Recently, diffusion models have emerged as a promising paradigm for molecular design and optimization. However, most diffusion-based molecular generative models focus on modeling 2D graphs or 3D geometries, with limited research on molecular sequence diffusion models. The International Union of Pure and Applied Chemistry (IUPAC) names are more akin to chemical natural language than the Simplified Molecular Input Line Entry System (SMILES) for organic compounds. In this work, we apply an IUPAC-guided conditional diffusion model to facilitate molecular editing from chemical natural language to chemical language (SMILES) and explore whether the pre-trained generative performance of diffusion models can be transferred to chemical natural language. We propose DiffIUPAC, a controllable molecular editing diffusion model that converts IUPAC names to SMILES strings. Evaluation results demonstrate that our model outperforms existing methods and successfully captures the semantic rules of both chemical languages. Chemical space and scaffold analysis show that the model can generate similar compounds with diverse scaffolds within the specified constraints. Additionally, to illustrate the model's applicability in drug design, we conducted case studies in functional group editing, analogue design and linker design.

Flavonoids are key bioactive components for evaluating the pharmacological activities of Chimonanthus praecox. Exploring the potential flavonoids and pharmacological mechanisms of C. praecox lays a foundation for the rational development and efficient utilization of this plant. This study employed ultra-performance liquid chromatography-tandem mass spectrometry-based widely targeted metabolomics to comprehensively identify the flavonoids in C. praecox. Network pharmacology was employed to explore the bioactive flavonoids and their mechanisms of action. Molecular docking was adopted to validate the predicted results. Finally, the content of bioactive flavonoids in different varieties of C. praecox was measured. The widely targeted metabolomics analysis identified 387 flavonoids in C. praecox, and the flavonoids varied among different varieties. Network pharmacology predicted 96 chemical components including 19 bioactive compounds, 181 corresponding targets and 2 504 disease targets, among which 99 targets were shared by the active components and the disease. Thirty-three core targets were predicted, involving 229 gene ontology terms and 99 pathways (P≤0.05), which indicated that the flavonoids components of C. praecox exhibited pharmacological activities including antioxidant, anti-inflammatory, antimicrobial, and antiviral activities. Topological analysis screened out five core components (salvigenin, laricitrin, isorhamnetin, quercetin, and 6-hydroxyluteolin) and five core targets (SRC, PIK3R1, AKT1, ESR1, and AKR1C3). The predicted bioactive flavonoids from C. praecox stably bound to key targets, which indicated that these flavonoids possessed potential bioactivities in their interactions with the targets. The flavonoids in C. praecox exerted pharmacological activities in a multi-component, multi-target, and multi-pathway manner. The combined application of metabolomics and network pharmacology provides a theoretical basis for in-depth studies on the pharmacological effects and mechanisms of C. praecox.
Flavonoids/metabolism* ; Network Pharmacology ; Metabolomics/methods* ; Molecular Docking Simulation ; Calycanthaceae/chemistry* ; Tandem Mass Spectrometry ; Drugs, Chinese Herbal/chemistry*

Prunus mume is an ecologically and economically valuable plant with both medicinal and edible values. However, drought severely limits the promotion and cultivation of P. mume in the arid and semi-arid areas in northern China. In this study, we treated P. mume 'Meiren' with natural drought and then assessed photosynthetic and physiological indexes such as osmoregulatory substances, photosynthetic parameters, and antioxidant enzyme activities. Furthermore, we employed transcriptome sequencing to explore the internal regulatory mechanism of P. mume under drought stress. As the drought stress aggravated, the levels of chlorophyll a (Chla), chlorophyll b (Chlb), chlorophyll (a+b)[Chl(a+b)], and soluble protein (SP) in P. mume first elevated and then declined. The net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), maximum photochemical efficiency (Fv/Fm), effective photochemical quantum yield [Y(Ⅱ)], photochemical quenching (qP), and relative electron transport rate (ETR) all kept decreasing, while the levels of malondialdehyde, superoxide dismutase (SOD), peroxidase (POD), and osmoregulatory substances rose. Transcriptome sequencing revealed a total of 24 853 high-quality genes. Gene ontology (GO) enrichment showed that differentially expressed genes (DEGs) were the most under severe drought. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that the DEGs during the four drought periods were mainly involved in the biosynthesis of secondary metabolites, plant-pathogen interaction, plant hormone signal transduction, starch and sucrose metabolism, and mitogen-activated protein kinase signaling pathways. Furthermore, we identified 16 key genes associated with the drought tolerance of P. mume 'Meiren'. This study discovered that P. mume might up-regulate or down-regulate the expression of drought tolerance-related genes such as SUS, P5CS, LEA, SOD, POD, SOD1, TPPD, and TPPA via transcription factors like MYB, ERF, bHLH, NAC, and WRKY to promote the accumulation of osmoregulatory substances like sucrose and enhance the activities of antioxidant enzymes such as SOD and POD, thus reducing the harm of reactive oxygen species and protecting the structure and function of the membrane system under drought stress. The findings provide theoretical references for further exploration of candidate genes of P. mume in response to drought stress and breeding of drought-tolerant varieties.
Droughts ; Photosynthesis/physiology* ; Gene Expression Regulation, Plant ; Stress, Physiological/genetics* ; Prunus/genetics* ; Chlorophyll/metabolism* ; Plant Proteins/genetics*

We studied the genetic diversity and established the DNA molecular identify for Prunus mume with both ornamental and edible values, aiming to collect, identify, evaluate, and breed new varities of this plant and promote the upgrading of the P. mume industry chain in northern China. We employed 13 pairs of primers with good polymorphism, clear bands, and good repeatability to analyze the genetic diversity and establish the molecular identify of 68 germplasm accessions of P. mume with both ornamental and edible values from Xingtai, Hebei Province. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance. After that, we analyzed the genetic structure of the 68 germplasm accessions based on a Bayesian model. The 13 pairs of SSR primers amplified a total of 124 alleles from 68 P. mume germplasm accessions, with the mean number of alleles (Na) of 9.538 5, the minor allele frequency (MAF) of 0.369 3, the mean number of effective alleles (Ne) of 4.483 5, and the mean Shannon genetic diversity index (I) of 1.712 4. The mean Nei's gene diversity index (H) of 0.763 7, the mean observed heterozygosity (Ho) of 0.719 5, the mean expected heterozygosity (He) of 0.769 3, the mean polymorphism information content (PIC) of 0.733 6, and the mean genetic similarity (GS) of 0.772 9 suggested that there were significant genetic differences and rich genetic diversity among the studied P. mume germplasm accessions. The cluster analysis revealed that the 68 accessions were classified into three groups, with the mean genetic distance of 0.622 6. The population structure analysis classified the germplasm accessions into two populations. According to the PIC of primers, we selected primers for combination and constructed the combination with the fewest primers required for germplasm differentiation of P. mume with both ornamental and edible values. This study provides a theoretical basis for the innovation and industrial upgrading of P. mume with both ornamental and edible values in gardening and the improvement of breeding efficiency.
Prunus/classification* ; Microsatellite Repeats/genetics* ; Genetic Variation ; China ; Phylogeny ; Polymorphism, Genetic ; DNA, Plant/genetics* ; Alleles

Objective:To construct the clinical practice pathway for narrative medicine in traditional Chinese medicine(TCM),with a view to providing clinical practice guidelines for narrative medicine in TCM for frontline practitioners.Methods:Using the realistic literature review and the Nominal Group Technique(NGT),the paper systematically sorted out the practices of humanistic care in ancient Chinese medical books and famous medical cases,as well as constructed the first draft of the clinical practice pathway and details for narrative medicine in TCM.Subsequently,experts from multiple fields were invited to demonstrate by using the NGT.After in-depth discussion and collective voting,various operational modules,and their detailed rules and supporting tools were determined,thus completing the construction of the entire practical pathway.Results:A complete set of clinical practice pathways for narrative medicine in TCM had been established.It encompassed six core modules,including"start of diagnosis and treatment","communication of disease conditions","diagnosis and explanation","joint decision-making","end of diagnosis and treatment",and"reflection and summary".Besides,detailed operating rules and supporting tools were also provided.Conclusion:The clinical practice pathway for narrative medicine in TCM integrates the humanistic spirit of TCM,the core concepts of narrative medicine,and the communication skills of psychology,providing medical workers with standardized,procedural,and operationally flexible practice guidance,which helps both doctors and patients to better communicate,empathize,and make joint decisions throughout the entire process of diagnosis and treatment.

Objective:To analyze the effect of birth parity on life expectancy (LE) and healthy life expectancy (HLE) among rural women.Method:A total of 15 304 women aged 40 to 79 years who participated in baseline and follow-up surveys were selected from a rural cohort in Henan province. The LE and HLE of women with different birth parity were calculated by using multi-state life table.Results:There were 1 195 (7.8%), 7 782 (50.8%), 3 867 (25.3%) and 2 460 (16.1%) women with 1, 2, 3 and 4 birth parities, respectively, and the M ( Q1 and Q3) of age were 50.3 (47.3, 53.4) and 53.3 (48.8, 60.7), 62.6 (55.4, 66.9) and 69.5 (64.7, 73.4) years old, respectively. LE at 40 years old was 44.5, 44.8, 45.1 and 45.4 years old, and HLE was 17.7, 18.3, 18.8 and 19.3 years old, respectively. LE at age 40 increased by 0.3, 0.6, and 0.9 years in women with 2, 3, and 4 birth parities or more and HLE increased by 0.5, 1.1, and 1.6 years, respectively, compared with women with 1 birth parity. For women with higher and lower socioeconomic status who had 4 birth parities or more, the LE at age 40 was 47.1 and 43.9 years, respectively, an increase of 0.2 and 0.1 years over women with 1 birth parity, respectively; and the HLE was 20.4 and 18.7 years, respectively, an increase of 1.4 and 1.3 years over women with 1 birth parity, respectively. Conclusion:LE and HLE show an upward trend with the increase of birth parity among rural women.

Objective:To analyze the effect of birth parity on life expectancy (LE) and healthy life expectancy (HLE) among rural women.Method:A total of 15 304 women aged 40 to 79 years who participated in baseline and follow-up surveys were selected from a rural cohort in Henan province. The LE and HLE of women with different birth parity were calculated by using multi-state life table.Results:There were 1 195 (7.8%), 7 782 (50.8%), 3 867 (25.3%) and 2 460 (16.1%) women with 1, 2, 3 and 4 birth parities, respectively, and the M ( Q1 and Q3) of age were 50.3 (47.3, 53.4) and 53.3 (48.8, 60.7), 62.6 (55.4, 66.9) and 69.5 (64.7, 73.4) years old, respectively. LE at 40 years old was 44.5, 44.8, 45.1 and 45.4 years old, and HLE was 17.7, 18.3, 18.8 and 19.3 years old, respectively. LE at age 40 increased by 0.3, 0.6, and 0.9 years in women with 2, 3, and 4 birth parities or more and HLE increased by 0.5, 1.1, and 1.6 years, respectively, compared with women with 1 birth parity. For women with higher and lower socioeconomic status who had 4 birth parities or more, the LE at age 40 was 47.1 and 43.9 years, respectively, an increase of 0.2 and 0.1 years over women with 1 birth parity, respectively; and the HLE was 20.4 and 18.7 years, respectively, an increase of 1.4 and 1.3 years over women with 1 birth parity, respectively. Conclusion:LE and HLE show an upward trend with the increase of birth parity among rural women.

Objective:To analyze the clinical manifestations and explore the etiology in a family with congenital aniridia and to analyze the influence of candidate variants on the protein structure.Methods:A pedigree investigation was performed.A Han Chinese family with congenital aniridia of two generations consisting of three members from Henan Province, including one patient diagnosed with congenital aniridia, was identified and studied following their admission to Henan Eye Hospital in June 2023.A thorough medical history was obtained for the patient and their family members.Comprehensive ophthalmologic examinations were conducted, including visual acuity, intraocular pressure, anterior segment photography, color fundus photography, ultrasound biomicroscopy, and optical coherence tomography, etc.Peripheral blood samples were obtained from the family members and whole exome sequencing (WES) was performed on the patient and validated by Sanger sequencing for other members.The pathogenicity and protein structure of newly identified variant sites were analyzed.This study adhered to the Declaration of Helsinki.The study protocol was approved by the Ethics Committee of Henan Eye Hospital (No.HNEECKY-2023[06]).Written informed consent was obtained from each subject.Results:The proband is a 23-year-old male presenting with poor binocular vision, aniridia, corneal degeneration, mild lens opacity, shallow anterior chamber, elevated intraocular pressure, peripheral retinal degeneration, and macular dysplasia.The clinical phenotype of the proband's parents did not show any significant abnormality.WES identified a heterozygous frameshift and nonsense varint c. 734_735del (p.Arg245Asnfs*20) in exon 10 of the PAX6 gene, which consisited of two bases deletion at positions 734 to 735, resulting in the mutation of its arginine at position 245 to asparagine and the early appearance of a termination codon at the next 19 amino acids.The variant had not been identified in the HGMD, Clinvar, 1 000 Genomes, and gnomAD databases.Neither of the proband's parents carried the variant, consistent with the pattern of family co-segregation.Substructural analysis using the SMART tool indicated that the variant is situated within the HOX domain.Amino acid conservation analysis demonstrated that the arginine residue at position 245 in the PAX6 gene is highly conserved across multiple species, including human, house mouse, domestic dog, African clawed frog, and macaque.The variant was classified as pathogenic (PVS1+ PS2+ PM2+ PP3) based on the ACMG standards and guidelines for the interpretation of sequence variants.Protein structure analysis revealed the absence of both the homologous domain and the proline-serine-threonine-rich domain in the PAX6 protein. Conclusions:A novel pathogenic variant, c.734_735del (p.Arg245Asnfs*20), in the PAX6 gene has been identified in a family affected by congenital aniridia.This variant results in the deletion of both the PAX6 protein homology domain and the proline-serine-threonine-rich domain.

Objective:To select the differential prognostic lactic acid metabolism-related genes(LRGs)of the head and neck squamous cell carcinoma(HNSCC)to construct the LRGs prognostic model of HNSCC,and to clarify the potential mechanism.Methods:The HNSCC gene expression and clinical data were obtained from The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)Databases,the LRGs were identified through GeneCards Database,and R software was used to screen out the LRGs of HNSCC;univariate Cox regression analysis was used to identify prognosis-related genes;two different subtypes were identified based on the prognostis-related LRGs;Kaplan-Meier(K-M)curve analysis was used to compare the prognosis of the patients between two groups;CIBERSORT algorithm was used to perform the immuno-correlation analysis between two groups;multivariate Cox regression analysis and LASSO regression analysis were used to construct the prognostic model;receiver operating characteristic curve(ROC)and K-M survival curve were used to assess the relationship between LRGs and survival and prognosis of the HNSCC patients.The prognostic model was validated by GSE27020,GSE41613,and GSE65858 datasets.The experiment were grouped based on risk score,and immune-related analysis and tumor score analysis were performed.Results:The TCGA Database differential analysis results showed that 1 196 LRGs were identified from HNSCC samples;univariate Cox regression analysis selected 27 differentially expressed genes(DEGs)associated with the prognosis of the HNSCC patients.Two different LRGs subtypes(Group 1 and Group 2)were identified according to the prognosis-related genes.The K-M survival curves results showed that the overall survival(OS)of the patients in Group 2 was significantly higher than that in Group 1,and the immune cell expression amount of the patients in Group 2 was also higher than that in group 1.The multivariate Cox regression and LASSO regression analysis results screened out 9 LRGs,including hypoxanthine phosphoribosyltransferase 1(HPRT1),amyloid precursor protein(APP),glycogen phosphorylase L(PYGL),urokinase-type plasminogen activator(PLAU),cannabinoid receptor 2(CNR2),stanniocalcin 2(STC2),nucleotide binding oligomerization domain-like receptor protein 1(NLRP1),integrin-linked kinase(ILK),and forkhead box B1(FOXB1);the prognostic model was constructed.The K-M and ROC curve results indicated that the expression levels of above 9 genes were associated with the survival and prognosis of the HNSCC patients,providing good 1-year,2-year,and 3-year survival prediction effect,and the area under ROC curve(AUC)values were all greater than 0.650.Furthermore,the predictive ability of the prognosis model was validated in GSE27020,GSE41613,and GSE65858 datasets.The patients classified based on the risk scores had distinguishable immune statuses.Conclusion:The differentially expressed LRGs of HNSCC screened by bioinformatics methods are related to the survival and prognosis of the HNSCC patients;the prognostic model constructed by 9 LRGs can predict the survival status and treatment response of the HNSCC patients.

Intracerebral hemorrhage (ICH) is a hemorrhagic cerebrovascular disease with high incidence and mortality. Oxidative stress response plays an important role in the pathological and physiological processes of ICH, and is also a potential effective target for clinical treatment. In this paper, the pathogenesis of oxidative stress after ICH, mechanism of nerve and vascular injury in oxidative stress, and detection and treatment of oxidative stress are reviewed in order to provide references for basic research and clinical practice in ICH.