ABSTRACT
Objective: The objective of this paper was to investigate hub genes of postmenopausal osteoporosis (PO) utilizing benchmarked dataset and gene regulatory network (GRN). Materials and Methods: To achieve this goal, the first step was to benchmark the dataset downloaded from the ArrayExpress database by adding local noise and global noise. Second, differentially expressed genes (DEGs) between PO and normal controls were identified using the Linear Models for Microarray Data package based on benchmarked dataset. Third, five kinds of GRN inference methods, which comprised Zscore, GeneNet, context likelihood of relatedness (CLR) algorithm, Partial Correlation coefficient with Information Theory (PCIT), and GEne Network Inference with Ensemble of trees (Genie3), were described and evaluated by receiver operating characteristic (ROC) and precision and recall (PR) curves. Finally, GRN constructed according to the method with best performance was implemented to conduct topological centrality (closeness) for the purpose of investigate hub genes of PO. Results:A total of 236 DEGs were obtained based on benchmarked dataset of 20,554 genes. By assessing Zscore, GeneNet, CLR, PCIT, and Genie3 on the basis of ROC and PR curves, Genie3 had a clear advantage than others and was applied to construct the GRN which was composed of 236 nodes and 27,730 edges. Closeness centrality analysis of GRN was carried out, and we identified 14 hub genes (such as TTN, ACTA1, and MYBPC1) for PO. Conclusion: In conclusion, we have identified 14 hub genes (such as TN, ACTA1, and MYBPC1) based on benchmarked dataset and GRN. These genes might be potential biomarkers and give insights for diagnose and treatment of PO
ABSTRACT
Objective To observe the deposition of PM2.5 in the contact lens and its influence on the oxygen permeability and refractive index of the contact lens.Methods Atmospheric PM2.5 was collected for preparation of 1 mg · mL-1 PM2.5 suspension.Then,18 rigid gas permeable contact lenses (RGPCL) and 18 soft contact lens lenses (SCL) were grouped in control,experimental and PBS-rinse group,with 6 RGPCL and 6 SCL in each group.RGPCL and SCL in the experimental and PBS-rinse groups were incubated in 1 mg · mL-1 PM2.5 solution for 24 h,followed by PBS-rinse group were further washed for 1 h in PBS,whereas the controls were incubated in PBS for 24 h.All of them were examined with field scanning electron microscopy.Meanwhile,oxygen permeability and refractive index of contact lens were measured using the polar graphic devices and refractometry respectively.All the obtained data were quantitatively and statistically analyzed.Results After treatment in PM2.5 solution,there was a large amount of PM2.5 deposition on the RGPCL surface in the experimental group,and the amount of PM2.5 was counted (3.19 ± 1.64) · 100 μm-2,while no atmospheric particulate matter was found in the control group;following the treatment of PBS,a lot of PM2.5 attached on the surface of RGPCL remained visible,and the number of particles was (5.12 ± 1.27) · 100 μm-2.And the difference was statistically significant between the control group and PBS-rinse group (P ＜0.05).In addition,and the amount of PM2.5 attached on the surface of SCL in the exPerimental group was (2.16 ± 1.19) · 100 μm-2,while there wasn t any atmospheric particulate matter in the control group;and,after a wash of SCL in PBS,the amount of PM2.5 on SCL surface was (0.56 ±0.39) · 100 μm-2 in the PBS-rinse group,indicating a statistically difference between the control group and PBS-rinse group (P ＜0.05).Moreover,the amount of PM2.5 attachment on SCL surface in the experimental group was significantly lower than that of the control group,and the difference was statistically significant (P ＜ 0.05).After PM2.5 solution treatment,oxygen permeability of RGPCL and SCL was 100.00 ± 3.17 and 42.00 ± 2.57 respectively in the experimental group,as well as 100.00 ±2.36 and 41.00 ± 3.44 in the control group,with no statistically significant difference between the two groups (all P ＞ 0.05);while refractive index of RGPCL and SCL was 1.415 6 ±0.000 4 and 1.3737 ±0.000 7 respectively in the experimental group,as well as 1.415 3 ±0.000 4 and 1.373 7 ±0.000 l in the control group,with no statistically significant difference between the two groups either (all P ＞ 0.05).Conclusion PM2.5 can be attached to the surface of RGPCL and SCL,and PM2.5 is easier to adhere to RGPCL surface and is not easy to elute when compared with SCL,but PM2.5 deposition do not affect oxygen permeability and refractive index of contact lenses over a short span of time.