1.Lung ultrasound for the diagnosis of pneumonia in children in recent 5 years: a meta-analysis
Ningxin LUO ; Wanru CAI ; Hui XIA ; Yazhen XU ; Shuwen ZHONG ; Li ZHAO
Chinese Pediatric Emergency Medicine 2022;29(4):301-306
Objective:To assess the accuracy of lung ultrasound(LUS) to predict pneumonia in pediatric patients using meta-analysis.Methods:The PubMed, the Cochrane Library, EMbase databases from January 2015 to March 2020 were searched.The retrieved outcome data to evaluate the efficacy of LUS for the diagnosis of pneumonia in patients under 18 years of age were included.Two reviewers independently screened literature, extracted data and assessed the risk of bias of included studies.Meta-analysis was then conducted using MetaDisc 1.4, RevMan 5.3 and Stata 15.0 softwares.Results:Twelve diagnostic studies were included, which involved 2 484 patients.The results of meta-analysis showed that compared with the gold standard, the sensitivity, specificity, positive and negative likelihood ratios, diagnostic odds ratio of LUS were 0.90(95% CI 0.88-0.91), 0.88(95% CI 0.85-0.90), 8.64(95% CI 3.79-19.72), 0.12(95% CI 0.06-0.26) and 77.58(95% CI 28.39-211.99), respectively.The area under the summary receiver operating characteri stic curve was 0.96.Subgroup analysis showed that there was no difference in LUS′s diagnostic accuracy for pneumonia with different department, different diagnostic gold standard, and different level of sonographer training. Conclusion:Current evidence shows that LUS has a high accuracy in the diagnosis of pneumonia in children.
2.Correlation analysis between depression and gambling behavior using graph theory
Ningxin MA ; Yu WANG ; Hongbing XIAO ; Suxia XING ; Ran XU
Chinese Journal of Medical Physics 2024;41(11):1374-1382
The correlations of global/local properties of brain networks with gambling behavioral scales in depression are explored.The task-state brain functional magnetic resonance imaging data of 24 patients with gambling behavior and depression and 24 healthy controls are analyzed,and preprocessed by SPM software.Graph theory analysis method is used to establish the functional brain networks in which local and global properties are calculated.Two sets of local attribute index including node degree and node efficiency are used to make edge analysis in different depression groups(major,moderate and mild depression groups,with 8 patients in each group)and healthy control group,and the changes in global properties are also discussed.Additionally,the correlations of scoring scale related to gambling behavior with 3 criteria on the global properties(small world attribute,global efficiency and local efficiency)are analyzed.The two-sample t-tests on depression groups and healthy control group confirm the significant connections among brain regions(P<0.05),and reveal the significant negative correlations between the global brain network attribute indexes and different behavioral scales,which fully verifies the correlation between gambling behavior and depression,and provides the basis for further exploring correlation between the individual behavior attribute and depression,thereby assisting clinical diagnosis and treatment of depression patients.
3.High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads
Wang BO ; Yang XIAOFEI ; Jia YANYAN ; Xu YU ; Jia PENG ; Dang NINGXIN ; Wang SONGBO ; Xu TUN ; Zhao XIXI ; Gao SHENGHAN ; Dong QUANBIN ; Ye KAI
Genomics, Proteomics & Bioinformatics 2022;20(1):4-13
Arabidopsis thaliana is an important and long-established model species for plant molec-ular biology,genetics,epigenetics,and genomics.However,the latest version of reference genome still contains a significant number of missing segments.Here,we reported a high-quality and almost complete Col-0 genome assembly with two gaps(named Col-XJTU)by combining the Oxford Nanopore Technologies ultra-long reads,Pacific Biosciences high-fidelity long reads,and Hi-C data.The total genome assembly size is 133,725,193 bp,introducing 14.6 Mb of novel sequences compared to the TAIR1 0.1 reference genome.All five chromosomes of the Col-XJTU assembly are highly accurate with consensus quality(QV)scores>60(ranging from 62 to 68),which are higher than those of the TAIR10.1 reference(ranging from 45 to 52).We completely resolved chro-mosome(Chr)3 and Chr5 in a telomere-to-telomere manner.Chr4 was completely resolved except the nucleolar organizing regions,which comprise long repetitive DNA fragments.The Chr1 cen-tromere(CEN1),reportedly around 9 Mb in length,is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats.Using the cutting-edge sequencing data and novel computational approaches,we assembled a 3.8-Mb-long CEN1 and a 3.5-Mb-long CEN2.We also investigated the structure and epigenetics of centromeres.Four clusters of CEN180 monomers were detected,and the centromere-specific histone H3-like protein(CENH3)exhibited a strong preference for CEN 180 Cluster 3.Moreover,we observed hypomethylation patterns in CENH3-enriched regions.We believe that this high-quality genome assembly,Col-XJTU,would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms,as well as the genetic and epigenetic features in plants.
4.Comprehensive protein kinase inhibition analysis reveals the molecu-lar mechanism of KG-1 proliferation
Yu DUAN ; Ningxin XU ; Qiong CAO ; Kai YANG ; Jinjuan WANG ; Sijin LIU ; Fengfeng JIA ; Jianbing LIU ; Li LI
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(6):621-628
AIM:To investigate the molecular mechanisms of KG-1 cell proliferation by profiling its responses to various protein kinase inhibitors.METHODS:CCK-8 assay,real time quantitative PCR(qRT-PCR)and Western-blot were used to detect the effect of various protein kinase inhibitors on KG-1 cell proliferation,the expression levels of mRNA and phosphorylation level of signaling pro-teins in the FGFR1 downstream pathways.RE-SULTS:NVP-BGJ398 and PD173074 effectively in-hibited the proliferation of KG-1 cells,indicative of a crucial role of FGFR downstream signaling.After treatment with FGFR inhibitors,the levels of p-FG-FR1OP2-FGFR1 and p-STAT5 decreased significantly(P<0.001),p-AKT decreased slightly(P<0.05),with-out affecting the p-ERK level(P>0.05).CONCLU-SION:FGFR1OP2-FGFR1 mainly acts on the down-stream STAT5 signaling pathway to promote cell proliferation.Comprehensive protein kinase inhibi-tion analysis is a reliable and direct approach to identify functional drivers of cancer cell prolifera-tion.