1.Computational pathology in precision oncology: Evolution from task-specific models to foundation models.
Yuhao WANG ; Yunjie GU ; Xueyuan ZHANG ; Baizhi WANG ; Rundong WANG ; Xiaolong LI ; Yudong LIU ; Fengmei QU ; Fei REN ; Rui YAN ; S Kevin ZHOU
Chinese Medical Journal 2025;138(22):2868-2878
With the rapid development of artificial intelligence, computational pathology has been seamlessly integrated into the entire clinical workflow, which encompasses diagnosis, treatment, prognosis, and biomarker discovery. This integration has significantly enhanced clinical accuracy and efficiency while reducing the workload for clinicians. Traditionally, research in this field has depended on the collection and labeling of large datasets for specific tasks, followed by the development of task-specific computational pathology models. However, this approach is labor intensive and does not scale efficiently for open-set identification or rare diseases. Given the diversity of clinical tasks, training individual models from scratch to address the whole spectrum of clinical tasks in the pathology workflow is impractical, which highlights the urgent need to transition from task-specific models to foundation models (FMs). In recent years, pathological FMs have proliferated. These FMs can be classified into three categories, namely, pathology image FMs, pathology image-text FMs, and pathology image-gene FMs, each of which results in distinct functionalities and application scenarios. This review provides an overview of the latest research advancements in pathological FMs, with a particular emphasis on their applications in oncology. The key challenges and opportunities presented by pathological FMs in precision oncology are also explored.
Humans
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Precision Medicine/methods*
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Medical Oncology/methods*
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Artificial Intelligence
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Neoplasms/pathology*
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Computational Biology/methods*
2.Microbiome, metabolome, and transcriptome analyses in esophageal squamous cell carcinoma: insights into immune modulation by F. nucleatum.
Xue ZHANG ; Jing HAN ; Yudong WANG ; Li FENG ; Zhisong FAN ; Yu SU ; Wenya SONG ; Lan WANG ; Long WANG ; Hui JIN ; Jiayin LIU ; Dan LI ; Guiying LI ; Yan LIU ; Jing ZUO ; Zhiyu NI
Protein & Cell 2025;16(6):491-496
3.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.
4.Mechanisms of Fufang Biejia Ruangan Pills Against Alcoholic Liver Disease via Regulating Liver-brain Dialogue Mediated by HMGB1-BDNF Axis
Yudong LIU ; Xiangying YAN ; Tao LI ; Chu ZHANG ; Bingbing CAI ; Zhaochen MA ; Na LIN ; Yanqiong ZHANG
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(23):214-223
ObjectiveTo systematically and objectively characterize the pharmacological effects of Fufang Biejia Ruangan pills (FBRP) in the intervention of alcoholic liver disease (ALD) using acute and chronic ALD mouse models and to elucidate its molecular mechanisms. MethodFifty SPF-grade male BALB/c mice were randomly divided into the normal group, model group, and FBRP low-, medium-, and high-dose groups (9.6, 19.2, 38.4 mg·kg-1). Except for the normal group, the remaining groups were given 56° white wine by gavage to establish the acute ALD model, with samples collected after 4 weeks. Thirty SPF-grade male C57BL/6N mice were randomly divided into the normal group, model group, and FBRP medium-dose group (19.2 mg·kg-1). The chronic ALD mouse model was established using the Lieber-DeCarli method over a 10-week period. Inflammatory markers in liver tissues were assessed using hematoxylin-eosin (HE), Sirius Red, oil red O staining, and enzyme-linked immunosorbent assay (ELISA). Intoxication behaviors of each group were objectively evaluated through sobering-up time, net-catching, and pole-climbing tests. Further bioinformatics analyses based on clinical transcriptomic data were conducted to identify key targets and molecular mechanisms of FBRP in alleviating ALD through liver-brain dialogue, with experimental validation by ELISA, Western blot, and immunohistochemical staining. ResultCompared with the normal group, the levels of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in liver tissues of mice in the acute and chronic ALD model groups were significantly increased (P<0.05). Compared with the model group, the levels of AST and ALT in liver tissue of mice in FBRP groups were significantly decreased (P<0.05). Compared with the normal group, the time of grasping the net and climbing the pole in the acute ALD model group was significantly decreased within 4 weeks (P<0.01). Compared with the model group, the grasping and climbing time of FBRP high dose groups increased significantly within 4 weeks (P<0.05). Compared with the normal group, the expression of high mobility group protein B1 (HMGB1) protein in liver tissue and prefrontal lobe tissue of mice in the chronic ALD model group was significantly increased (P<0.01). Compared with the model group, the expression of HMGB1 protein in FBRP medium dose group was significantly decreased (P<0.05,P<0.01). Compared with the normal group, the expression of brain-derived neurotrophic factor (BDNF) protein and the release of γ-aminobutyric acid (GABA) in the prefrontal cortex of the model group were significantly decreased (P<0.01). Compared with the model group, the expression of BDNF protein and the release of GABA in the FBRP medium dose group were significantly increased (P<0.05). ConclusionThis study revealed that FBRP improved key pathological changes in ALD by modulating liver-brain dialogue mediated by the HMGB1-BDNF axis. These findings provide experimental evidence for the clinical use of FBRP in treating ALD and offer new insights for the development of ALD therapeutic agents.
5.Design and Fabrication of Porous Implants Manufactured by 3D Printing
Yan WU ; Yudong WANG ; Mengxing LIU ; Dufang SHI ; Nan HU ; Wei FENG
Chinese Journal of Medical Instrumentation 2024;48(1):15-19
Different porous structures were studied through finite element analysis and then optimal porous structure was selected for the orthopedic applications.The optimal Voronoi structure was designed and fabricated using 3D printing.The mechanical properties and osseointegration ability were both investigated.The mechanical tests showed that the tensile strength,compressive strength and bending strength of Voronoi structures were obviously higher than that of the human bone,and the modulus of Voronoi structures were similar to human bone.In addition,the animal experimental results exhibited that obvious bone ingrowth was found from Month 1 to Month 6.This study provides some theoretical references for the orthopedic application of porous structures.
6.Research progress in the treatment of intrahepatic cholangiocarcinoma
Chaobo CHEN ; Shuo ZHANG ; Yan ZHOU ; Yudong QIU
Chinese Journal of Hepatobiliary Surgery 2024;30(6):464-468
Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor derived from the biliary epithelial cells of the liver. Radical surgical resection remains the only potentially curative treatment but still with a dismal prognosis. In light of research progress in tumor immunotherapy, the combination of chemotherapy and immunotherapy has recently emerged as a first-line regimen for a significantly improved survival in patients with ICC. Genomics-based targeted therapy can benefit ICC patients with specific gene mutations. Additionally, systemic combined with local treatment can also benefit a group of patients with ICC. The management of ICC remains challenging and we hereby reviewed the treatment strategies of ICC to provide valuable references for clinical diagnosis, treatment, and basic research of ICC.
7.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.
8.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.
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.Effects of combined spinal-epidural anesthesia on postoperative pain and short-term cognitive function in elderly patients undergoing hip fracture surgery
Yudong YAN ; Shuai ZHOU ; Zhenqing LI
Chinese Journal of Postgraduates of Medicine 2023;46(4):361-364
Objective:To investigate the effects of combined spinal-epidural anesthesia (CSEA) on postoperative pain and short-term cognitive function in elderly patients undergoing hip fracture surgery.Methods:A total of 60 elderly patients undergoing hip fracture surgery in Dongchangfu District of Liaocheng People′s Hospital from October 2018 to September 2020 were selected as subjects and they were divided into the control group and the observation group by performed different anaesthesias methods, with 30 patients in each group. The control group underwent total intravenous anesthesia (TIVA), and the observation group underwent CSEA. The scores of visual analogue scale (VAS) at different points and the analgesic recovery rate within 48 h of the two groups were compared, and mini mental state evaluation (MMSE) scores of two groups at different points were evaluated. The levels of serum interleukin (IL)-6, IL-10 and tumor necrosis factor-α (TNF-α) of the two groups before the surgery and on the 1 d after the surgery were compared, and adverse events after the surgery were observed.Results:The analgesic recovery rate within 48 h in the observation group was lower than that in the control group: 3.33%(1/30) vs. 26.67%(8/30), the difference was statistically significant ( χ2 = 6.40, P<0.05). The VAS scores at 4, 6, 12, 24, 48 h after the surgery in the observation group were lower than those in the control group ( P<0.05). The scores of MMSE at 1 and 3 d after the surgery in the observation group were higher than those in the control group: (25.38 ± 2.86) scores vs. (22.17 ± 2.72) scores, (26.89 ± 3.04) scores vs. (25.17 ± 2.69) scores, the differences were statistically significant ( P<0.05). At 1 d after the surgery, the levels of IL-6, TNF-α in the observation group were lower than those in the control group: (67.59 ± 15.47) ng/L vs. (86.75 ± 17.88) ng/L, (18.75 ± 4.23) ng/L vs. (22.81 ± 4.30) ng/L; and the level of IL-10 was higher than that in the control group: (39.78 ± 8.31) ng/L vs. (34.76 ± 7.54) ng/L, the differences were statistically significant ( P<0.05). There was no statistical difference in the total incidence of postoperative adverse events between the two groups ( P>0.05). Conclusions:CSEA can effectively relieve postoperative pain, improve short-term cognitive function, reduce inflammatory response in elderly patients with hip fracture surgery, and with great safety.

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