1.HerbGL: a network propagation and graph regularization-based framework for herb pairs prediction in traditional Chinese medicine
Weixiang Liu ; Qian Yuan ; Junjie Zhang ; Xinliang Sun ; Kongfa Hu ; Tao Yang
Digital Chinese Medicine 2026;9(2):265-277
Objective:
To address the challenges of systematically identifying herb pairs in traditional Chinese medicine (TCM), we proposed HerbGL, a framework for predicting potential herb pairs that integrates network propagation and graph regularization.
Methods:
Based on the assumption that herbal actions induce subtle perturbations in biological systems, a framework named HerbGL was proposed. Random walk with restart (RWR) was first applied to the protein-protein interaction (PPI) network to reconstruct herb-specific perturbation effects and generate weighted subnetworks. Then, to quantify affinity between herb pairs, two network-proximity metrics, Closeness and PageRank, were computed from the weighted subnetworks to construct herb-pair affinity matrices. Finally, these matrices, together with known herb pairs (derived from co-occurrence analysis of TCM formulas with a threshold determined from the inflection point of the frequency distribution), were incorporated into a graph regularization model to predict potential herb pairs. Model performance was assessed through baseline comparison, ablation and robustness experiment under different ratios of positive and negative samples, using the area under the receiver operating characteristic curve (AUROC), the area under the precision-recall curve (AUPRC), accuracy, and precision as evaluation metrics. Furthermore, the predicted herb pairs were validated through both literature evidence and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.
Results:
The weighted subnetworks constructed by RWR provided a refined simulation of herb-specific perturbation effects, which formed the basis for subsequent affinity modeling and prediction. Analysis of herb pair co-occurrence frequencies revealed a marked change around 150, which was selected as the threshold to distinguish herb pairs from non-herb pairs. HerbGL exhibited superior predictive performance compared with baseline models (AUROC = 0.970 5, AUPRC = 0.955 5, accuracy = 0.726 6, precision = 0.970 6). Ablation results showed that removing the Closeness and PageRank metrics substantially degraded performance (AUROC = 0.819 1, AUPRC = 0.876 8), confirming their necessity. Robustness evaluation under an imbalanced positive-to-negative sample ratio of 1 : 5 yielded AUROC = 0.969 6 and AUPRC = 0.840 4, indicating stable predictive ability. Moreover, multiple case studies further validated the rationality of the predicted herb pairs, such as Fangfeng (Saposhnikoviae Radix) and Qingpi (Citri Reticulatae Pericarpium Viride) which are recorded in Liangpeng Huiji (《良朋汇集》, Collection of Excellent Recipes) Vol. 3: Fangfeng Shengma Tang (防风升麻汤). Additionally, pathway enrichment analysis of the Renshen (Ginseng Radix et Rhizoma) and Lianqiao (Forsythiae Fructus) pair further supported the biological plausibility of their compatibility.
Conclusion
HerbGL offers an effective and biologically informed framework for identifying herb pairs in TCM. Beyond improving herb pair prediction, the framework also provides data support for research on herb compounds and mechanisms, thereby supporting data-driven exploration of TCM compatibility.
2.A case of recurrent atypical lipomatous tumor originating from cervical lipoma
Yi GAO ; Tingting LIU ; Weixiang NI ; Junwei FANG ; Weixuan HONG ; Lie WANG ; Chunhong XIAO
Journal of Clinical Surgery 2025;33(8):895-896
Adipocytic tumors are the most common type of soft tissue tumors,which can be divided into lipomas and liposarcomas.Studies have found that benign lipomas resected from the same site can transform into liposarcomas,especially atypical lipomatous tumors(ALT),suggesting an underlying biological association.In this case,the patient underwent resection of a right neck mass in our hospital in 2017,and the pathology showed fibrolipoma.One year later,the mass recurred at the original site but was not treated.By 2023,the mass had significantly enlarged and extended deeply.MRI showed that the lesion had an unclear boundary with the surrounding fat,suggesting liposarcoma.Puncture and molecular pathology showed MDM2 gene amplification,and the diagnosis of ALT was made,which was confirmed by pathology after complete surgical resection.It can be seen that adipocytic tumors have great differences in biological behavior,and benign lipomas can transform into liposarcomas(especially ALT).Clinically,it is necessary to combine imaging,pathology and molecular detection(such as MDM2/CDK4)for differentiation to formulate treatment plans.
3.A case of recurrent atypical lipomatous tumor originating from cervical lipoma
Yi GAO ; Tingting LIU ; Weixiang NI ; Junwei FANG ; Weixuan HONG ; Lie WANG ; Chunhong XIAO
Journal of Clinical Surgery 2025;33(8):895-896
Adipocytic tumors are the most common type of soft tissue tumors,which can be divided into lipomas and liposarcomas.Studies have found that benign lipomas resected from the same site can transform into liposarcomas,especially atypical lipomatous tumors(ALT),suggesting an underlying biological association.In this case,the patient underwent resection of a right neck mass in our hospital in 2017,and the pathology showed fibrolipoma.One year later,the mass recurred at the original site but was not treated.By 2023,the mass had significantly enlarged and extended deeply.MRI showed that the lesion had an unclear boundary with the surrounding fat,suggesting liposarcoma.Puncture and molecular pathology showed MDM2 gene amplification,and the diagnosis of ALT was made,which was confirmed by pathology after complete surgical resection.It can be seen that adipocytic tumors have great differences in biological behavior,and benign lipomas can transform into liposarcomas(especially ALT).Clinically,it is necessary to combine imaging,pathology and molecular detection(such as MDM2/CDK4)for differentiation to formulate treatment plans.
4.Discussion on the Targeting Mechanism of Qingre Huoxue Formula (清热活血方) for Treatment of Rheumatoid Arthritis by Regulating “Inflammation-Bone Destruction”:Based on LRG1/TGF- β Signalling Axis
Weixiang LIU ; Yu SHI ; Yanqiong ZHANG ; Xun GONG ; Quan JIANG
Journal of Traditional Chinese Medicine 2024;65(7):691-696
Based on the previous publications, it is believed that damp-heat syndrome is the core syndrome of rheumatoid arthritis (RA), and Qingre Huoxue Formula (清热活血方) is an effective formula for the treatment of damp-heat syndrome of RA. “Inflammation-bone destruction” is a key pathological link of RA, and it is also the advantage of the effectiveness of Qingre Huoxue Formula. Leucine rich α-2-glycoprotein 1 (LRG1) can mediate the transforming growth factor-β (TGF-β) signalling pathway to participate in the pathogenic process of “inflammation-bone destruction” of RA, and it can be used as a target protein in the treatment of damp-heat syndrome of RA by Qingre Huoxue Formula. Accordingly, a scientific hypothesis was proposed that Qingre Huoxue Formula may regulate TGF-β signalling pathway mediated by LRG1 to improve “inflammation-bone destruction” of RA, and it was envisioned that the clinical effect of Qingre Huoxue Formula on LRG1 could be confirmed through clinical studies, and the mechanism of action of Qingre Huoxue Formula on the LRG1/TGF-β signalling axis as well as the influence of the expression or non-expression of the LRG1/TGF-β signalling axis on the therapeutic effectiveness of Qingre Huoxue Formula could be clarified through animal experiments.
5.Application progresses of new ultrasonic technologies for assisting diagnosis of BI-RADS 4 lesions
Jiahong LI ; Pengji LIN ; Tianqi WU ; Mingsong XUE ; Tingwei CHEN ; Weixiang LIANG ; Tao LIU
Chinese Journal of Interventional Imaging and Therapy 2024;21(1):52-55
The ultrasonic manifestations of benign and malignant breast imaging-reporting and data system(BI-RADS)4 lesions overlap in some degrees,is able to result in unnecessary biopsy or untimely therapy.Accurate classifying the nature of BI-RADS 4 breast lesions can provide reliable references for clinical decision-making.The progresses of application of new ultrasonic technologies,including automated breast volume scanner,superb micro-vascular imaging,elastography,contrast-enhanced ultrasound and artificial intelligence for assisting diagnosis of BI-RADS 4 lesions were reviewed in this article.
6.Pharmacological inhibition of BAP1 recruits HERC2 to competitively dissociate BRCA1-BARD1, suppresses DNA repair and sensitizes CRC to radiotherapy.
Xin YUE ; Tingyu LIU ; Xuecen WANG ; Weijian WU ; Gesi WEN ; Yang YI ; Jiaxin WU ; Ziyang WANG ; Weixiang ZHAN ; Ruirui WU ; Yuan MENG ; Zhirui CAO ; Liyuan LE ; Wenyan QIU ; Xiaoyue ZHANG ; Zhenyu LI ; Yong CHEN ; Guohui WAN ; Xianzhang BU ; Zhenwei PENG ; Ran-Yi LIU
Acta Pharmaceutica Sinica B 2023;13(8):3382-3399
Radiotherapy is widely used in the management of advanced colorectal cancer (CRC). However, the clinical efficacy is limited by the safe irradiated dose. Sensitizing tumor cells to radiotherapy via interrupting DNA repair is a promising approach to conquering the limitation. The BRCA1-BARD1 complex has been demonstrated to play a critical role in homologous recombination (HR) DSB repair, and its functions may be affected by HERC2 or BAP1. Accumulated evidence illustrates that the ubiquitination-deubiquitination balance is involved in these processes; however, the precise mechanism for the cross-talk among these proteins in HR repair following radiation hasn't been defined. Through activity-based profiling, we identified PT33 as an active entity for HR repair suppression. Subsequently, we revealed that BAP1 serves as a novel molecular target of PT33 via a CRISPR-based deubiquitinase screen. Mechanistically, pharmacological covalent inhibition of BAP1 with PT33 recruits HERC2 to compete with BARD1 for BRCA1 interaction, interrupting HR repair. Consequently, PT33 treatment can substantially enhance the sensitivity of CRC cells to radiotherapy in vitro and in vivo. Overall, these findings provide a mechanistic basis for PT33-induced HR suppression and may guide an effective strategy to improve therapeutic gain.
7.Application of thinking visual guidance teaching model in anesthesia clinical practice teaching
Weixiang MIN ; Yan YAN ; Yu LIU ; Yunfei LIU ; Shuting LIU ; Dexiang MA
Chinese Journal of Medical Education Research 2022;21(9):1186-1190
Objective:To analyze the application of thinking visual guidance teaching model in anesthesia clinical practice teaching.Methods:Taking the implementation time (March 2019) of thinking visual guidance teaching model in our hospital as the limit, 56 interns who came to our hospital for anesthesia practice before the implementation were included as control group, and 61 interns enrolled after the implementation (from March 2019 to March 2020) were included in study group. The mastery status of professional skills (duration of anesthesia operation, success rate of one-time anesthesia puncture and success rate of one - time tracheal intubation), professional knowledge assessment results and professional attitude changes were compared between the two groups at 2 months and 6 months of training. Self-evaluation after 6 months of training was compared between the two groups. SPSS 18.0 was used for t test and chi-square test. Results:After 6 months of training, the mastery status of professional skills (duration of anesthesia operation, success rate of one-time anesthesia puncture, and success rate of one-time tracheal intubation) of the two groups of interns were significantly improved compared with those after 2 months of training, and the above indicators of study group were significantly better than those of control group (all P<0.05). After 6 months of training, the scores of assessment results of professional knowledge (basic knowledge, understanding and memory, case analysis, emergency handling) and professional attitude (behavior, language, initiative and adaptability) in the two groups of interns were significantly higher than those after 2 months of training, and the above indicators scores of study group were significantly higher than those of control group (all P<0.05). The scores of self-evaluation (learning efficiency, learning atmosphere, learning ability, self-confidence and satisfaction) of study group at 6 months of training were significantly higher than those of control group at the same period (all P<0.05). Conclusion:Thinking visual guidance teaching model can effectively improve the professional knowledge and operation skills of anesthesia clinical interns, and it has a good application effect.
8.Preliminary clinical application of catheter - directed thrombolysis with urokinase for acute limb ischemia
Yujin LIU ; Xiaojun ZHANG ; Weixiang SONG ; Xubo SHEN ; Liubo LI
Journal of Interventional Radiology 2018;27(3):262-265
Objective To evaluate the curative effect and feasibility of catheter-directed thrombolysis with urokinase for acute limb ischemia. Methods The clinical data of a total of 21 patients with acute limb ischemia, who were treated with infusion of urokinase through UniFuse thrombolytic catheter, were retrospectively analyzed. The clinical curative efficacy, prognosis and complications of catheter - directed thrombolysis (CDT) were summarized. Results In all patients, thrombolysis therapy was effective, the clinical symptoms were alleviated, and successful limb salvage was achieved. One patient died of cerebral hemorrhage due to renal decompensation. No other serious complications such as hemorrhage, hematoma or disability occurred. Conclusion Preliminary clinical study shows that CDT with urokinase is effective and safe for the treatment of acute limb ischemia. This therapy can help reduce unnecessary surgical procedures or stent implantation, and the risk of thrombolysis is controllable. (J Intervent Radiol, 2018, 27: 262-265)
9.Effect evaluation of a 2 dose varicella vaccine immunization strategy implemented to control outbreaks in school and kindergarten settings.
Luodan SUO ; Juan LI ; Dan ZHAO ; Fan YANG ; Weixiang LIU ; Jiang WU ; Xinghuo PANG ; Ying DENG ; Li LU ; Email: LULIBJ@SINA.COM.
Chinese Journal of Preventive Medicine 2015;49(6):485-489
OBJECTIVETo evaluate the effect of outbreaks control in school settings after a 2 dose varicella vaccine immunization strategy implemented in Beijing.
METHODSEpidemiological data of varicella outbreaks in school and kindergarten settings, which were reported by all 16 districts (county) during 2007-2013 according to the technical management norms of Beijing, was collected. The first dose and second dose varicella vaccine coverage rate of eligible children after the 2 dose varicella vaccine immunization strategy implementation were estimated through BJIIMS. Based on above we analyzed the changes of outbreak quantity, case quantity and the distribution characteristics between the pre-adjustment era (2007-2011 years) and late adjustment era (2013) of the 2 dose immunization strategy.
RESULTSIn pre-adjustment era (2007-2011 years), an average of 74 (95% CI: 60-89) outbreaks was reported and 964 (95% CI: 812-1 116) cases were involved per year. In late adjustment era (2013): Outbreaks (35) declined 52.7%, involved cases (371) declined 61.5%; Outbreaks epidemic duration shortened from 22 days of pre-adjustment era to 18 days; Outbreaks involved 10-24 cases declined 64.7% (from 34 to 12); Outbreaks involved ≥ 25 cases declined 71.4% (from 7 to 2); Outbreaks of different school type as well as different regions without exception declined dramatically. Cumulative one-dose vaccine coverage in children of 2-6 yr of age was 89.6% (812 859/907 579), and cumulative second-dose vaccine coverage in children of 4-7 yr of age was 44.3% (289 764/647 732).
CONCLUSIONImplementation of a 2 dose varicella vaccine immunization strategy effectively controlled outbreaks in school and kindergarten settings.
Chickenpox ; Chickenpox Vaccine ; Child ; Child, Preschool ; Disease Outbreaks ; Epidemics ; Humans ; Schools ; Students ; Vaccination
10.Waveflex elastic fixation and discectomy annulus in repair and reconstruction of spinal stability in patients with lumbar disc herniation
Zhaochuan ZHANG ; Xiaowei JIANG ; Weixiang DAI ; Dehui WU ; Chao MA ; Zhaohong WANG ; Meng HAN ; Jie FENG ; Guangpu LIU
Chinese Journal of Tissue Engineering Research 2015;(44):7131-7136
BACKGROUND:For reason of pathological particularity, treatments for young adult patients with lumbar disc herniation require more demanding procedures. Traditional discectomy and rigid fixation and fusion receive a lower clinical satisfaction rate because of their concomitant complications. Waveflex is a semi-rigid fixation system with non-fusion pedicle screws. Once combined with the technology of annulus repair, it can maintain the normal movement of the segments, and can thus raise clinical satisfaction rate. OBJECTIVE:To evaluate the short-term efficacy of the treatment of young adult lumbar disc herniation through the technology of the posterior Waveflex non-fusion pedicle screw elastic fixed smal window nucleus pulposus extirpation associated with annulus repair. METHODS: Thirty-eight patients with lumbar disc herniation were involved in this study, among which, 18 cases in the elastic fixation group were subjected to a posterior lumbar smal window nucleuspulposus extraction along with annulus repair together bound with Waveflex elastic fixation; the rest 20 cases in the nucleus pulposus removal group underwent simple nucleus pulposus extirpation. After these operations, a series of folow-up study was conducted, including: folow-up analysis of clinical efficacy and complications, colection of low-back pain visual analogue scores, colection of Japanese Orthopaedic Association scores (JOA), regular assessment of Oswestry dysfunction index, and reevaluation of the lumbar lateral radiographs related indicators. RESULTS AND CONCLUSION:Folow-up visits to the patients were conducted 12-20 months later since the operations. Both groups showed a better performance than before treatment in the pain visual analogue scale, low back pain JOA score, and Oswestry dysfunction index of low-back pain (P < 0.05) during the last visit. The pain visual analogue scale, low back pain JOA score, and Oswestry dysfunction index of low-back pain in the dynamic fixation group were superior to those in the nucleus pulposus removal group (P <0.05). Stil in the last folow-up, operative segment disc height in the dynamic fixation group was greater than that before treatment, and the operative segment range of motion was smaler than that before treatment (P <0.05). These results suggest that compared to nucleus pulposus removal, Waveflex system associated with nucleus pulposus excision annulus repair has a more satisfactory effect in the early recovery of lumbar spine function and exerts a positive effect on the stability of the operated segments in the treatment of lumbar protrusion of the intervertebral disc in young adults.

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