1.Identify drug-drug interactions via deep learning: A real world study.
Jingyang LI ; Yanpeng ZHAO ; Zhenting WANG ; Chunyue LEI ; Lianlian WU ; Yixin ZHANG ; Song HE ; Xiaochen BO ; Jian XIAO
Journal of Pharmaceutical Analysis 2025;15(6):101194-101194
Identifying drug-drug interactions (DDIs) is essential to prevent adverse effects from polypharmacy. Although deep learning has advanced DDI identification, the gap between powerful models and their lack of clinical application and evaluation has hindered clinical benefits. Here, we developed a Multi-Dimensional Feature Fusion model named MDFF, which integrates one-dimensional simplified molecular input line entry system sequence features, two-dimensional molecular graph features, and three-dimensional geometric features to enhance drug representations for predicting DDIs. MDFF was trained and validated on two DDI datasets, evaluated across three distinct scenarios, and compared with advanced DDI prediction models using accuracy, precision, recall, area under the curve, and F1 score metrics. MDFF achieved state-of-the-art performance across all metrics. Ablation experiments showed that integrating multi-dimensional drug features yielded the best results. More importantly, we obtained adverse drug reaction reports uploaded by Xiangya Hospital of Central South University from 2021 to 2023 and used MDFF to identify potential adverse DDIs. Among 12 real-world adverse drug reaction reports, the predictions of 9 reports were supported by relevant evidence. Additionally, MDFF demonstrated the ability to explain adverse DDI mechanisms, providing insights into the mechanisms behind one specific report and highlighting its potential to assist practitioners in improving medical practice.
2.Application value of gastric suspension method in supra-pancreatic lymph node dissection of laparoscopic radical gastrectomy of gastric cancer
Mengmeng LE ; Jingyang HE ; Siwei PAN ; Xiangliu CHEN ; Can HU ; Yanqiang ZHANG ; Jianfa YU ; Zhiyuan XU
Chinese Journal of Digestive Surgery 2025;24(3):389-393
Objective:To investigate the application value of gastric suspension method in supra-pancreatic lymph node dissection of laparoscopic radical gastrectomy of gastric cancer.Method:The retrospective cohort study was conducted. The clinicopathological data of 84 patients who under-went laparoscopic radical gastrectomy of gastric cancer at Zhejiang Cancer Hospital from August 2023 to July 2024 were collected. There were 61 males and 23 females, aged (64±11)years. Of the 84 patients, 42 patients undergoing supra-pancreatic lymph node dissection during laparoscopic radical gastrectomy of gastric cancer with traditional method for surgical field exposure were divided into the control group, and 42 patients undergoing supra-pancreatic lymph node dissection during laparoscopic radical gastrectomy of gastric cancer with gastric suspension method for surgical field exposure were divided into the suspension group. Observation indicators: (1) surgical conditions; (2) postoperative conditions. Comparison of measurement data with normal distribution between groups was conducted using the independent sample t test. Comparison of measurement data with skewed distribution between groups was conducted using the Mann-Whitney U test. Comparison of count data between groups was conducted using the chi-square test. Results:(1) Surgical condi-tions. The time for supra-pancreatic lymph node dissection of the control group was (78±14)minutes. Number of grasping operations was 116±34, number of bleeding sites caused by grasping operations was 7.8±2.7, and operation time was (3.9±0.8)hours. The above indicators of the suspension group were (59±12)minutes, 68±19, 2.1±1.5, and (3.3±0.7)hours, respectively. There were significant diffe-rences in the above indicators between the two groups ( t=5.42, 8.10, 8.31, 3.14, P<0.05). (2) Post-operative conditions. The tumor diameter was 2.5(2.0,3.5)cm for patients of the control group, versus 3.0(2.4, 4.4)cm for patients of the suspension group, showing a significant difference between the two groups ( Z=-1.98, P<0.05). Conclusion:Compared with the traditional non-suspension method, the gastric suspension method in laparoscopic radical gastrectomy of gastric cancer for supra-pancreatic lymph node dissection is associated with shorter operation time and less trauma.
3.Exploration on Shengmai Decoction Targeting Bcl-2/Bax/Caspase-3 Pathway to Mediate Mitochondrial Apoptosis in Treatment of Heart Failure Based on Network Pharmacology
Xuan LIU ; He FENG ; Jingyang WANG ; Yuting WANG ; Rui ZHANG ; Zilian ZHAN ; Qiang XU
Chinese Journal of Information on Traditional Chinese Medicine 2025;32(9):22-30
Objective To explore the mechanism of Shengmai Decoction in improving heart failure by regulating mitochondrial apoptosis based on network pharmacology and experimental verification;To provide a basis for its clinical application.Methods The active components and targets of Shengmai Decoction were obtained through TCMSP and TCMID databases.Heart failure and mitochondrial apoptosis related targets were retrieved from GeneCards,OMIM,DrugBank,PharmGKB and TTD databases.A protein-protein interaction(PPI)network at the intersection of drugs and diseases was constructed using the STRING database,and a component-target network was constructed using Cytoscape 3.8.2 software.GO and KEGG pathway enrichment analysis was performed on intersecting targets using the DAVID database.Molecular docking was conducted to assess the binding affinity of key components to core target proteins.A rat model of heart failure was established,and the cardiac function of rats were detected by echocardiogram,ELISA was used to detect serum contents of BNP and NT-proBNP,mitochondrial ultrastructure was observed by transmission electron microscope,and Western blot was used to detect protein expressions of Bcl-2/Bax/Caspase-3 signaling pathway.Results A total of 66 active components and 146 targets of Shengmai Decoction were identified,and 22 intersecting targets with heart failure and mitochondrial apoptosis,including key proteins such as TNF,Bcl-2,Bax and Caspase-3.GO enrichment analysis revealed that the intersecting targets were closely associated with inflammation and cell signaling,while KEGG pathway analysis showed that the targets were primarily involved in the TNF signaling pathway,IL-17 signaling pathway,and mitochondrial function regulation.Molecular docking results indicated that Ginsenoside rh2,Beta-sitosterol and other components of Shengmai Decoction exhibited strong binding affinities with Bcl-2,Bax and Caspase-3.Animal experiments demonstrated that Shengmai Decoction significantly improved cardiac function(P<0.05,P<0.01),reduced serum BNP and NT-proBNP contents(P<0.01),alleviated mitochondrial damage,and inhibited mitochondrial apoptosis by upregulating Bcl-2 and downregulating Bax and Caspase-3 protein expression(P<0.01),thereby protecting cardiomyocytes.Conclusion Shengmai Decoction can target and regulate the Bcl-2/Bax/Caspase-3 signaling pathway,improving pathological processes associated with heart failure,which can provide a foundation for clinical optimization of Shengmai Decoction.
4.Identify drug-drug interactions via deep learning:A real world study
Jingyang LI ; Yanpeng ZHAO ; Zhenting WANG ; Chunyue LEI ; Lianlian WU ; Yixin ZHANG ; Song HE ; Xiaochen BO ; Jian XIAO
Journal of Pharmaceutical Analysis 2025;15(6):1249-1263
Identifying drug-drug interactions(DDIs)is essential to prevent adverse effects from polypharmacy.Although deep learning has advanced DDI identification,the gap between powerful models and their lack of clinical application and evaluation has hindered clinical benefits.Here,we developed a Multi-Dimensional Feature Fusion model named MDFF,which integrates one-dimensional simplified molec-ular input line entry system sequence features,two-dimensional molecular graph features,and three-dimensional geometric features to enhance drug representations for predicting DDIs.MDFF was trained and validated on two DDI datasets,evaluated across three distinct scenarios,and compared with advanced DDI prediction models using accuracy,precision,recall,area under the curve,and F1 score metrics.MDFF achieved state-of-the-art performance across all metrics.Ablation experiments showed that integrating multi-dimensional drug features yielded the best results.More importantly,we obtained adverse drug reaction reports uploaded by Xiangya Hospital of Central South University from 2021 to 2023 and used MDFF to identify potential adverse DDIs.Among 12 real-world adverse drug reaction reports,the predictions of 9 reports were supported by relevant evidence.Additionally,MDFF demon-strated the ability to explain adverse DDI mechanisms,providing insights into the mechanisms behind one specific report and highlighting its potential to assist practitioners in improving medical practice.
5.Preliminary exploration of esophagogastrostomy with modified Toupet-like anastomosis (mToupet-like) anastomosis after proximal gastrectomy
Yanqiang ZHANG ; Jingyang HE ; Mengmeng LE ; Jianfa YU ; Chan HU ; Zhiyuan XU
Chinese Journal of Gastrointestinal Surgery 2025;28(7):773-776
Objective:To evaluate the functional outcomes and postoperative complications associated with modified Toupet-like (mToupet-like) anastomosis following proximal gastrectomy for patients with gastric tumors.Methods:After proximal gastrectomy, barbed sutures (2-3 stitches) in the seromuscular layer were used to secure the anterior wall of the stomach at a distance of 1-2 cm from the closure line and the posterior wall of the esophagus at a distance of 5.0 cm from the closure line. The remnant stomach was then positioned posterior to the esophagus on the greater curvature side. Esophagogastric anterior wall anastomosis (manual or circular stapling) was performed at the greater curvature of the remnant stomach, 3 cm distal to the gastroesophageal fixation point. A Toupet-like folding procedure was conducted by folding the reconstructed gastric fundus and wall anteriorly from behind the esophagus and embedding the esophagus within a 270° wrap at the site of stomach-esophagus fixation.Results:Twelve patients with gastric tumors underwent proximal partial gastrectomy with mToupet-like anastomosis in the Department of Gastric Surgery at Zhejiang Cancer Hospital from January to March 2024. Among them, 10 diagnosed as upper gastric adenocarcinoma, and 2 diagnosed as gastric gastrointestinal stromal tumors. The cohort included nine male patients and three female patients, aged 46 to 77 years old, with a body mass index (BMI) ranging from 19.7 to 27.3 kg/m2. The maximum tumor diameter was less than 4 cm, and the predicted residual gastric volume exceeded one-half. Laparoscopic surgery was performed in 11 patients, while only 1 patient underwent open surgery. The mean duration of mToupet-like anastomosis was 48.3±8.7 minutes with an estimated intraoperative blood loss was 53.0±11.2 ml. All the 12 patients successfully achieved R0 resection. Among these patietns, the median postoperative hospital stay was 8.5 (7.0, 11.0) days, and the average hospitalization cost was 5.0±0.2 ten thousand yuan. No Clavien-Dindo grade II or higher complications were observed during the perioperative period. Patients were followed up for 6 to 8 months after operation, and no cases of reflux esophagitis were detected by gastroscopy, and no patient required long-term oral proton pump inhibitors.Conclusions:mToupet-like anastomosis for digestive tract reconstruction after proximal gastrectomy is a safe and feasible technique, demonstrating favorable preliminary efficacy.
6.Preliminary exploration of esophagogastrostomy with modified Toupet-like anastomosis (mToupet-like) anastomosis after proximal gastrectomy
Yanqiang ZHANG ; Jingyang HE ; Mengmeng LE ; Jianfa YU ; Chan HU ; Zhiyuan XU
Chinese Journal of Gastrointestinal Surgery 2025;28(7):773-776
Objective:To evaluate the functional outcomes and postoperative complications associated with modified Toupet-like (mToupet-like) anastomosis following proximal gastrectomy for patients with gastric tumors.Methods:After proximal gastrectomy, barbed sutures (2-3 stitches) in the seromuscular layer were used to secure the anterior wall of the stomach at a distance of 1-2 cm from the closure line and the posterior wall of the esophagus at a distance of 5.0 cm from the closure line. The remnant stomach was then positioned posterior to the esophagus on the greater curvature side. Esophagogastric anterior wall anastomosis (manual or circular stapling) was performed at the greater curvature of the remnant stomach, 3 cm distal to the gastroesophageal fixation point. A Toupet-like folding procedure was conducted by folding the reconstructed gastric fundus and wall anteriorly from behind the esophagus and embedding the esophagus within a 270° wrap at the site of stomach-esophagus fixation.Results:Twelve patients with gastric tumors underwent proximal partial gastrectomy with mToupet-like anastomosis in the Department of Gastric Surgery at Zhejiang Cancer Hospital from January to March 2024. Among them, 10 diagnosed as upper gastric adenocarcinoma, and 2 diagnosed as gastric gastrointestinal stromal tumors. The cohort included nine male patients and three female patients, aged 46 to 77 years old, with a body mass index (BMI) ranging from 19.7 to 27.3 kg/m2. The maximum tumor diameter was less than 4 cm, and the predicted residual gastric volume exceeded one-half. Laparoscopic surgery was performed in 11 patients, while only 1 patient underwent open surgery. The mean duration of mToupet-like anastomosis was 48.3±8.7 minutes with an estimated intraoperative blood loss was 53.0±11.2 ml. All the 12 patients successfully achieved R0 resection. Among these patietns, the median postoperative hospital stay was 8.5 (7.0, 11.0) days, and the average hospitalization cost was 5.0±0.2 ten thousand yuan. No Clavien-Dindo grade II or higher complications were observed during the perioperative period. Patients were followed up for 6 to 8 months after operation, and no cases of reflux esophagitis were detected by gastroscopy, and no patient required long-term oral proton pump inhibitors.Conclusions:mToupet-like anastomosis for digestive tract reconstruction after proximal gastrectomy is a safe and feasible technique, demonstrating favorable preliminary efficacy.
7.Application value of gastric suspension method in supra-pancreatic lymph node dissection of laparoscopic radical gastrectomy of gastric cancer
Mengmeng LE ; Jingyang HE ; Siwei PAN ; Xiangliu CHEN ; Can HU ; Yanqiang ZHANG ; Jianfa YU ; Zhiyuan XU
Chinese Journal of Digestive Surgery 2025;24(3):389-393
Objective:To investigate the application value of gastric suspension method in supra-pancreatic lymph node dissection of laparoscopic radical gastrectomy of gastric cancer.Method:The retrospective cohort study was conducted. The clinicopathological data of 84 patients who under-went laparoscopic radical gastrectomy of gastric cancer at Zhejiang Cancer Hospital from August 2023 to July 2024 were collected. There were 61 males and 23 females, aged (64±11)years. Of the 84 patients, 42 patients undergoing supra-pancreatic lymph node dissection during laparoscopic radical gastrectomy of gastric cancer with traditional method for surgical field exposure were divided into the control group, and 42 patients undergoing supra-pancreatic lymph node dissection during laparoscopic radical gastrectomy of gastric cancer with gastric suspension method for surgical field exposure were divided into the suspension group. Observation indicators: (1) surgical conditions; (2) postoperative conditions. Comparison of measurement data with normal distribution between groups was conducted using the independent sample t test. Comparison of measurement data with skewed distribution between groups was conducted using the Mann-Whitney U test. Comparison of count data between groups was conducted using the chi-square test. Results:(1) Surgical condi-tions. The time for supra-pancreatic lymph node dissection of the control group was (78±14)minutes. Number of grasping operations was 116±34, number of bleeding sites caused by grasping operations was 7.8±2.7, and operation time was (3.9±0.8)hours. The above indicators of the suspension group were (59±12)minutes, 68±19, 2.1±1.5, and (3.3±0.7)hours, respectively. There were significant diffe-rences in the above indicators between the two groups ( t=5.42, 8.10, 8.31, 3.14, P<0.05). (2) Post-operative conditions. The tumor diameter was 2.5(2.0,3.5)cm for patients of the control group, versus 3.0(2.4, 4.4)cm for patients of the suspension group, showing a significant difference between the two groups ( Z=-1.98, P<0.05). Conclusion:Compared with the traditional non-suspension method, the gastric suspension method in laparoscopic radical gastrectomy of gastric cancer for supra-pancreatic lymph node dissection is associated with shorter operation time and less trauma.
8.Exploration on Shengmai Decoction Targeting Bcl-2/Bax/Caspase-3 Pathway to Mediate Mitochondrial Apoptosis in Treatment of Heart Failure Based on Network Pharmacology
Xuan LIU ; He FENG ; Jingyang WANG ; Yuting WANG ; Rui ZHANG ; Zilian ZHAN ; Qiang XU
Chinese Journal of Information on Traditional Chinese Medicine 2025;32(9):22-30
Objective To explore the mechanism of Shengmai Decoction in improving heart failure by regulating mitochondrial apoptosis based on network pharmacology and experimental verification;To provide a basis for its clinical application.Methods The active components and targets of Shengmai Decoction were obtained through TCMSP and TCMID databases.Heart failure and mitochondrial apoptosis related targets were retrieved from GeneCards,OMIM,DrugBank,PharmGKB and TTD databases.A protein-protein interaction(PPI)network at the intersection of drugs and diseases was constructed using the STRING database,and a component-target network was constructed using Cytoscape 3.8.2 software.GO and KEGG pathway enrichment analysis was performed on intersecting targets using the DAVID database.Molecular docking was conducted to assess the binding affinity of key components to core target proteins.A rat model of heart failure was established,and the cardiac function of rats were detected by echocardiogram,ELISA was used to detect serum contents of BNP and NT-proBNP,mitochondrial ultrastructure was observed by transmission electron microscope,and Western blot was used to detect protein expressions of Bcl-2/Bax/Caspase-3 signaling pathway.Results A total of 66 active components and 146 targets of Shengmai Decoction were identified,and 22 intersecting targets with heart failure and mitochondrial apoptosis,including key proteins such as TNF,Bcl-2,Bax and Caspase-3.GO enrichment analysis revealed that the intersecting targets were closely associated with inflammation and cell signaling,while KEGG pathway analysis showed that the targets were primarily involved in the TNF signaling pathway,IL-17 signaling pathway,and mitochondrial function regulation.Molecular docking results indicated that Ginsenoside rh2,Beta-sitosterol and other components of Shengmai Decoction exhibited strong binding affinities with Bcl-2,Bax and Caspase-3.Animal experiments demonstrated that Shengmai Decoction significantly improved cardiac function(P<0.05,P<0.01),reduced serum BNP and NT-proBNP contents(P<0.01),alleviated mitochondrial damage,and inhibited mitochondrial apoptosis by upregulating Bcl-2 and downregulating Bax and Caspase-3 protein expression(P<0.01),thereby protecting cardiomyocytes.Conclusion Shengmai Decoction can target and regulate the Bcl-2/Bax/Caspase-3 signaling pathway,improving pathological processes associated with heart failure,which can provide a foundation for clinical optimization of Shengmai Decoction.
9.Construction and validation of Alignment Diagram model for risk of parenteral nutrition-associated cholestasis in extremely/ultra-low birth weight infants
Shuyan CHEN ; Jinglin XU ; Yali CAI ; Yunting HU ; Qingling ZHU ; Zhiyong LIU ; He WANG ; Jingyang ZHENG ; Dongmei CHEN
Chinese Pediatric Emergency Medicine 2024;31(2):114-119
Objective:To explore the high-risk factors for parenteral nutrition associated cholestasis(PNAC)in extremely/ultra-low birth weight infants,and establish a risk Alignment Diagram prediction model.Methods:We retrospectivly analyzed the clinical data of hospitalized extremely/ultra-low birth weight infants admitted to Neonatology Department at Quanzhou Children's Hospital from January 2019 to December 2020,using multivariate Logistic regression analysis to screen for independent risk factors for the occurrence of PNAC.An Alignment Diagram model prediction model for PNAC was constructed by using R software,and the performance of the model was evaluated through receiver operating characteristic curves.Results:A total of 203 extremely/ultra-low birth weight infants were included,with a median gestational age of 29.14(28.00,30.86)weeks and a median birth weight of 1 170(1 000,1 300)g.Among them,26(12.81%)cases developed PNAC.Multivariate Logistic regression analysis showed that the duration of parenteral nutrition( OR=1.015 ,95% CI 1.003-1.034),the cumulative amount of glucose( OR=1.014 ,95% CI 1.001-1.028),small for gestational age( OR=3.455 ,95% CI 1.127-10.589),and neonatal sepsis( OR=3.142 ,95% CI 1.039-9.503)were independent risk factors for PNAC( P<0.05);The four independent risk factors mentioned above were introduced into R software to construct an Alignment Diagram model,the area under the receiver operating characteristic curve was 0.835(95% CI 0.842-0.731),and the results of the Hosmer Limeshow goodness of fit test show that:χ 2=5.34,degree of freedom=8, P=0.72.A calibration curve indicated good consistency between the predicted probability of the model and the actual occurrence rate,with good accuracy. Conclusion:The Alignment Diagram model constructed based on four independent risk factors of the duration of parenteral nutrition,glucose accumulation,small for gestational age infants,and neonatal sepsis exhibits high predictive ability,and is expected to provide an intuitive and convenient visualization tool for preventing or reducing the occurrence of PNAC in extremely/ultra-low birth weight infants
10.Construction of Aβ1-42 plasmid and its binding to calmodulin
Shuang QI ; Xuanxuan SUN ; Qixuan WANG ; Yiting HE ; Jiarui LI ; Jingyang SU ; Liying HAO
Journal of China Medical University 2024;53(6):495-500
Objective To investigate the involvement of calmodulin(CaM)in the pathogenesis of Alzheimer disease(AD)and the mechanism by which CaM binds to amyloid-β(Aβ).Methods The hub genes expressed in AD and predicted to be the target proteins for AD prevention and treatment were obtained using bioinformatics methods.The GST-Aβ1-42 recombinant plasmid was constructed through genetic recombination and was then sequenced.The recombinant plasmids were identified using agarose gel electrophoresis,while the extracted and purified GST-Aβ1-42 fusion protein was confirmed using SDS-PAGE gel electrophoresis.GST pull-down assay was used to detect the interaction between GST-Aβ1-42 protein and CaM,expressed in the plasmid.Results The top 20 hub genes in degree ranking were obtained.The DNA sequencing results of the plasmid proved that the recombinant plasmid was successfully constructed.The agarose gel electrophoresis results indicated that the fragment digested by the enzyme was similar to the molecular weight of the Aβ1-42 gene seg-ments,further proving the successful construction of the recombinant plasmid.Binding of GST-Aβ1-42 protein to CaM in a concentration dependent manner was revealed through the GST pull down experiment.Conclusion The GST-Aβ1-42 recombinant plasmid is success-fully constructed and is shown to bind to CaM.

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