Objective To investigate the levels of hypoxia-inducible factor 1α(HIF-1α)and lipopolysaccha-ride signal receptor(CD14)in gingival crevicular fluid of preschool children with dental caries and their clini-cal significance.Methods A total of 468 preschool children(aged 3-6 years)who underwent oral examina-tions in the hospital from April 2022 to May 2024 were selected as the research objects and were divided into the observation group(with dental caries,n=107)and the healthy group(without dental caries,n=361)based on the presence or absence of dental caries.The observation group was further divided into three sub-groups according to the degree of caries activity test(CAT)score:low activity group(n=29),moderate activ-ity group(n=46),and high activity group(n=32).The children in the observation group were followed up for 6 months,and then divided into the occurrence group(n=36)and the non-occurrence group(n=71)based on whether chronic apical periodontitis occurred during the follow-up period.The levels of HIF-1α and CD14 in gingival crevicular fluid in the research objects were detected.The relationship between the levels of HIF-1α and CD14 in gingival crevicular fluid of preschool children with dental caries and CAT score was ex-plored by Pearson correlation analysis.The predictive value of HIF-1α and CD14 levels in gingival crevicular fluid for chronic apical periodontitis in preschool children with dental caries was explored by receiver operating characteristic(ROC)curve.Results The levels of HIF-1α and CD14 in gingival crevicular fluid in the obser-vation group were higher than those in the healthy group(P＜0.05).With the increase of CAT score,the lev-els of HIF-1α and CD14 in gingival crevicular fluid gradually increased(high activity group＞moderate activi-ty group＞low activity group),and the differences were statistically significant(P＜0.05).The levels of HIF-1α and CD14 in gingival crevicular fluid of preschool children with dental caries were positively correlated with CAT score(r=0.526,0.634,P＜0.001).The levels of HIF-1α and CD14 in gingival crevicular fluid in the occurrence group were significantly higher than those in the non-occurrence group(P＜0.05).ROC curve analysis showed that the area under the curve(AUC)of combined prediction of HIF-1α and CD14 levels in gingival crevicular fluid for chronic apical periodontitis in preschool children with dental caries was 0.902(95％CI:0.857-0.952),which was higher than 0.709(95％CI:0.664-0.759)and 0.825(95％CI:0.775-0.870)of individual prediction of HIF-1α and CD14 levels in gingival crevicular fluid.Conclusion HIF-1α and CD14 are highly expressed in gingival crevicular fluid of preschool children with dental caries,and their levels are related to the activity of dental caries and the occurrence of chronic apical periodontitis in preschool chil-dren with dental caries.The combined detection of the two can be used as effective indicators for predicting the occurrence of chronic apical periodontitis in preschool children with dental caries.

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.

Complex structural variants(CSVs)are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants.How-ever,detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy.As a result,there has been limited progress for CSV discovery com-pared with simple structural variants.Here,we systematically analyzed the multi-breakpoint con-nection feature of CSVs,and proposed Mako,utilizing a bottom-up guided model-free strategy,to detect CSVs from paired-end short-read sequencing.Specifically,we implemented a graph-based pattern growth approach,where the graph depicts potential breakpoint connections,and pattern growth enables CSV detection without pre-defined models.Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms.Notably,validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70％,where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp,respectively.Moreover,the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types,including two novel types of adjacent segment swap and tandem dispersed duplication.Further analysis of these CSVs also revealed the impact of sequence homology on the formation of CSVs.Mako is publicly available at https://github.com/xjtu-omics/Mako.