Objective To explore the predictive value of fibrin degradation product to albumin ratio(FDP/ALB),neutrophil to lymphocyte and platelet ratio(NLPR)for the severity of elderly community-acquired pneumonia(CAP).Methods 147 elderly CAP patients hospitalized in the Department of Respiratory and Critical Care,Affiliated Hospital of Chengde Medical University from March 2021 to March 2023 were selected and divided into non severe CAP group(n=94)and severe CAP group(n=53)according to the severity of the disease.The general and clinical data of two groups of patients were recorded,and calculated neutrophil to lymphocyte ratio(NLR),platelet to lymphocyte ratio(PLR),C-reactive protein(CRP)to albumin ratio(CAR),FDP/ALB,NLPR,and oxygenation index,the differences between two groups of the above indicators were compared and correlation analysis were conducted;The predictive value of FDP/ALB,NLPR,and other traditional inflammatory indicators on the severity of elderly CAP were compared.Results CRP,procalcitonin(PCT),white blood cells(WBC),neutrophil(NEU),fibrin degradation product(FDP),NLR,CAR,CURB-65 scores,FDP/ALB,and NLPR in severe CAP group were significantly higher than those in non severe CAP group,while lymphocyte(LYM),platelet(PLT)and albumin(ALB)were significantly lower than those in non severe CAP group(P＜0.05);There were no statistically significant differences in age,gender,smoking history,underlying diseases,and PLR between two groups(P＞0.05).Spearman correlation analysis showed a positive correlation between FDP/ALB,NLPR and CRP,PCT,WBC,NLR,CAR CURB-65 scores,while a negative correlation with oxygenation index(P＜0.05).Multivariate Logistic regression analysis showed that FDP/ALB and NLPR were independent risk factors for severe CAP in the elderly(P＜0.05).The analysis of receiver operating characteristic curve showed that the ability of FDP/ALB,NLPR,NLR,CAR,PCT,NEU,CURB-65 score,CRP,and WBC to predict the severity of elderly CAP gradually decreased(P＜0.05).Conclusion The predictive value of FDP/ALB and NLPR for the severity of elderly CAP is significantly better than traditional inflammatory indicators(CRP,PCT,WBC,NEU,NLR,CAR,CURB-65 scores),which should be taken seriously by clinical workers.

Objective·To investigate the changes in transcriptome and chromatin accessibility during the differentiation of human embryonic stem cells(hESCs)into neural progenitor cells(NPCs)using in vitro differentiation models and high-throughput multi-omics sequencing technologies.Methods·hESCs were first induced to differentiate into NPCs in vitro using the embryoid body formation method,and cells at both stages were collected.The cell phenotypes were identified by reverse transcription-quantitative real-time PCR(RT-qPCR)and immunofluorescence(IF)staining.Transcriptome sequencing(RNA-seq)was conducted to detect and analyze the differentially expressed genes(DEGs)between hESCs and NPCs.The assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq)was employed to assess chromatin accessibility changes between hESCs and NPCs.Motif enrichment analysis was performed on differentially accessible chromatin regions to discover potential regulatory transcription factors.Finally,an integrated analysis of RNA-seq and ATAC-seq data and the protein-protein interaction(PPI)network were performed to identify key genes and regulatory pathways involved in the early stages of neural differentiation in vitro.Results·Both RT-qPCR and IF results indicated that the expression levels of pluripotency markers(NANOG and POU5F1)were high at the hESC stage but significantly decreased at the NPC stage,while early neural differentiation markers(PAX6,SOX1,and NES)were minimally expressed at the hESC stage but markedly upregulated at the NPC stage.RNA-seq analysis revealed that compared to the hESC stage,there were 5 597 genes upregulated and 3 654 genes downregulated at the NPC stage.Gene function enrichment analysis showed that the upregulated genes at the NPC stage were enriched in the functions related to neural development.ATAC-seq analysis demonstrated a total of 27 491 genomic regions had significant changes in chromatin accessibility during the differentiation from hESC to NPC,with 12 381 regions showing increased accessibility and 15 110 regions showing decreased accessibility.Motif enrichment analysis revealed that transcription factor genes such as DLX1 and LHX2 might play an important role in the differentiation process from hESCs into NPCs.Integrated analysis of RNA-seq and ATAC-seq data revealed that overlapping genes with high expression at the NPC stage were mainly enriched in axon guidance,forebrain development,and neuron migration.After neural differentiation,the expression levels of CTNND2 and LHX2 genes increased,and the chromatin accessibility of related genomic regions also increased.PPI network analysis indentified candidate downstream genes including PRKACA,CDH2,and ERBB4.Conclusion·The in vitro differentiation model of hESCs combined with high-throughput multi-omics sequencing technologies can be used to depict the changes in transcriptome and chromatin accessibility during the differentiation of hESCs into NPCs.In this process,the expression levels of genes related to axon guidance,forebrain development,and neuronal migration pathways increase and related chromatin accessibility is enhanced.

Objective·To investigate the changes in transcriptome and chromatin accessibility during the differentiation of human embryonic stem cells(hESCs)into neural progenitor cells(NPCs)using in vitro differentiation models and high-throughput multi-omics sequencing technologies.Methods·hESCs were first induced to differentiate into NPCs in vitro using the embryoid body formation method,and cells at both stages were collected.The cell phenotypes were identified by reverse transcription-quantitative real-time PCR(RT-qPCR)and immunofluorescence(IF)staining.Transcriptome sequencing(RNA-seq)was conducted to detect and analyze the differentially expressed genes(DEGs)between hESCs and NPCs.The assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq)was employed to assess chromatin accessibility changes between hESCs and NPCs.Motif enrichment analysis was performed on differentially accessible chromatin regions to discover potential regulatory transcription factors.Finally,an integrated analysis of RNA-seq and ATAC-seq data and the protein-protein interaction(PPI)network were performed to identify key genes and regulatory pathways involved in the early stages of neural differentiation in vitro.Results·Both RT-qPCR and IF results indicated that the expression levels of pluripotency markers(NANOG and POU5F1)were high at the hESC stage but significantly decreased at the NPC stage,while early neural differentiation markers(PAX6,SOX1,and NES)were minimally expressed at the hESC stage but markedly upregulated at the NPC stage.RNA-seq analysis revealed that compared to the hESC stage,there were 5 597 genes upregulated and 3 654 genes downregulated at the NPC stage.Gene function enrichment analysis showed that the upregulated genes at the NPC stage were enriched in the functions related to neural development.ATAC-seq analysis demonstrated a total of 27 491 genomic regions had significant changes in chromatin accessibility during the differentiation from hESC to NPC,with 12 381 regions showing increased accessibility and 15 110 regions showing decreased accessibility.Motif enrichment analysis revealed that transcription factor genes such as DLX1 and LHX2 might play an important role in the differentiation process from hESCs into NPCs.Integrated analysis of RNA-seq and ATAC-seq data revealed that overlapping genes with high expression at the NPC stage were mainly enriched in axon guidance,forebrain development,and neuron migration.After neural differentiation,the expression levels of CTNND2 and LHX2 genes increased,and the chromatin accessibility of related genomic regions also increased.PPI network analysis indentified candidate downstream genes including PRKACA,CDH2,and ERBB4.Conclusion·The in vitro differentiation model of hESCs combined with high-throughput multi-omics sequencing technologies can be used to depict the changes in transcriptome and chromatin accessibility during the differentiation of hESCs into NPCs.In this process,the expression levels of genes related to axon guidance,forebrain development,and neuronal migration pathways increase and related chromatin accessibility is enhanced.

Objective To explore the predictive value of fibrin degradation product to albumin ratio(FDP/ALB),neutrophil to lymphocyte and platelet ratio(NLPR)for the severity of elderly community-acquired pneumonia(CAP).Methods 147 elderly CAP patients hospitalized in the Department of Respiratory and Critical Care,Affiliated Hospital of Chengde Medical University from March 2021 to March 2023 were selected and divided into non severe CAP group(n=94)and severe CAP group(n=53)according to the severity of the disease.The general and clinical data of two groups of patients were recorded,and calculated neutrophil to lymphocyte ratio(NLR),platelet to lymphocyte ratio(PLR),C-reactive protein(CRP)to albumin ratio(CAR),FDP/ALB,NLPR,and oxygenation index,the differences between two groups of the above indicators were compared and correlation analysis were conducted;The predictive value of FDP/ALB,NLPR,and other traditional inflammatory indicators on the severity of elderly CAP were compared.Results CRP,procalcitonin(PCT),white blood cells(WBC),neutrophil(NEU),fibrin degradation product(FDP),NLR,CAR,CURB-65 scores,FDP/ALB,and NLPR in severe CAP group were significantly higher than those in non severe CAP group,while lymphocyte(LYM),platelet(PLT)and albumin(ALB)were significantly lower than those in non severe CAP group(P＜0.05);There were no statistically significant differences in age,gender,smoking history,underlying diseases,and PLR between two groups(P＞0.05).Spearman correlation analysis showed a positive correlation between FDP/ALB,NLPR and CRP,PCT,WBC,NLR,CAR CURB-65 scores,while a negative correlation with oxygenation index(P＜0.05).Multivariate Logistic regression analysis showed that FDP/ALB and NLPR were independent risk factors for severe CAP in the elderly(P＜0.05).The analysis of receiver operating characteristic curve showed that the ability of FDP/ALB,NLPR,NLR,CAR,PCT,NEU,CURB-65 score,CRP,and WBC to predict the severity of elderly CAP gradually decreased(P＜0.05).Conclusion The predictive value of FDP/ALB and NLPR for the severity of elderly CAP is significantly better than traditional inflammatory indicators(CRP,PCT,WBC,NEU,NLR,CAR,CURB-65 scores),which should be taken seriously by clinical workers.

Objective: To reveal the molecular mechanism underlying the compatibility of Salvia miltiorrhiza Bge (S. miltiorrhiza, Dan Shen) and C. tinctorius L. (C. tinctorius, Hong Hua) as an herb pair through network pharmacology and subsequent experimental validation. Methods: Network pharmacology was applied to construct an active ingredient-efficacy target-disease protein network to reveal the unique regulation pattern of S. miltiorrhiza and C. tinctorius as herb pair. Molecular docking was used to verify the binding of the components of these herbs and their potential targets. An H9c2 glucose hypoxia model was used to evaluate the efficacy of the components and their synergistic effects, which were evaluated using the combination index. Western blot was performed to detect the protein expression of these targets. Results: Network pharmacology analysis revealed 5 pathways and 8 core targets of S. miltiorrhiza and C. tinctorius in myocardial protection. Five of the core targets were enriched in the hypoxia-inducible factor-1 (HIF-1) signaling pathway. S. miltiorrhiza-C. tinctorius achieved vascular tone mainly by regulating the target genes of the HIF-1 pathway. As an upstream gene of the HIF-1 pathway, STAT3 can be activated by the active ingredients cryptotanshinone (Ctan), salvianolic acid B (Sal. B), and myricetin (Myric). Cell experiments revealed that Myric, Sal. B, and Ctan also exhibited synergistic myocardial protective activity. Molecular docking verified the strong binding of Myric, Sal. B, and Ctan to STAT3. Western blot further showed that the active ingredients synergistically upregulated the protein expression of STAT3. Conclusion The pharmacodynamic transmission analysis revealed that the active ingredients of S. miltiorrhiza and C. tinctorius can synergistically resist ischemia through various targets and pathways. This study provides a methodological reference for interpreting traditional Chinese medicine compatibility.

Objective:High-throughput screening to obtain small molecular compounds against Gram-negative bacilli by targeting BamA outer membrane protein.Methods:The sybyl-X2.1 software was used to perform high-throughput virtual screening of small molecular compounds in Chemdiv compound library based on the molecular docking. The top 150 hits by high-throughput screening were re-screened through in vitro biological experiments. The top 4 small molecules with obvious antibacterial activity were selected for in-depth molecular docking analysis, and the small molecule 8308-0401 with the highest docking score was selected for further experiments. The antibacterial effect of 8308-0401 combined with rifampicin was tested by checkerboard assay. Finally, the affinity between 8308-0401 and BamA was tested by plasma surface resonance assay. Results:The docking score of the top 150 hits calculated by high-throughput virtual screening had a mean value of 5.63. In vitro biological experiments showed that small molecules 8308-0401, 8365-1335, C066-2507 and L582-0346 exhibited strong antibacterial activity. Among those molecules, 8308-0401 showed the highest molecular docking score, and synergistic antibacterial activity against both types of strains and clinical isolates when combined with rifampicin. 8308-0401 has a strong affinity to BamA with binding a constant of 182 μmol/L. Conclusion:The small molecule 8308-0401 exerts antibacterial activity against Gram negative bacilli by targeting the outer membrane protein BamA.

Objective·To study the relationship between evolution and the developmental process from the perspective of DNA sequence conservation,and explore their inherent principles.Methods·First,conservation rate(CR)was established by analyzing the conservation of amino acid sequences of coding genes in 100 species to quantify the evolutionary conservation of genes.The relationship between CR and developmental potential was verified by using the feature genes involved in embryonic stem cells pathways.Secondly,cell type-specific genes and their characteristics in conservation were studied by analyzing the RNA sequencing(RNA-seq)data of the three early germ layers(ectoderm,mesoderm and endoderm)and their corresponding mature organs(brain,heart,liver,etc).Then,chromatin immunoprecipitation sequencing(ChIP-seq)data of enhancer histone H3 acetylated at lysine 27(H3K27ac)from early germ layers and mature organs were collected to search for enhancer sites and identify super enhancers in various cells and tissues by using the ROSE procedure.Functional enrichment and signaling pathway analysis of genes was used to examine the identity correlation between SEs-regulated genes and the corresponding cell characteristics,to clarify whether the SEs identified in this study were consistent with the characteristics reported in previous studies.Finally,PhastCons program was used to calculate the DNA conservation score(CS)of non-coding regulatory regions to study their relationship with developmental potential.Results·In the coding region of DNA,CR was successfully established to quantify the conservation of genes.The gene expression data of early germ layers and mature organs showed that the genes with higher conservation rate were more relevant to the stemness and early developmental process,and the differences between the tissues from early and late development could be distinguished by using CR.In the non-coding regions of DNA,it was found that the conservation of regulatory regions was also correlated with development.The CS of the SE sequences in the early developmental germ layers was significantly higher than that of the SE sequences in the corresponding mature organs.However,cell-specific typical enhancers(TEs)did not show such a trend.Conclusion·During the developmental process,CR of genes expressed in the coding region decreases,and CS of super-enhancer DNA in the non-coding region decreases.

ObjectiveTo study the relationship between the exposure to two kinds of phthalate esters （PAEs） ［Di-N-butyl phthalate，（DBP） and Di-（2-ethylhexyl）phthalate （DEHP）］ and estrogen homeostasis in pregnant women. MethodsIn 2021， we classified the Jiading District of Shanghai into five geographical areas， east， west， south， north and central. A total of 151 pregnant women from each area were selected for questionnaire survey， with random urine samples during first， second， and third trimesters collected. A DBP metabolite ［Mono-N-butyl phthalate （MBP）］ and two DEHP metabolites ［Mono（2-ethylhexyl） phthalate （MEHP）， Mono（2-ethyl5-oxohexyl） phthalate， （MEOHP）］ and three estrogens ［estrone （E₁）， 17β -estradiol （E₂）， and estriol （E₃）］ in urine were determined by ultra-performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry. After a natural logarithmic transformation of PAEs metabolite levels and estrogen concentration， multivariable linear regression was used to control potential confounders and determine the relationship between PAEs metabolite levels and estrogen concentration. ResultsThe detection rates of three PAEs metabolites in urine of pregnant women were more than 98%. The median corrected concentrations of MBP， MEHP and MEOHP were 5.18， 0.59 and 4.23 mg·kg^-1， respectively. During the whole pregnancy， MEOHP was positively correlated with E₁ （β=0.450， 95%CI： 0.057‒0.844）， and MBP was positively correlated with E₃ （β=0.250， 95%CI： 0.034‒0.465）. Stratified by trimesters， MBP was positively correlated with E₃ in the first trimester （β=0.428， 95%CI： 0.103‒0.752）. MEOHP was positively correlated with E₁ in the second trimester （β=0.734， 95%CI： 0.130‒0.752）， and had a possitive trend with E₁ in the third trimester （β=0.744， 95%CI： -0.140‒1.629）. In addition， MEHP had a negative correlation with E₁ in the second trimester （β=-0.498， 95%CI： -1.063‒0.066）. MEOHP had a positive correlation trend with E₂ （β=0.628， 95%CI： -0.101‒1.356） in the third trimester. ConclusionPAEs exposure may interfere with estrogen homeostasis during pregnancy and differs by trimesters. Given the cross-sectional nature of this study， it warrants further study to validate the findings.

The importance of structural variants(SVs)for human phenotypes and diseases is now recognized.Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed,few benchmarking procedures are available to confidently assess their performances in biological and clinical research.To facilitate the validation and application of these SV detection approaches,we established an Asian reference material by characterizing the genome of an Epstein-Barr virus(EBV)-immortalized B lymphocyte line along with identified benchmark regions and high-confidence SV calls.We established a high-confidence SV callset with 8938 SVs by integrating four alignment-based SV callers,including 109x Pacific Biosciences(PacBio)continuous long reads(CLRs),22 x PacBio circular consensus sequencing(CCS)reads,104x Oxford Nanopore Technologies(ONT)long reads,and 114×Bionano optical mapping plat-form,and one de novo assembly-based SV caller using CCS reads.A total of 544 randomly selected SVs were validated by PCR amplification and Sanger sequencing,demonstrating the robustness of our SV calls.Combining trio-binning-based haplotype assemblies,we established an SV benchmark for identifying false negatives and false positives by constructing the continuous high-confidence regions(CHCRs),which covered 1.46 gigabase pairs(Gb)and 6882 SVs supported by at least one diploid haplotype assembly.Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology,disease,and clinical research.

Objective: To determine the in vitro and in vivo absorption properties of active ingredients of the Chinese medicine, baicalein, to enrich mechanistic understanding of oral drug absorption. Methods: The Biopharmaceutic Classification System (BCS) category was determined using equilibrium solubility, intrinsic dissolution rate, and intestinal permeability to evaluate intestinal absorption mech-anisms of baicalein in rats in vitro. Physiologically based pharmacokinetic (PBPK) model commercial software GastroPlus?was used to predict oral absorption of baicalein in vivo. Results: Based on equilibrium solubility, intrinsic dissolution rate, and permeability values of main absorptive segments in the duodenum, jejunum, and ileum, baicalein was classified as a drug with low solubility and high permeability. Intestinal perfusion with venous sampling (IPVS) revealed that baicalein was extensively metabolized in the body, which corresponded to the low bioavailability predicted by the PBPK model. Further, the PBPK model predicted the key indicators of BCS, leading to reclassification as BCS-II. Predicted values of peak plasma concentration of the drug (Cmax) and area under the curve (AUC) fell within two times of the error of the measured results, highlighting the superior prediction of ab-sorption of baicalein in rats, beagles, and humans. The PBPK model supported in vitro and in vivo evi-dence and provided excellent prediction for this BCS class Ⅱ drug. Conclusion: BCS and PBPK are complementary methods that enable comprehensive research of BCS parameters, intestinal absorption rate, metabolism, prediction of human absorption fraction and bioavailability, simulation of PK, and drug absorption in various intestinal segments across species. This combined approach may facilitate a more comprehensive and accurate analysis of the absorption characteristics of active ingredients of Chinese medicine from in vitro and in vivo perspectives.