septic shock and sepsis in the discovery dataset. Further gene set enrichment analysis identified upregulated neutrophil activation and impaired T-cell activation in septic shock. Co-expression analysis revealed nine co-expressed gene modules. In addition, we determined twenty-one prognostic SSAGs using cox regression analysis in an independent dataset. Moreover, protein-protein interaction (PPI) network revealed two clusters. Among these neutrophil activation was enriched in the most positively-related modules and the cluster2 PPI network, while T-cell activation was enriched in both the most negatively-related module and one of the most positively-related modules as well as the cluster1 PPI network. ELANE, LCN2 and IFI44 were identified as hub genes with CytoHubba methods and semantic similarity analysis. Notably, ELANE was the only prognostic gene and was further validated in an external dataset. Blood neutrophil count was demonstrated to increase in septic shock and be a risky factor of prognosis based on clinical data. In conclusions, septic shock is associated with upregulated neutrophil activation and dysregulated T-cell activation. Three hub genes might have potentials as sensitive markers for the further translational research and ELANE could be a robust prognostic biomarker and effective therapeutic target.

Improved targeting of the 16S rDNA nanopore sequencing method enables rapid pathogen identification in bacterial pneumonia in children.

Objectives: To develop a rapid and low-cost method for 16S rDNA nanopore sequencing. Methods: This was a prospective study on a 16S rDNA nanopore sequencing method. We developed this nanopore barcoding 16S sequencing method by adding barcodes to the 16S primer to reduce the reagent cost and simplify the experimental procedure. Twenty-one common pulmonary bacteria (7 reference strains, 14 clinical isolates) and 94 samples of bronchoalveolar lavage fluid from children with severe pneumonia were tested. Results indicating low-abundance pathogenic bacteria were verified with the polymerase chain reaction (PCR). Further, the results were compared with those of culture or PCR. Results: The turnaround time was shortened to 6~8 hours and the reagent cost of DNA preparation was reduced by employing a single reaction adding barcodes to the 16S primer in advance. The accuracy rate for the 21 common pulmonary pathogens with an abundance ≥ 99% was 100%. Applying the culture or PCR results as the gold standard, 71 (75.5%) of the 94 patients were positive, including 25 positive cultures (26.6%) and 52 positive quantitative PCRs (55.3%). The median abundance in the positive culture and qPCR samples were 29.9% and 6.7%, respectively. With an abundance threshold increase of 1%, 5%, 10%, 15% and 20%, the test sensitivity decreased gradually to 98.6%, 84.9%, 72.6%, 67.1% and 64.4%, respectively, and the test specificity increased gradually to 33.3%, 71.4%, 81.0%, 90.5% and 100.0%, respectively. Conclusions: The nanopore barcoding 16S sequencing method can rapidly identify the pathogens causing bacterial pneumonia in children.

Discovery and validation of novel biomarkers for detection of cervical cancer.

AIMS: To investigate novel biomarker for diagnosis of cervical cancer, we analyzed the datasets in Gene Expression Omnibus (GEO) and confirmed the candidate biomarker in patient sample. MATERIALS AND METHODS: We collected major datasets of cervical cancer in GEO, and analyzed the differential expression of normal and cancer samples online with GEO2R and tested the differences, then focus on the GSE63514 to screen the target genes in different histological grades by using the R-Bioconductor package and R-heatmap. Then human specimens from the cervix in different histological grades were used to confirm the top 8 genes expression by immunohistochemical staining using Ki67 as a standard control. RESULTS: We identified genes differentially expressed in normal and cervical cancer, 274 upregulated genes and 206 downregulated genes. After intersection with GSE63514, we found the obvious tendency in different histological grades. Then we screened the top 24 genes, and confirmed the top 8 genes in human cervix tissues. Immunohistochemical (IHC) results confirmed that keratin 17 (KRT17) was not expressed in normal cervical tissues and was over-expressed in cervical cancer. Cysteine-rich secretory protein-2 (CRISP2) was less expressed in high-grade squamous intraepithelial lesions (HSILs) than in other histological grades. CONCLUSION: For the good repeatability and consistency of KRT17 and CRISP2, they may be good candidate biomarkers. Combined analysis of KRT17, CRISP2 expression at both genetic and protein levels can determine different histological grades of cervical squamous cell carcinoma. Such combined analysis is capable of improving diagnostic accuracy of cervical cancer.

Sensitivity-Compensated Micro-Pressure Flexible Sensor for Aerospace Vehicle.

When flight vehicles (e.g., aerospace vehicles, Low Earth Orbit (LEO) satellites, near-space aircrafts, Unmanned Aerial Vehicles (UAVs) and drones) fly at high speed, their surfaces suffer the micro-pressure from high-altitude thin air. The long-term effect of this pressure causes the surface components of flight vehicle to deform or fall off, which can lead to a serious accident. To solve this problem, this paper proposes a sensitivity-compensated micro-pressure flexible sensor based on hyper-elastic plastic material and plate parallel capacitance. The sensor is able to measure a range of 0⁻6 kPa micro-pressure suffered by the flight vehicle's surface with high sensitivity and flexible devices. In this paper, we propose the principle, structure design and fabrication of the sensitivity-compensated micro-pressure flexible sensor. We carried out experiments to obtain the static characteristic curve between micro-pressure and the output capacitance of the sensor devices, and investigated the relationship between sensitivity and geometric parameters. We also compared the performance of the flexible sensor before and after sensitivity compensation. The result shows that the sensor can measure a range of 0⁻2 kPa and 2⁻6 kPa with a sensitivity of 0.27 kPa-1 and 0.021 kPa-1, which are 80% and 141.38% higher than the sensor before compensation; a linearity of 1.39% and 2.88%, which are 51.7% and 13.1% higher than the sensor before compensation; and a hysteresis and repeatability of 4.95% and 2.38%, respectively. The sensor has potential applications in flight vehicles to measure the micro-pressure with high sensitivity and flexibility.