1.Fingerprint-enhanced hierarchical molecular graph neural networks for property prediction
Shuo LIU ; Mengyun CHEN ; Xiaojun YAO ; Huanxiang LIU
Journal of Pharmaceutical Analysis 2025;15(6):1311-1320
Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials.Traditional methods based on manually crafted features and graph-based methods have shown promising results in molecular property prediction.However,traditional methods rely on expert knowledge and often fail to capture the complex structures and interactions within molecules.Similarly,graph-based methods typically overlook the chemical structure and function hidden in molecular motifs and struggle to effectively integrate global and local molecular information.To address these limitations,we propose a novel fingerprint-enhanced hierarchical graph neural network(FH-GNN)for molecular property prediction that simultaneously learns information from hierarchical molecular graphs and fingerprints.The FH-GNN captures diverse hierarchical chemical information by applying directed message-passing neural networks(D-MPNN)on a hierarchical molecular graph that integrates atomic-level,motif-level,and graph-level information along with their relationships.Addi-tionally,we used an adaptive attention mechanism to balance the importance of hierarchical graphs and fingerprint features,creating a comprehensive molecular embedding that integrated hierarchical mo-lecular structures with domain knowledge.Experiments on eight benchmark datasets from MoleculeNet showed that FH-GNN outperformed the baseline models in both classification and regression tasks for molecular property prediction,validating its capability to comprehensively capture molecular informa-tion.By integrating molecular structure and chemical knowledge,FH-GNN provides a powerful tool for the accurate prediction of molecular properties and aids in the discovery of potential drug candidates.
2.Epidemiologic evidence of proteus mirabilis infection in patients with rheumatoid arthritis:A systematic evaluation and Meta-analysis of included global controlled studies
Jiawei ZHANG ; Li JI ; Guoyong DING ; Shuman LIU ; Mengyun WU ; Xue ZHANG ; Aihong ZHOU
China Modern Doctor 2025;63(18):18-24
Objective To systematically evaluate the level of proteus mirabilis(PM)infection in patients with rheumatoid arthritis(RA)and to investigate its potential association with the development of RA.Methods Based on Meta-analysis of observational studies in epidemiology and preferred reporting items for systematic review and Meta-analysis guide,a comprehensive search of PubMed,Web of Science and Embase databases was conducted to screen relevant literature published up to December 2024 for studies comparing the levels of anti-PM antibodies between RA patients and healthy populations,and the quality of the included studies was assessed by using the Newcastle-Ottawa scale.Heterogeneity among studies was assessed by Q-test and I2-test,and accordingly,fixed-effects or random-effects models were selected,and the robustness of the results was assessed by sensitivity analyses,Begg's test,and clipping and patching method.Results Finally,18 eligible articles were included,involving 753 RA patients and 716 healthy controls.The total antibody levels[weighted mean difference(WMD)=0.86,95%CI:0.38-1.34,I2=98.3%,P=0.000]and IgA antibody levels(WMD=0.17,95%CI:0.06-0.28,I2=96.7%,P=0.000)of RA patients were higher than those of healthy controls,and subgroup analyses revealed significant heterogeneity among geographic regions and testing methods.Conclusion Prevention and treatment of PM infections may be a complementary strategy for RA management and provide evidence-based support for the"PM antigen-genitourinary tract mucosa-autoimmunity"pathology hypothesis.
3.Exploring the Mechanism of Qingwen Baidu Drink on Lung Injury in Septic Mice Based on the Caspase11-GSDMD-GD-MD-N Pathway
Yupei ZHAO ; Yu BAI ; Binchan HE ; Wei PANG ; Mengyun LIU ; Yimin ZHU
Journal of Nanjing University of Traditional Chinese Medicine 2025;41(3):333-340
OBJECTIVE To explore the mechanism of Qingwen Baidu Drink in treating sepsis-induced lung injury.METHODS One hundred C57BL/6 mice were randomly divided into blank group,model group,Qingwen Baidu Drink low-dose group,Qingwen Baidu Drink medium-dose group,and Qingwen Baidu Drink high-dose group,with 20 mice in each group.HE staining was used to examine the pathological changes of lung tissues.ELISA was used to detect the expression levels of serum interleukin-1β(IL-1β),tumor necrosis factor-α(TNF-α),chemokine ligand 10(CXCL10)and plasma coagulation factor Ⅲ(F3).qPCR was used to detect the mRNA expression levels of monocyte chemoattractant protein-1(MCP-1),cyclooxygenase-2(COX-2)and interferon-γ(IFN-γ)in lung tissues.The number of platelets(PLT)in plasma was analyzed by routine blood analysis instrument.Immunofluorescence a-nalysis was used to detect vascular endothelial cadherin(VE-cadherin),endothelial adhesion junction marker occludin 5(CLDN5)and pericyte marker neuronal collagen antigen 2(NG2)in alveolar capillary endothelial cells.Western blot was used to detect the pro-tein expression levels of cysteine-containing aspartate proteinase 11(Caspase11),GSDMD and GSDMD-N in mouse lung tissues.RESULTS Compared with the blank group,the lung tissue of the mice in the model group showed obvious pathological dam-age.The levels of serum IL-1β,TNF-α,and CXCL10 and the mRNA expression levels of MCP-1,COX-2,and IFN-γ in lung tis-sue were significantly increased(P<0.01),and the number of PLT and the content of F3 in plasma were significantly decreased(P<0.01).The fluorescence expression of VE-cadherin,CLDN5,and NG2 proteins in lung tissue was significantly enhanced(P<0.01),while the expression of Caspase11 and GSDMD-N proteins was increased(P<0.01).Compared with the model group,the pathological damage of the lung tissue of the mice in all doses of Qingwen Baidu Drink groups was alleviated,the levels of serum IL-1β,TNF-α,and CXCL10 and the mRNA expression levels of MCP-1,COX-2,and IFN-γ in lung tissue were significantly decreased(P<0.05,P<0.01),and the number of PLT and the content of F3 in plasma were increased(P<0.05,P<0.01);the fluorescence expression of VE-cadherin,CLDN5,and NG2 proteins in lung tissues was weakened(P<0.05,P<0.01),and the expression of Caspase11 and GSDMD-N/GSDMD proteins was reduced(P<0.05,P<0.01).CONCLUSION Qingwen Baidu Drink can inhibit the activation of GSDMD-N and Caspase11,reduce the release of inflammatory factors,decrease blood loss and damage to vascular barrier function,and thus improve the lung injury caused by sepsis.
4.Analysis of C4BPA gene polymorphism and its correlation with milk quality in Chinese Holstein cows
Mengyun ZHU ; Ping JIANG ; Xuanxu CHEN ; Zhongqun TANG ; Haibin YU ; Yanlong ZHOU ; Xianghao LIU ; Zhihui ZHAO ; Ziwei LIN
Chinese Journal of Veterinary Science 2025;45(1):138-144
The complement component 4 binding protein alpha(C4BPA)gene is the alpha chain of complement binding protein 4.As a plasma protein involved in the complement and coagulation systems,it can influence immune responses and lipid metabolism.In order to study the polymor-phism of C4BPA gene and its correlation with milk quality traits in Chinese Holstein cows,genom-ic DNA was extracted from blood samples of 92 Chinese Holstein cows,and the target fragment of C4BPA gene was amplified by PCR,and the association analysis was performed by using direct se-quencing to obtain the SNP loci and milk quality traits.The results showed that among the four SNPs found at the third intron of the C4BPA gene,I3-11 G>A was highly significantly correlated with milk protein and urea nitrogen(P<0.05),I3-291 T>G was significantly correlated with lac-tose(P<0.05),I3-374 C>T was highly significantly correlated with lactose and urea nitrogen(P<0.05),and I3-375 T>G was highly significantly correlated with lactose(P<0.05),milk pro-tein and urea nitrogen.The chi-square test values for each point indicated that the population was in genetic equilibrium.Individuals of haplotype combination H1 H1 had the highest lactose content,and haplotype combination H1H2 can be used as the best haplotype combination in the molecular selection work of dairy cows.
5.Fingerprint-enhanced hierarchical molecular graph neural networks for property prediction.
Shuo LIU ; Mengyun CHEN ; Xiaojun YAO ; Huanxiang LIU
Journal of Pharmaceutical Analysis 2025;15(6):101242-101242
Accurate prediction of molecular properties is crucial for selecting compounds with ideal properties and reducing the costs and risks of trials. Traditional methods based on manually crafted features and graph-based methods have shown promising results in molecular property prediction. However, traditional methods rely on expert knowledge and often fail to capture the complex structures and interactions within molecules. Similarly, graph-based methods typically overlook the chemical structure and function hidden in molecular motifs and struggle to effectively integrate global and local molecular information. To address these limitations, we propose a novel fingerprint-enhanced hierarchical graph neural network (FH-GNN) for molecular property prediction that simultaneously learns information from hierarchical molecular graphs and fingerprints. The FH-GNN captures diverse hierarchical chemical information by applying directed message-passing neural networks (D-MPNN) on a hierarchical molecular graph that integrates atomic-level, motif-level, and graph-level information along with their relationships. Additionally, we used an adaptive attention mechanism to balance the importance of hierarchical graphs and fingerprint features, creating a comprehensive molecular embedding that integrated hierarchical molecular structures with domain knowledge. Experiments on eight benchmark datasets from MoleculeNet showed that FH-GNN outperformed the baseline models in both classification and regression tasks for molecular property prediction, validating its capability to comprehensively capture molecular information. By integrating molecular structure and chemical knowledge, FH-GNN provides a powerful tool for the accurate prediction of molecular properties and aids in the discovery of potential drug candidates.
6.Acupuncture combined with blade needle therapy for knee osteoarthritis:a randomized controlled trial.
Xiao LI ; Yujie CUI ; Wenjin YANG ; Yuanyuan LI ; Xiao GUO ; Di LIU ; Mengyun YU ; Hui HU ; Hua LI
Chinese Acupuncture & Moxibustion 2025;45(11):1571-1576
OBJECTIVE:
To observe the clinical efficacy and safety of acupuncture combined with blade needle therapy for knee osteoarthritis (KOA).
METHODS:
A total of 60 patients with KOA were randomly divided into an observation group and a control group, 30 cases each group. The control group received acupuncture at Neixiyan (EX-LE4),Dubi (ST35), Yinlingquan (SP9), Liangqiu (ST34), Xuehai (SP10), Yanglingquan (GB34) and Zusanli (ST36) on the affected side, once every other day, 3 times a week. The observation group received blade needle therapy on the basis of the treatment in the control group, once every 3 days, 2 times a week. Both groups were treated for 4 weeks. Before treatment, after 2, 4 weeks of treatment, and after 1 month of treatment completion (in follow-up), the scores of pain visual analogue scale (VAS), Western Ontario and McMaster Universities osteoarthritis index (WOMAC) and Lequesne index were observed in the two groups, and the clinical efficacy and safety were evaluated.
RESULTS:
After 2, 4 weeks of treatment and in follow-up, the pain VAS scores, Lequesne index scores, and pain, stiffness, function scores of WOMAC in both groups were decreased compared with those before treatment (P<0.05), and the VAS scores, Lequesne index scores and pain, function scores of WOMAC in the observation group were lower than those in the control group (P<0.05). The effective response rate in the observation group was 76.7% (23/30), while that in the control group was 70.0% (21/30), there was no statistically significant difference in the effective response rates between the two groups (P>0.05). No adverse reactions were observed in either group.
CONCLUSION
Acupuncture combined with blade needle therapy could alleviate pain and promote functional recovery in KOA patients, and achieve long-lasting improvements.
Humans
;
Osteoarthritis, Knee/physiopathology*
;
Acupuncture Therapy/instrumentation*
;
Male
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Female
;
Middle Aged
;
Aged
;
Acupuncture Points
;
Treatment Outcome
;
Adult
;
Needles
;
Combined Modality Therapy
7.Causal relationship of liposomes and circulating metabolomes to schizophrenia: a two-step, two-sample Mendelian randomization study
Mengyun LEI ; Yanhong DU ; Yao GAO ; Huaili DENG ; Binhong WANG ; Zhiyong REN ; Sha LIU
Sichuan Mental Health 2025;38(3):223-228
BackgroundSchizophrenia is a complex, chronic and severe mental disorder, and the pathogenesis of which has not been fully elucidated. The abnormalities in lipid metabolism and circulating metabolomes have already been implicated in the pathophysiology of schizophrenia. However, available studies have mainly focused on a few liposomes and circulating metabolites, failing to systematically reveal the mediating role of circulating metabolomes in the causal relationship between liposomes and schizophrenia. ObjectiveTo uncover mediating role of circulating metabolomes in the causal relationship between liposomes and schizophrenia, thereby providing biomarkers and potential therapeutic targets for the prevention and treatment of schizophrenia. MethodsData from Genome-Wide Association Studies (GWAS) were analyzed, taking data on 179 liposomes as exposure variables, data on 123 circulating metabolites as intermediate variables, and data on schizophrenia as outcome variable. A two-step, two-sample Mendelian randomization analysis was conducted using the inverse-variance weighted (IVW), MR- Egger, Weighted median, and Weighted mode methods to study the causal relationship of liposomes with schizophrenia and the mediating role of circulating metabolomes in the relationship. ResultsIVW model identified 8 lipids associated with schizophrenia without reverse causality. There were 5 circulating metabolomes strongly associated with schizophrenia. Acetate played a significant mediating role in the causal relationship between phosphatidylinositol (18:0_18:2) and schizophrenia (P=0.023, 95% CI: 0.036~0.532), accounting for 28.4% of the causal relationship. ConclusionThis study demonstrates a causal relationship between liposomes and schizophrenia, with phosphatidylinositol being a risk factor in the progression of schizophrenia, and acetate playing a mediating role in this process. [Fund by National Natural Science Foundation of China General Program (number, 82271546); Shanxi Merit Funding for Overseas Students Sci-Tech Activities Project (number, 20240041); Shanxi Province Science and Technology Innovation Leading Talent Team Project (number, 202304051001049); Shanxi Scientific Research Foundation for the Returned Overseas Chinese Scholars (number, 2022-190); "Six Measures for Health Care Prosperity" Specialized Research Program (number, Y2024008)]
8.Research progress on the immunological pathogenesis of bronchial asthma
Ruli ZHAO ; Mengyun LIU ; Yimei MA ; Xiao WANG ; Xiaoying LIU
Immunological Journal 2025;41(11):842-848
Bronchial asthma is a common chronic heterogeneous airway disease that is pathologically characterized by airway hyperresponsiveness and chronic inflammation.The pathogenesis of this disease is complex.Essentially,it is an airway inflammatory response driven by abnormal activation of the immune system.Its occurrence and development involve the participation of various immune cells and immune factors,including B lymphocytes,T lymphocytes,mast cells,macrophages and dendritic cells,as well as key cytokines such as interleukin(IL)-4,IL-5,IL-13,and interferon(IFN)-γ.And key cytokines such as interleukin(IL)-4,IL-5,IL-13 and interferon-γ.The complex interactions between these immune cells and mediators cause a series of pathological changes such as increased airway mucus secretion,smooth muscle contraction and airway remodeling,ultimately leading to the appearance of clinical symptoms,such as chest tightness,shortness of breath,wheezing and coughing.This article conducts systematically reviews current understanding of the immunological pathogenesis of bronchial asthma,thereby providing theoretical references for drug development and clinical diagnosis and treatment.
9.Exploring the Mechanism of Qingwen Baidu Drink on Lung Injury in Septic Mice Based on the Caspase11-GSDMD-GD-MD-N Pathway
Yupei ZHAO ; Yu BAI ; Binchan HE ; Wei PANG ; Mengyun LIU ; Yimin ZHU
Journal of Nanjing University of Traditional Chinese Medicine 2025;41(3):333-340
OBJECTIVE To explore the mechanism of Qingwen Baidu Drink in treating sepsis-induced lung injury.METHODS One hundred C57BL/6 mice were randomly divided into blank group,model group,Qingwen Baidu Drink low-dose group,Qingwen Baidu Drink medium-dose group,and Qingwen Baidu Drink high-dose group,with 20 mice in each group.HE staining was used to examine the pathological changes of lung tissues.ELISA was used to detect the expression levels of serum interleukin-1β(IL-1β),tumor necrosis factor-α(TNF-α),chemokine ligand 10(CXCL10)and plasma coagulation factor Ⅲ(F3).qPCR was used to detect the mRNA expression levels of monocyte chemoattractant protein-1(MCP-1),cyclooxygenase-2(COX-2)and interferon-γ(IFN-γ)in lung tissues.The number of platelets(PLT)in plasma was analyzed by routine blood analysis instrument.Immunofluorescence a-nalysis was used to detect vascular endothelial cadherin(VE-cadherin),endothelial adhesion junction marker occludin 5(CLDN5)and pericyte marker neuronal collagen antigen 2(NG2)in alveolar capillary endothelial cells.Western blot was used to detect the pro-tein expression levels of cysteine-containing aspartate proteinase 11(Caspase11),GSDMD and GSDMD-N in mouse lung tissues.RESULTS Compared with the blank group,the lung tissue of the mice in the model group showed obvious pathological dam-age.The levels of serum IL-1β,TNF-α,and CXCL10 and the mRNA expression levels of MCP-1,COX-2,and IFN-γ in lung tis-sue were significantly increased(P<0.01),and the number of PLT and the content of F3 in plasma were significantly decreased(P<0.01).The fluorescence expression of VE-cadherin,CLDN5,and NG2 proteins in lung tissue was significantly enhanced(P<0.01),while the expression of Caspase11 and GSDMD-N proteins was increased(P<0.01).Compared with the model group,the pathological damage of the lung tissue of the mice in all doses of Qingwen Baidu Drink groups was alleviated,the levels of serum IL-1β,TNF-α,and CXCL10 and the mRNA expression levels of MCP-1,COX-2,and IFN-γ in lung tissue were significantly decreased(P<0.05,P<0.01),and the number of PLT and the content of F3 in plasma were increased(P<0.05,P<0.01);the fluorescence expression of VE-cadherin,CLDN5,and NG2 proteins in lung tissues was weakened(P<0.05,P<0.01),and the expression of Caspase11 and GSDMD-N/GSDMD proteins was reduced(P<0.05,P<0.01).CONCLUSION Qingwen Baidu Drink can inhibit the activation of GSDMD-N and Caspase11,reduce the release of inflammatory factors,decrease blood loss and damage to vascular barrier function,and thus improve the lung injury caused by sepsis.
10.Analysis of risk factors for amputation in patients with diabetic foot ulcer
Jie WANG ; Tianjian ZHA ; Mengyun LIU ; Xiaolong LIU ; Junjie YAO ; Jian ZHANG
Journal of Chinese Physician 2025;27(3):402-407
Objective:To investigate the risk factors of amputation in patients with diabetic foot ulcer (DFU) in order to improve the prognosis and reduce the amputation rate.Methods:The clinical data of 359 DFU patients admitted to the People′s Hospital of Xinjiang Uygur Autonomous Region from January 2017 to August 2021 were retrospectively analyzed, and they were divided into amputation group (161 cases) and non-amputation group (198 cases) according to whether amputation surgery was performed. Demographic characteristics, Wagner grading and other data of the two groups were collected. Forward step logistic regression analysis was used to identify independent risk factors for amputation, and receiver operating characteristic (ROC) curves were used to evaluate the predictive value of each risk factor for amputation in DFU patients.Results:There were significant differences between the amputation and non-amputation groups in terms of previous amputation history, peripheral vascular diseases (PVD), diabetic foot secondary osteomyelitis, diabetic nephropathy (DN), history of angioplasty, Wanger grade, K +, age, white blood cell count, C-reactive protein, high density lipoprotein cholesterol (HDL-C), estimated glomerular filtration rate, cardiac troponin T, and cardiac troponin I, lactic acid (all P<0.05). Previous amputation history ( OR=2.329, 95% CI: 1.092-4.970, P=0.029), DN ( OR=4.091, 95% CI: 2.222-7.532, P<0.001), PVD ( OR=2.556, 95% CI: 1.487-4.395, P=0.001), diabetic foot secondary osteomyelitis ( OR=6.332, 95% CI: 3.595-11.153, P<0.001), Wagner grade were independent risk factors for amputation in DFU patients, HDL-C ( OR=0.392, 95% CI: 0.182-0.842, P=0.016) were protective factors for amputation in DFU patients. Moreover, the combined accuracy of the above factors in predicting amputation in DFU patients was high, and the area under ROC curve was 0.839 (95% CI: 0.798-0.880), sensitivity was 83%, and specificity was 73% ( OR=0.05). Conclusions:Previous amputation history, DN, PVD, diabetic foot secondary osteomyelitis and Wagner grade are independent risk factors for amputation in DFU patients, while HDL-C is a protective factor for amputation in DFU patients. Further investigation will help to establish a stratified system for predicting the risk of diabetic foot, so as to achieve better individualized treatment.

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