1.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.
2.Da Vinci robot assisted total gastrectomy plus hand-sewn esophagojejunostomy for gastric carcinaoma
Wanbo HUANG ; Jianming XIE ; Jiabin YANG ; Yongfang YIN ; Haixiang DING ; Xiuchong YU ; Zhilong YAN
Chinese Journal of General Surgery 2024;39(10):758-763
Objective:To evaluate the safety and feasibility of robot assisted total gastrectomy plus hand-sewn esophagojejunostomy.Methods:The clinical data of 72 patients diagnosed with gastric cancer and undergoing total gastrectomy at the First Affiliated Hospital of Ningbo University from Nov 2021 to May 2024 were retrospectively analyzed. They were divided into two groups: robot-assisted total gastrectomy (RATG) group, consisting of 30 patients, and laparoscopic assisted total gastrectomy (LATG) group, consisting of 42 patients . In the RATG group, the digestive tract was reconstructed by manual suture under the robot scope and Roux-Y reconstruction was performed . In LATG group, digestive tract reconstruction was performed using an in vitro stapler and Roux-Y. The clinicopathological data, perioperative indexes, and postoperative follow-up data of both groups were observed and analyzed.Results:All 72 patients successfully completed the operation without conversion to open laparotomy. The total operation time in RATG group was longer than that in LATG group [(235.2±25.8) min vs. (200.7±40.6) min, t=4.099, P<0.05)].RATG was superior to LATG group in terms of digestive tract reconstruction time, postoperative fluid intake time and hospitalization days,the difference was statistically significant [(36.9±3.0) min vs.(39.4±4.5) min, (4.2±0.5) d vs. (5.2±0.6) d、(9.5±1.6) d vs. (10.8±2.4)d, t=-2.554,-7.135,-2.595, all P<0.05]; In terms of postoperative pathology, the number of lymph node dissection in RATG group was higher than that in LATG group [(29.8±6.2) vs. (26.3±7.5), t=2.197, P<0.05]. Conclusion:The application of delayed disconnection hand-sewn esophagojejunostomy in Da Vinci robot total gastrectomy is safe and feasible for cure-intent total gastrectomy in patients of gastric carcinoma.
3.Analysis of infection and related risk factors after heart transplantation in a third-grade class-A hospital from 2018 to 2023
Linlin GUO ; Lu XIE ; Yongfang LIU ; Panpan LI ; Lin GUO
Journal of Clinical Medicine in Practice 2024;28(6):104-107
Objective To investigate the infection status after heart transplantation (HT) in a third-grade class-A hospital from 2018 to 2023, and explore its risk factors. Methods A retrospective analysis was conducted on the data of 314 patients who underwent HT surgery from January 2018 to July 2023, they were divided into infection group and control group according to postoperative infection situation, the possible influencing factors of HT postoperative infection were analyzed by univariate analysis, and the risk factors of HT postoperative infection were screened by multivariate Logistic regression analysis. Results A total of 91 patients(28.98%)developed postoperative infections, with infection sites of respiratory tract and blood. Logistic regression analysis showed that the main risk factors for postoperative infection in HT patients included complicating with chronic lung disease, surgical time ≥5 h, long retention time of postoperative thoracic drainage tube, long postoperative urinary tube retention time, long postoperative mechanical ventilation time, and preoperative Alb < 35 g/L. Conclusion Complicating chronic lung disease, surgical time ≥5 h, long postoperative thoracic drainage tube retention time, long postoperative urinary tube retention time, long postoperative mechanical ventilation time, preoperative Alb < 35 g/L are related to postoperative infection of HT. Therefore, active intervention should be carried out for the above factors in patients to reduce the risk of infection.
4.Comparison of clinical effects of a novel stent assisted intestinal bypass and temporary loop ileostomy in laparoscopic low anterior resection of rectal cancer
Liushiyang XU ; Shiyu HU ; Wanbo HUANG ; Jianming XIE ; Jiabin YANG ; Yongfang YIN ; Haixiang DING ; Zhilong YAN
Chinese Journal of General Surgery 2023;38(6):401-406
Objective:To compare the clinical value of stent assisted intestinal bypass and temporary loop ileostomy in laparoscopic low anterior resection of rectal cancer.Method:In this retrospective analysis, 57 patients undergoing laparoscopic low anterior resection for rectal cancer in the First Affiliated Hospital of Ningbo University from Jan 2020 to Jan 2022 were divided into intestinal bypass group (36 cases) and loop ileostomy group (21 cases).Result:There were no significant differences in postoperative GI function recovery and postoperative complication rate between the two groups (all P>0.05). The levels of albumin, prealbumin and hemoglobin in the intestinal bypass group were better than those in the ileostomy group when evaluated on 3rd months after operation [(40.5±2.3) g/L vs. (38.1±2.6)g/L、(26.4±2.7)mg/dl vs. (24.5±2.0)mg/dl、(137.6±5.9) g/L vs. (134.0±7.0) g/L, t=3.605、2.743、2.085, all P<0.05]. Hospital expenses of the intestinal bypass group was lower [(571 000±7 500) yuan vs. (69 300±9 100) yuan, t=-5.477, P<0.05]. Conclusion:Compared with traditional ileostomy, the stent assisted intestinal bypass reduces trauma with lower expenses and improves patients' status after laparoscopic low anterior resection for rectal cancer.
5.Medication evaluation and adverse reaction monitoring in patient on peritoneal dialysis with pancytopenia induced by vancomycin
Bin ZHANG ; Yunling DONG ; Yingxin XIE ; Yueyue LI ; Xiuxiu JIAO ; Yongfang YUAN
Journal of Pharmaceutical Practice 2021;39(2):169-173
Objective To provide reference for anti-infection treatment and individual pharmaceutical care in patient on peritoneal dialysis. Methods The plasma concentration of vancomycin in patient on peritoneal dialysis was monitored by clinical pharmacists. The anti-infection treatment plan was evaluated and adjusted according to the bacterial culture and drug sensitivity results of the abdominal dialysis fluid. The adverse reactions of pancytopenia induced by vancomycin were documented. Results Infection in the patient on peritoneal dialysis was effectively controlled. The related indicators of pancytopenia were improved. Conclusion A case of pancytopenia induced by vancomycin in the patient on peritoneal dialysis was analyzed to get clinical staff's attention to this adverse reaction and improve the safety of vancomycin administration.
6.SURF4 maintains stem-like properties via BIRC3 in ovarian cancer cells
Yongfang YUE ; Lili XIA ; Shanshan XU ; Conghui WANG ; Xinyu WANG ; Weiguo LU ; Xing XIE
Journal of Gynecologic Oncology 2020;31(4):e46-
Objective:
As cancer stem cells (CSCs) are considered as the origin of tumor development, recurrence, and drug resistance, we aimed to explore the mechanism related to modulating stemness in CSCs, thus facilitating to search for new therapeutic strategy for ovarian cancer.
Methods:
In this study, ovarian cancer stem cells (OCSCs) induced from cell line 3AO and A2780 were enriched in serum-free medium (SFM). The effect of SURF4 on CSC-like properties was evaluated by sphere-forming assays, re-differentiation assays, quantitative real-time polymerase chain reaction, flow cytometry, Western blotting, cell viability assays and in vivo xenograft experiments. The downstream molecule participating in SURF4 maintaining stemness was screened by RNA-sequencing and identified by the experiments of gene function.
Results:
SURF4 was upregulated expressed in OCSCs. Knockdown of SURF4 reduced the expression of the related stem markers (SOX2 and c-MYC), inhibited self-renewal ability, and improved the sensitivity to chemotherapeutic drugs (paclitaxel and cisplatin) in OCSCs.SURF4 knockdown also inhibited tumorigenesis in nonobese diabetic/severe combined immunodeficiency mice. BIRC3 expression was controlled by SURF4, and BIRC3 showed the similar effect as SURF4 did, and BIRC3 overexpression partially recovered stem-like properties abolished by SURF4 knockdown.
Conclusion
Our findings suggest that SURF4 possesses the ability to maintain stemness of OCSCs via BIRC3, and may serve as a potential target in stem cell-targeted therapy for ovarian cancer.
7.Effects of honokiol on activation of transient receptor potential channel in rat spinal dorsal root ganglion cells and pruritus in mouse models
Bo XIE ; Yongfang WANG ; Shasha SONG ; Jianbing WU ; Xinyu LI
Chinese Journal of Dermatology 2019;52(7):455-460
Objective To evaluate the effect of honokiol on the activation of transient receptor potential (TRP) channel in rat spinal dorsal root ganglion cells and pruritus in mouse models.Methods Healthy male ICR mice aged 4-6 weeks were used to establish histamine-induced and acetone/ether/water (AEW)-induced itching models separately.Totally,mice were randomly divided into 7 groups (histamineinduced model experiment) or 6 groups (AEW-induced model experiment):normal control group and model group both gavaged with sodium chloride physiological solution,solvent group gavaged with sodium carboxymethylcellulose solution,chlorphenamine group (only set up in the histamine-induced model experiment) gavaged with chlorphenamine,50,25 and 12.5 mg/kg honokiol groups gavaged with 50,25 and 12.5 mg/kg honokiol respectively.In the histamine-induced model experiment,the mice were all injected with histamine except the normal control group injected with sodium chloride physiological solution 24 hours after the gavage treatment,while the mice in the AEW-induced model experiment were all topically treated with AEW except the normal control group topically treated with sodium chloride physiological solution for 4 days,followed by gavage with different drugs.The anti-itch effect of each treatment was evaluated by counting the scratching frequency within 30 minutes.Rat spinal dorsal root ganglion (DRG)cells were isolated and subjected to a primary culture.Then,the DRG cells were divided into 6 groups:capsaicin or allyl isothiocyanate (AITC)-induced model group pre-incubated with Hank's balanced salt solution (HBSS),500 μmol/L capsazepine or 10 μmol/L HSC030031 group pre-incubated with capsazepine or HSC030031,solvent group pre-incubated with dimethyl sulfoxide (DMSO),3 honokiol groups preincubated with 7.81,15.63 and 31.25 mg/L honokiol respectively,and Ca2+ fluorescence imaging system was used to observe changes of Ca2+ influx in these cells after capsaicin or AITC stimulation.Statistical analysis was carried out with SPSS 20.0 software by using one-way analysis of variance and Dunnett-t test.Results In the histamine-induced mouse models,the scratching frequency was significantly lower in the 50 and 25 mg/kg honokiol groups than in the model group (21.88 and 21.14 vs.63.70,t =3.48,3.49 respectively,both P =0.003),while no significant difference in the scratching frequency was observed between the 12.5 mg/kg honokiol group and the model group (t =2.01,P =0.062).After the treatment with 50 mg/kg honokiol in the AEW-induced mouse models,the scratching frequency significantly decreased compared with the model group (61.4 vs.101.17,t =0.45,P =0.009),while there were no significant differences among the 25,12.5 mg/kg honokiol groups and the model group (all P > 0.05).Compared with the capsaicin or AITC-induced model group,the increase of Ca2+ fluorescence signal in the DRG cells was significantly inhibited in the 31.25 mg/L honokiol group:at the 45th second,the rate of relative fluorescence intensity change (AF/F0) was 1.11 in the model group,but-0.11 in the 31.25 mg/L honokiol group in the capsaicin-induced model experiment,and 0.56 in the model group,but 0.00 in the 31.25 mg/L honokiol group in the AITC-induced model experiment.Conclusion Honokiol shows an inhibitory effect on mouse models of pruritus induced by histaminergic or non-histaminergic factors,likely by inhibiting Ca2+ influx through activated TRPV 1 and TRPA 1 channels in the DRG cells.
8.Evaluation of Renal Pathophysiological Processes Induced by an Iodinated Contrast Agent in a Diabetic Rabbit Model Using Intravoxel Incoherent Motion and Blood Oxygenation Level-Dependent Magnetic Resonance Imaging
Yongfang WANG ; Xin ZHANG ; Bin WANG ; Yang XIE ; Yi WANG ; Xuan JIANG ; Rongjia WANG ; Ke REN
Korean Journal of Radiology 2019;20(5):830-843
OBJECTIVE: To examine the potential of intravoxel incoherent motion (IVIM) and blood oxygen level-dependent (BOLD) magnetic resonance imaging for detecting renal changes after iodinated contrast-induced acute kidney injury (CI-AKI) development in a diabetic rabbit model. MATERIALS AND METHODS: Sixty-two rabbits were randomized into 2 groups: diabetic rabbits with the contrast agent (DCA) and healthy rabbits with the contrast agent (NCA). In each group, 6 rabbits underwent IVIM and BOLD imaging at 1 hour, 1 day, 2 days, 3 days, and 4 days after an iohexol injection while 5 rabbits were selected to undergo blood and histological examinations at these specific time points. Iohexol was administrated at a dose of 2.5 g I/kg of body weight. Further, the apparent transverse relaxation rate (R2*), average pure molecular diffusion coefficient (D), pseudo-diffusion coefficient (D*), and perfusion fraction (f) were calculated. RESULTS: The D and f values of the renal cortex (CO) and outer medulla (OM) were significantly decreased compared to baseline values in the 2 groups 1 day after the iohexol injection (p < 0.05). A marked reduction in the D* values for both the CO and OM was also observed after 1 hour in each group (p < 0.05). In the OM, a persistent elevation of the R2* was detected for 4 days in the DCA group (p < 0.05). Histopathological changes were prominent, and the pathological features of CI-AKI aggravated in the DCA group until day 4. The D, f, and R2* values significantly correlated with the histological damage scores, hypoxia-inducible transcription factor-1α expression scores, and serum creatinine levels. CONCLUSION: A combination of IVIM and BOLD imaging may serve as a noninvasive method for detecting and monitoring CI-AKI in the early stages in the diabetic kidney.
Acute Kidney Injury
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Body Weight
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Creatinine
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Diffusion
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Iohexol
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Kidney
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Magnetic Resonance Imaging
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Methods
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Oxygen
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Perfusion
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Rabbits
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Relaxation
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Vascular Endothelial Growth Factor A
9. Serosal and muscular layers incision and use of submucosal layers exfoliation technique in laparoscopic surgery for gastric gastrointestinal stromal tumors
Jianming XIE ; Moucheng ZHANG ; Yongfang YIN ; Zhiping ZHANG ; Jiaming ZHOU ; Zhilong YAN
Chinese Journal of General Surgery 2019;34(11):956-958
Objective:
To explore the feasibility and clinical efficacy of serosal muscular layers incision and submucosal layers exfoliation technique in laparoscopic surgery for gastric gastrointestinal stromal tumors(GIST).
Methods:
28 patients with gastric GIST underwent serosal muscular layers incision and submucosal layers exfoliation technique under laparoscopic surgery. Patients′clinicopathologic characteristics, operative outcomes, postoperative complications, and follow up results were analyzed retrospectively.
Results:
Surgery was successfully completed in all patients, and no one was converted to open surgery.The average operation time was (66±15) min, and the intra operative blood loss was (16±10) ml, the time of passage of gas by anus after operation was (20±10)h, the time starting liquid diet was(2.5±1.6)d, and the length of postoperative hospital stay was (7±3)d. One patient had delayed gastric emptying, one had incisional infection. All the specimen had complete pseudocapsule and negative margin. pathology was all gastric GIST. After a median 22 months followed up, no recurrence or metastasis were found.
Conclusion
Serosal muscular layers incision and submucosal layers exfoliation under laparoscopic surgery is a safe and feasible procedure for treating gastric GIST.
10.Evaluation and Medication Reconciliation of Preoperative Medication in 210 Selective Surgery Elderly Patients
Weiwei ZHANG ; Huijie MENG ; Jike XIE ; Qing XI ; Yan YAN ; Yongfang HU
China Pharmacy 2019;30(1):110-114
OBJECTIVE: To investigate and evaluate perioperative medication in elective surgery elderly patients, and to provide reference for perioperative medication management of clinical pharmacists for elderly patients. METHODS: Totally 210 elective surgery elderly patients were selected from Beijing Tsinghua Chang Gung Hospital during Oct. 2015 to Oct. 2016. Pharmacists carried out drug reconstitution, obtained information about their diseases and medication, analyzed and evaluated perioperative medication (indication, usage and dosage, interaction, drug selection, if these drugs should be stopped before surgery) according to Optimal Guidelines for Preoperative Evaluation of Elderly Patients so as to put forward related medication suggestions. RESULTS: Among 210 patients, there were 132 males (62.86%) and 78 females (37.14%) with an average age of (69.96±7.67) years; 43.81% of patients had more than 3 kinds of diseases, and 13.33% of patients suffered from more than 5 kinds of diseases; 31.43% of patients took more than 5 kinds of drug for long term before surgery; 38.10% patients had more than 2 drug-induced risks; The preoperative medication of 110 patients (52.38%) included drugs that should be avoided before surgery (such as antiplatelet aggregation agents), 23 patients (10.95%) had potentially inappropriate medication (such as proton pump inhibitors), 12 patients (5.71%) should use drugs (such as aspirin) cautiously, 35 patients (16.67%) should use drugs (β receptor blocker) continuously during perioperative period. The pharmacists provided 177 times of medication suggestions such as stopping some medications for patients and physicians through medication reconciliation and preoperative medication evaluation (71 times for patients, 106 times for physicians); the final adoption rates were 100% and 95.28%, respectively. CONCLUSIONS: The elderly patients have many preoperative complications, various risk factors, multiple medications, so it is vital for their preoperative medication management. The medication reconciliation is an effective way to evaluate preoperative medication in elderly patients, preoperative medication evaluation and analysis in elderly patients is of great significance to ensure the safety of clinical medication.


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