1.A tailored database combining reference compound-derived metabolite, metabolism platform and chemical characteristic of Chinese herb followed by activity screening: Application to Magnoliae Officinalis Cortex.
Zhenzhen XUE ; Yudong SHANG ; Lan YANG ; Tao LI ; Bin YANG
Journal of Pharmaceutical Analysis 2025;15(4):101066-101066
A strategy combining a tailored database and high-throughput activity screening that discover bioactive metabolites derived from Magnoliae Officinalis Cortex (MOC) was developed and implemented to rapidly profile and discover bioactive metabolites in vivo derived from traditional Chinese medicine (TCM). The strategy possessed four characteristics: 1) The tailored database consisted of metabolites derived from big data-originated reference compound, metabolites predicted in silico, and MOC chemical profile-based pseudomolecular ions. 2) When profiling MOC-derived metabolites in vivo, attentions were paid not only to prototypes of MOC compounds and metabolites directly derived from MOC compounds, as reported by most papers, but also to isomerized metabolites and the degradation products of MOC compounds as well as their derived metabolites. 3) Metabolite traceability was performed, especially to distinguish isomeric prototypes-derived metabolites, prototypes of MOC compounds as well as phase I metabolites derived from other MOC compounds. 4) Molecular docking was utilized for high-throughput activity screening and molecular dynamic simulation as well as zebrafish model were used for verification. Using this strategy, 134 metabolites were swiftly characterized after the oral administration of MOC to rats, and several metabolites were reported for the first time. Furthermore, 17 potential active metabolites were discovered by targeting the motilin, dopamine D2, and the serotonin type 4 (5-HT4) receptors, and part bioactivities were verified using molecular dynamic simulation and a zebrafish constipation model. This study extends the application of mass spectrometry (MS) to rapidly profile TCM-derived metabolites in vivo, which will help pharmacologists rapidly discover potent metabolites from a complex matrix.
2.Adaptive multi-view learning method for enhanced drug repurposing using chemical-induced transcriptional profiles, knowledge graphs, and large language models.
Yudong YAN ; Yinqi YANG ; Zhuohao TONG ; Yu WANG ; Fan YANG ; Zupeng PAN ; Chuan LIU ; Mingze BAI ; Yongfang XIE ; Yuefei LI ; Kunxian SHU ; Yinghong LI
Journal of Pharmaceutical Analysis 2025;15(6):101275-101275
Drug repurposing offers a promising alternative to traditional drug development and significantly reduces costs and timelines by identifying new therapeutic uses for existing drugs. However, the current approaches often rely on limited data sources and simplistic hypotheses, which restrict their ability to capture the multi-faceted nature of biological systems. This study introduces adaptive multi-view learning (AMVL), a novel methodology that integrates chemical-induced transcriptional profiles (CTPs), knowledge graph (KG) embeddings, and large language model (LLM) representations, to enhance drug repurposing predictions. AMVL incorporates an innovative similarity matrix expansion strategy and leverages multi-view learning (MVL), matrix factorization, and ensemble optimization techniques to integrate heterogeneous multi-source data. Comprehensive evaluations on benchmark datasets (Fdataset, Cdataset, and Ydataset) and the large-scale iDrug dataset demonstrate that AMVL outperforms state-of-the-art (SOTA) methods, achieving superior accuracy in predicting drug-disease associations across multiple metrics. Literature-based validation further confirmed the model's predictive capabilities, with seven out of the top ten predictions corroborated by post-2011 evidence. To promote transparency and reproducibility, all data and codes used in this study were open-sourced, providing resources for processing CTPs, KG, and LLM-based similarity calculations, along with the complete AMVL algorithm and benchmarking procedures. By unifying diverse data modalities, AMVL offers a robust and scalable solution for accelerating drug discovery, fostering advancements in translational medicine and integrating multi-omics data. We aim to inspire further innovations in multi-source data integration and support the development of more precise and efficient strategies for advancing drug discovery and translational medicine.
3.Association of sleep duration and physical exercise with dyslipidemia in older adults aged 80 years and over in China
Bing WU ; Yang LI ; Lanjing XU ; Zheng ZHANG ; Jinhui ZHOU ; Yuan WEI ; Chen CHEN ; Jun WANG ; Changzi WU ; Zheng LI ; Ziyu HU ; Fanye LONG ; Yudong WU ; Xuehua HU ; Kexin LI ; Fangyu LI ; Yufei LUO ; Yingchun LIU ; Yuebin LYU ; Xiaoming SHI
Chinese Journal of Epidemiology 2024;45(1):48-55
Objective:To explore the impact of sleep duration, physical exercise, and their interactions on the risk of dyslipidemia in older adults aged ≥80 (the oldest old) in China.Methods:The study subjects were the oldest old from four rounds of Healthy Aging and Biomarkers Cohort Study (2008-2009, 2011-2012, 2014 and 2017-2018). The information about their demographic characteristics, lifestyles, physical examination results and others were collected, and fasting venous blood samples were collected from them for blood lipid testing. Competing risk model was used to analyze the causal associations of sleep duration and physical exercise with the risk for dyslipidemia. Restricted cubic spline (RCS) function was used to explore the dose-response relationship between sleep duration and the risk for dyslipidemia. Additive and multiplicative interaction model were used to explore the interaction of sleep duration and physical exercise on the risk for dyslipidemia.Results:The average age of 1 809 subjects was (93.1±7.7) years, 65.1% of them were women. The average sleep duration of the subjects was (8.0±2.5) hours/day, 28.1% of them had sleep duration for less than 7 hours/day, and 27.2% had sleep for duration more than 9 hours/day at baseline survey. During the 9-year cumulative follow-up of 6 150.6 person years (follow-up of average 3.4 years for one person), there were 304 new cases of dyslipidemia, with an incidence density of 4 942.6/100 000 person years. The results of competitive risk model analysis showed that compared with those who slept for 7-9 hours/day, the risk for dyslipidemia in oldest old with sleep duration >9 hours/day increased by 22% ( HR=1.22, 95% CI: 1.07-1.39). Compared with the oldest old having no physical exercise, the risk for dyslipidemia in the oldest old having physical exercise decreased by 33% ( HR=0.67, 95% CI: 0.57-0.78). The RCS function showed a linear positive dose-response relationship between sleep duration and the risk for hyperlipidemia. The interaction analysis showed that physical exercise and sleep duration had an antagonistic effect on the risk for hyperlipidemia. Conclusion:Physical exercise could reduce the adverse effects of prolonged sleep on blood lipids in the oldest old.
4.Deep Learning-Based Artificial Intelligence Model for Automatic Carotid Plaque Identification
Lan HE ; E SHEN ; Zekun YANG ; Ying ZHANG ; Yudong WANG ; Weidao CHEN ; Yitong WANG ; Yongming HE
Chinese Journal of Medical Instrumentation 2024;48(4):361-366
This study aims at developing a dataset for determining the presence of carotid artery plaques in ultrasound images,composed of 1761 ultrasound images from 1165 participants.A deep learning architecture that combines bilinear convolutional neural networks with residual neural networks,known as the single-input BCNN-ResNet model,was utilized to aid clinical doctors in diagnosing plaques using carotid ultrasound images.Following training,internal validation,and external validation,the model yielded an ROC AUC of 0.99(95%confidence interval:0.91 to 0.84)in internal validation and 0.95(95%confidence interval:0.96 to 0.94)in external validation,surpassing the ResNet-34 network model,which achieved an AUC of 0.98(95%confidence interval:0.99 to 0.95)in internal validation and 0.94(95%confidence interval:0.95 to 0.92)in external validation.Consequently,the single-input BCNN-ResNet network model has shown remarkable diagnostic capabilities and offers an innovative solution for the automatic detection of carotid artery plaques.
5.Relationship between serum miR-21 and miR-27b levels and prognosis of patients with renal clear cell carcinoma
Shuang CHEN ; Na YANG ; Yudong HUANG ; Xiangfeng KONG ; Jintao LI ; Yizhong TANG ; Kex-Iong MA ; Yangyang ZHANG ; Yuandong ZHANG ; Chengde REN
The Journal of Practical Medicine 2024;40(3):343-347
Objective To explore the relationship between serum miRNA-21 and miR-27b levels and prognosis of patients with renal clear cell carcinoma.Methods A total of 118 patients with renal clear cell carcinoma admitted to the Qinghai University Hospital from February 2019 to April 2021 were selected as the study subjects,and another 118 healthy patients in the same period as the control group.Real time fluorescence quantitative polymerase chain reaction(PCR)was used to detect the expression of miR-21 and miR-27b in the serum of all subjects.The relative expression levels of serum miR-21 and miR-27b between the patients with renal clear cell carcinoma and healthy control patients were compared.The expression and correlation of serum miR-21 and miR-27b in the patients with renal clear cell carcinoma of different pathological stages and Fuhrman grading were analyzed.The relationship between the expression of serum miR-21 and miR-27b and the survival and prognosis of the patients was explored as well.Results The expression levels of serum miR-21 and miR-27b in the patients with renal clear cell carcinoma were higher than those in the healthy control group(P<0.05).The serum miR-21 expression level in stage Ⅲ patients was higher than in stageⅠ(P<0.05),while the serum miR-21 expression level in the stage Ⅳ patients was higher than that in stagesⅠ,Ⅱ,and Ⅲ(P<0.05).The expression level of miR-27b in the serum of patients gradually increased across the four stages,with a significant difference(P<0.05).The pathological staging was positively correlated with the expression of miR-21 and miR-27b(P<0.001).The expression levels of miR-21 and miR-27b in serum of patients gradually increased across grades Ⅰ,Ⅱ and Ⅲ by Fuhrman grading,with significant difference(P<0.05).Fuhrman grading was positively correlated with the serum miR-21 and miR-27b expression(P<0.001).There was a statistically significant difference in the survival curve between the miR-21 high expression group and the low expression group(P<0.05).There was a statistically significant difference in the survival curve between the high expression group and the low expression group of miR-27b(P<0.05).Conclusion The expression levels of serum miR-21 and miR-27b in patients with renal clear cell carcinoma is indicative of the progression and prognosis of the patient's condition.
6.Impact of peritoneal vaginoplasty combined with radical hysterectomy on the quality of sexual life for patients with early-stage cervical cancer: trial protocol for a multi-center superiority randomized controlled trial
Shimin YANG ; Yan DING ; Huaifang LI ; Sufang WU ; Weiwei FENG ; Yudong WANG ; Xipeng WANG ; Keqin HUA
Journal of Gynecologic Oncology 2024;35(3):e23-
Background:
Radical hysterectomy (RH) is commonly used to treat early-stage cervical cancer in women of childbearing age and sexual dysfunction due to postoperative vaginal shortening is a major concern. The impact of intraoperative vaginoplasty on prognosis and quality of sexual life in patients with early-stage cervical cancer remains controversial and lacks high-level evidence. However, there are few reports on vaginoplasty after RH to lengthen vagina in patients. This prospective, multi-center, randomized controlled trial aims to explore the impact of peritoneal vaginoplasty with or without ovarian transposition after laparoscopic RH on sexual dysfunction in patients with early-stage cervical cancer.
Methods
Eligible patients will be randomly assigned (1:1) to receive peritoneal vaginoplasty or not. The primary evaluation indicators are female sexual function index (FSFI) and male sexual satisfaction scale. The secondary evaluation indicators include EORTC QLQ-CX24, 2-year overall survival (OS), 5-year OS, 2-year progression-free survival (PFS), 5-year PFS and surgery-related complications. The trial will enroll 368 patients from 6 hospitals in China over a 3-year period and follow up for 5 years.Trial RegistrationChinese Clinical Trial Registry Identifier: ChiCTR2000040610SynopsisIt's a prospective, randomized controlled trial to explore the effect of peritoneal vaginoplasty with or without ovarian transposition following laparoscopic radical hysterectomy on sexual dysfunction in patients with cervical cancer. The trial will enroll 368 patients from 6 hospitals in China over a 3-year period and follow up for 5 years.
7.Effect of first drainage failure on postoperative prognosis of patients with perihilar cholangiocarci-noma
Aibaidula AILIXIER ; Liang MAO ; Yifei YANG ; Yi WANG ; Lei WANG ; Yudong QIU
Chinese Journal of Hepatobiliary Surgery 2024;30(2):108-113
Objective:To study the effect of first drainage failure on the prognosis of perihilar cholangiocarcinoma (PHCC).Methods:The clinical data of 68 patients with PHCC undergoing surgery in the Department of Pancreatic and Metabolic Surgery of Nanjing Drum Tower Hospital, Affiliated to the Medical School of Nanjing University, from April 2014 to December 2022 were retrospectively analyzed, including 46 males and 22 females, aged (63±9) (range, 39-80) years old. The patients were divided into two groups based on whether the first drainage was successful: successful group ( n=34) and failed group ( n=34). The patient's age, gender, first drainage, complications and other clinical data were collected. Patients were followed up by outpatient or telephone review. Kaplan-Meier method was used for survival analysis, and log-rank test was used for survival comparison. Results:Compared to the successful group, the drainage time [41(28, 52) d vs. 20(14, 28) d], the drainage tube adjustment rate [32.4%(11/34) vs. 0(0/34)], and the incidence of complications after drainage [88.2% (30/34) vs. 0(0/34)] were all increased in the failed group, with the adjustment rate of drainage position decreased [82.4%(28/34) vs. 100%(34/34)] (all P<0.05). Compared to the successful group, the incidence of abdominal infection was higher [70.6%(24/34) vs. 44.1%(15/34)] in the failed group ( P=0.027). The 5-year cumulative survival rates of the failed group and the successful group were 61.4% and 44.1%, respectively ( P>0.05). Conclusion:Compared to the patients of PHCC with first successful drainage, the risk of abdominal infection is increased when first drainage failed, while the incidence of postoperative complications, in-hospital mortality and long-term survival rate are comparable.
8.Analysis of surgical situations and prognosis of pancreaticoduodenectomy in Jiangsu province (a report of 2 886 cases)
Zipeng LU ; Xin GAO ; Hao CHENG ; Ning WANG ; Kai ZHANG ; Jie YIN ; Lingdi YIN ; Youting LIN ; Xinrui ZHU ; Dongzhi WANG ; Hongqin MA ; Tongtai LIU ; Yongzi XU ; Daojun ZHU ; Yabin YU ; Yang YANG ; Fei LIU ; Chao PAN ; Jincao TANG ; Minjie HU ; Zhiyuan HUA ; Fuming XUAN ; Leizhou XIA ; Dong QIAN ; Yong WANG ; Susu WANG ; Wentao GAO ; Yudong QIU ; Dongming ZHU ; Yi MIAO ; Kuirong JIANG
Chinese Journal of Digestive Surgery 2024;23(5):685-693
Objective:To investigate the surgical situations and perioperative outcome of pancreaticoduodenectomy in Jiangsu Province and the influencing factors for postoperative 90-day mortality.Methods:The retrospective case-control study was conducted. The clinicopathological data of 2 886 patients who underwent pancreaticoduodenectomy in 21 large tertiary hospitals of Jiangsu Quality Control Center for Pancreatic Diseases, including The First Affiliated Hospital of Nanjing Medical University, from March 2021 to December 2022 were collected. There were 1 732 males and 1 154 females, aged 65(57,71)years. Under the framework of the Jiangsu Provincial Pancreatic Disease Quality Control Project, the Jiangsu Quality Control Center for Pancreatic Diseases adopted a multi-center registration research method to establish a provincial electronic database for pancrea-ticoduodenectomy. Observation indicators: (1) clinical characteristics; (2) intraoperative and post-operative conditions; (3) influencing factors for 90-day mortality after pancreaticoduodenectomy. Measurement data with skewed distribution were represented as M( Q1, Q3) or M(IQR), and comparison between groups was conducted using the Mann-Whitney U test. Count data were expressed as absolute numbers or constituent ratio, and comparison between groups was conducted using the chi-square test, continuity correction chi-square test and Fisher exact probability. Maximal Youden index method was used to determine the cutoff value of continuous variables. Univariate analysis was performed using the corresponding statistical methods based on data types. Multivariate analysis was performed using the Logistic multiple regression model. Results:(1) Clinical characteristics. Of the 2 886 patients who underwent pancreaticoduodenectomy, there were 1 175 and 1 711 cases in 2021 and 2022, respectively. Of the 21 hospitals, 8 hospitals had an average annual surgical volume of <36 cases for pancreaticoduodenectomy, 10 hospitals had an average annual surgical volume of 36-119 cases, and 3 hospitals had an average annual surgical volume of ≥120 cases. There were 2 584 cases performed pancreaticoduodenectomy in thirteen hospitals with an average annual surgical volume of ≥36 cases, accounting for 89.536%(2 584/2 886)of the total cases. There were 1 357 cases performed pancrea-ticoduodenectomy in three hospitals with an average annual surgical volume of ≥120 cases, accounting for 47.020%(1 357/2 886) of the total cases. (2) Intraoperative and postoperative conditions. Of the 2 886 patients, the surgical approach was open surgery in 2 397 cases, minimally invasive surgery in 488 cases, and it is unknown in 1 case. The pylorus was preserved in 871 cases, not preserved in 1 952 cases, and it is unknown in 63 cases. Combined organ resection was performed in 305 cases (including vascular resection in 209 cases), not combined organ resection in 2 579 cases, and it is unknown in 2 cases. The operation time of 2 885 patients was 290(115)minutes, the volume of intra-operative blood loss of 2 882 patients was 240(250)mL, and the intraoperative blood transfusion rate of 2 880 patients was 27.153%(782/2 880). Of the 2 886 patients, the invasive treatment rate was 11.342%(327/2 883), the unplanned Intensive Care Unit (ICU) treatment rate was 3.087%(89/2 883), the reoperation rate was 1.590%(45/2 830), the duration of postoperative hospital stay was 17(11)days, the hospitalization mortality rate was 0.798%(23/2 882), and the failure rate of rescue data in 2 083 cases with severe complications was 6.529%(19/291). There were 2 477 patients receiving postoperative 90-day follow-up, with the 90-day mortality of 2.705%(67/2477). The total incidence rate of complication in 2 886 patients was 58.997%(1 423/2 412). The incidence rate of severe complication was 13.970%(291/2 083). The comprehensive complication index was 8.7(22.6) in 2 078 patients. (3) Influencing factors for 90-day mortality after pancreaticoduodenectomy. Results of multivariate analysis showed that age ≥ 70 years, postoperative invasive treatment, and unplanned ICU treatment were independent risk factors for 90-day mortality after pancreaticoduodenectomy ( odds ratio=2.403, 2.609, 16.141, 95% confidence interval as 1.281-4.510, 1.298-5.244, 7.119-36.596, P<0.05). Average annual surgical volume ≥36 cases in the hospital was an independent protective factor for 90-day mortality after pancreaticoduodenectomy ( odds ratio=0.368, 95% confidence interval as 0.168-0.808, P<0.05). Conclusions:Pancreaticoduodenectomy in Jiangsu Province is highly con-centrated in some hospitals, with a high incidence of postoperative complications, and the risk of postoperative 90-day mortality is significant higher than that of hospitallization mortality. Age ≥ 70 years, postoperative invasive treatment, and unplanned ICU treatment are independent risk factors for 90-day motality after pancreaticoduodenectomy, and average annual surgical volume ≥36 cases in the hospital is an independent protective factor.
9.Impact of peritoneal vaginoplasty combined with radical hysterectomy on the quality of sexual life for patients with early-stage cervical cancer: trial protocol for a multi-center superiority randomized controlled trial
Shimin YANG ; Yan DING ; Huaifang LI ; Sufang WU ; Weiwei FENG ; Yudong WANG ; Xipeng WANG ; Keqin HUA
Journal of Gynecologic Oncology 2024;35(3):e23-
Background:
Radical hysterectomy (RH) is commonly used to treat early-stage cervical cancer in women of childbearing age and sexual dysfunction due to postoperative vaginal shortening is a major concern. The impact of intraoperative vaginoplasty on prognosis and quality of sexual life in patients with early-stage cervical cancer remains controversial and lacks high-level evidence. However, there are few reports on vaginoplasty after RH to lengthen vagina in patients. This prospective, multi-center, randomized controlled trial aims to explore the impact of peritoneal vaginoplasty with or without ovarian transposition after laparoscopic RH on sexual dysfunction in patients with early-stage cervical cancer.
Methods
Eligible patients will be randomly assigned (1:1) to receive peritoneal vaginoplasty or not. The primary evaluation indicators are female sexual function index (FSFI) and male sexual satisfaction scale. The secondary evaluation indicators include EORTC QLQ-CX24, 2-year overall survival (OS), 5-year OS, 2-year progression-free survival (PFS), 5-year PFS and surgery-related complications. The trial will enroll 368 patients from 6 hospitals in China over a 3-year period and follow up for 5 years.Trial RegistrationChinese Clinical Trial Registry Identifier: ChiCTR2000040610SynopsisIt's a prospective, randomized controlled trial to explore the effect of peritoneal vaginoplasty with or without ovarian transposition following laparoscopic radical hysterectomy on sexual dysfunction in patients with cervical cancer. The trial will enroll 368 patients from 6 hospitals in China over a 3-year period and follow up for 5 years.
10.Impact of peritoneal vaginoplasty combined with radical hysterectomy on the quality of sexual life for patients with early-stage cervical cancer: trial protocol for a multi-center superiority randomized controlled trial
Shimin YANG ; Yan DING ; Huaifang LI ; Sufang WU ; Weiwei FENG ; Yudong WANG ; Xipeng WANG ; Keqin HUA
Journal of Gynecologic Oncology 2024;35(3):e23-
Background:
Radical hysterectomy (RH) is commonly used to treat early-stage cervical cancer in women of childbearing age and sexual dysfunction due to postoperative vaginal shortening is a major concern. The impact of intraoperative vaginoplasty on prognosis and quality of sexual life in patients with early-stage cervical cancer remains controversial and lacks high-level evidence. However, there are few reports on vaginoplasty after RH to lengthen vagina in patients. This prospective, multi-center, randomized controlled trial aims to explore the impact of peritoneal vaginoplasty with or without ovarian transposition after laparoscopic RH on sexual dysfunction in patients with early-stage cervical cancer.
Methods
Eligible patients will be randomly assigned (1:1) to receive peritoneal vaginoplasty or not. The primary evaluation indicators are female sexual function index (FSFI) and male sexual satisfaction scale. The secondary evaluation indicators include EORTC QLQ-CX24, 2-year overall survival (OS), 5-year OS, 2-year progression-free survival (PFS), 5-year PFS and surgery-related complications. The trial will enroll 368 patients from 6 hospitals in China over a 3-year period and follow up for 5 years.Trial RegistrationChinese Clinical Trial Registry Identifier: ChiCTR2000040610SynopsisIt's a prospective, randomized controlled trial to explore the effect of peritoneal vaginoplasty with or without ovarian transposition following laparoscopic radical hysterectomy on sexual dysfunction in patients with cervical cancer. The trial will enroll 368 patients from 6 hospitals in China over a 3-year period and follow up for 5 years.

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