1.Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions.
Fang REN ; Jing WEI ; Qingxin CHEN ; Mengling HU ; Lu YU ; Jianing MI ; Xiaogang ZHOU ; Dalian QIN ; Jianming WU ; Anguo WU
Acta Pharmaceutica Sinica B 2025;15(9):4327-4385
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline and memory loss, with few effective treatments currently available. The multifactorial nature of AD, shaped by genetic, environmental, and biological factors, complicates both research and clinical management. Recent advances in artificial intelligence (AI) and multi-omics technologies provide new opportunities to elucidate the molecular mechanisms of AD and identify early biomarkers for diagnosis and prognosis. AI-driven approaches such as machine learning, deep learning, and network-based models have enabled the integration of large-scale genomic, transcriptomic, proteomic, metabolomic, and microbiomic datasets. These efforts have facilitated the discovery of novel molecular signatures and therapeutic targets. Methods including deep belief networks and joint deep semi-non-negative matrix factorization have contributed to improvements in disease classification and patient stratification. However, ongoing challenges remain. These include data heterogeneity, limited interpretability of complex models, a lack of large and diverse datasets, and insufficient clinical validation. The absence of standardized multi-omics data processing methods further restricts progress. This review systematically summarizes recent advances in AI-driven multi-omics research in AD, highlighting achievements in early diagnosis and biomarker discovery while discussing limitations and future directions needed to advance these approaches toward clinical application.
2.Mechanism prediction and experimental verification of Maxing Shigan Decoction against influenza A virus infection based on UPLC-MS/MS and network pharmacology
Jiawang HUANG ; Jianing SHI ; Yang LIU ; Zhiying FENG ; Jingmin FU ; Siyu WANG ; Xuan JI ; Rong YU ; Ling LI
Digital Chinese Medicine 2025;8(4):532-542
Objective:
To investigate the chemical compositions of Maxing Shigan Decoction (麻杏石甘汤, MXSGD) and elucidate its anti-influenza A virus (IAV) mechanism from prediction to validation.
Methods:
Ultra high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was employed to analyze the chemical compositions of MXSGD. Network pharmacology theories were used to screen and identify shared targets of both the potential targets of active ingredients of MXSGD and IAV. A protein-protein interaction (PPI) network was then constructed, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The binding stability between core bioactive compounds and key targets was validated by molecular docking and dynamic simulations. A total of 24 BALB/c mice were infected with IAV to build IAV mouse models. After successful modelling, the mouse models were randomly divided into model, MXSGD high-dose (2.8 g/kg), MXSGD low-dose (1.4 g/kg), and oseltamivir (20.14 mg/kg) groups, with an additional normal mice as control group (n = 6 per group). The treatments were administered by gavage daily between 8:00 a.m. and 10:00 a.m. for five consecutive days. Upon completion of the administration, the body weight ratio, lung index, protein content in the bronchoalveolar lavage fluid (BALF), and the levels of inflammatory factors including interleukin (IL)-6 and tumor necrosis factor (TNF)-α in mice were measured to preliminarily analyze the therapeutic efficacy of MXSGD against IAV infection. Furthermore, the expression levels of mechanistic target of rapamycin (mTOR), hypoxia inducible factor (HIF)-1α, and vascular endothelial growth factor (VEGF) proteins in the HIF-1 signaling pathway, which was enriched by network pharmacology, were detected by Western blot.
Results:
A total of 212 chemical components in MXSGD were identified by the UPLC-MS/MS method. These chemical components can be classified into 9 primary categories and 31 secondary categories. After intersecting the chemical component targets with IAV-related targets, a total of 567 potential MXSGD components targeting IAV were identified. The construction of PPI network and the results of both GO and KEGG enrichment analyses revealed that the anti-IAV effects of MXSGD were associated with multiple pathways, including apoptosis, TNF, HIF-1, and IL-17 signaling pathways. The results of molecular docking demonstrated that the binding energies between the core compound 1-methoxyphaseollin and key targets including HIF-1α, mTOR, and VEGF were all lower than – 5.0 kcal/mol. Furthermore, molecular dynamics simulations confirmed the structural stability of the resulting complexes. Animal experiments showed that compared with the normal controls, IAV-infected mice showed significantly reduced body weight ratio, markedly increased lung index, protein content in BALF, and the levels of inflammatory factors such as IL-6 and TNF-α (P < 0.01), thereby causing damage to the lung tissue; consequently, the expression levels of mTOR, HIF-1α, and VEGF proteins in the lung tissues of these mice were significantly elevated (P < 0.01). However, after MXSGD treatment, the mouse models presented a significant increase in body weight ratio, as well as marked decreases in lung index, protein content in BALF, and the levels of inflammatory factors including IL-6 and TNF-α (P < 0.01). Furthermore, the therapy alleviated IAV-induced injuries and significantly downregulated the expression levels of mTOR, HIF-1α, and VEGF proteins in lung tissues (P < 0.01 or P < 0.05).
Conclusion
MXSGD exerts anti-IAV effects through multi-component, multi-target, and multi-pathway synergism. Among them, 1-methoxyphaseollin is identified as a potential key component, which alleviates virus-induced lung injury and inflammatory response via the regulation of HIF-1 signaling pathway, providing experimental evidence for the clinical application of MXSGD.
3.Research Progress in Data Acquisition and Intelligent Sensing Methods for Lumbar Electromyographic Signals
Jinghui FENG ; Yu YU ; Jianing XI
Chinese Journal of Medical Instrumentation 2024;48(2):119-125
Population aging trend is taking place in our country,and low back pain is a symptom of neuromuscular diseases of concern in the elderly.Accurately analyzing the disease of low back pain is important for both timely intervention and rehabilitation of patients.As a kind of bioelectrical signal,the acquisition and analysis of lumbar electromyography(EMG)signal is an important direction for the study of low back pain.The study reviews the acquisition of lumbar EMG by different types of sensors,introduces the signal characteristics of needle electrodes,surface electromyography electrodes and array electrodes,describes the use of signal algorithms,points out that wireless sensors and the use of deep learning algorithms are the direction of development,and puts forward prospects for its further development.
4.Predictive value of preoperative pelvic floor electrophysiological parameters on early urinary incontinence following radical prostatectomy
Shuhui YU ; Jianing HAN ; Lijun ZHONG ; Congyu CHEN ; Yunxiang XIAO ; Yanbo HUANG ; Yang YANG ; Xinyan CHE
Journal of Peking University(Health Sciences) 2024;56(4):594-599
Objective:To explore the predictive value of preoperative pelvic floor electromyography(EMG)parameters for the risk of urinary incontinence after prostate cancer surgery.Methods:This study retrospectively analyzed the medical records of 271 patients who underwent radical prostatectomy in the urology department of Peking University First Hospital from January 2020 to October 2022.The data included patient age,body mass index(BMI),international prostate symptom score(IPSS),prostate-specific antigen(PSA)levels,Gleason score,type of surgery,urethral reconstruction,lymph node dis-section,nerve preservation,catheterization duration,D'Amico risk classification,American Society of Anesthesiologists(ASA)score,Charlson comorbidity index,postoperative duration,prostate volume,and pelvic floor EMG parameters(pre-resting mean,fast muscle mean,and slow muscle mean scores).Independent risk factors affecting early postoperative urinary incontinence were identified through multiva-riate Logistic regression analysis.The predictive efficacy of pelvic floor EMG results was evaluated by cal-culating the area under the receiver operating characteristic(ROC)curve,and the optimal threshold for early postoperative urinary incontinence was determined based on the Youden index and clinical signifi-cance.Results:The study included 271 prostate cancer patients,with an 81.9%rate of voluntary urinary control post-surgery.The median score for fast pelvic floor muscles was 23.5(18.2,31.6),and for slow muscles,it was 12.5(9.6,17.3).Among the patients,179(66.1%)did not preserve nerves,and 110(40.6%)underwent urethral reconstruction.Advanced age and low fast muscle scores were identified as independent risk factors for urinary incontinence.Patients aged ≤60 had 5.482 times the voluntary urinary control rate compared with those aged ≥70(95%CI:1.532-19.617,P<0.05).There was a significant correlation between fast muscle scores and urinary incontinence recovery(OR=1.209,95%CI:1.132-1.291,P<0.05).When the optimal threshold for preoperative fast muscle score was set at 18.5,the ROC sensitivity and specificity were 80.6%and 61.2%,respectively.Con-clusion:Preoperative pelvic floor EMG parameters show good predictive accuracy and clinical applicabili-ty for the risk of urinary incontinence after prostate cancer surgery.These parameters can be used for ear-ly identification of urinary incontinence risk,with age and fast muscle scores being important predictors.
5.Study on identification of medicinal plant Gentiana scabra Bge. in Liaoning province based on DNA barcode sequences
Jianing XUE ; Rong ZHAO ; Ying YU ; Mingze GAO ; Haibo YIN
International Journal of Traditional Chinese Medicine 2024;46(1):103-107
Objective:To identify and analyze the genuine medicinal plant Gentiana scabra Bge. from 9 regions in Liaoning Province using DNA barcode technology based on the base sequence of internal transcribed spacer. Methods:DNA was extracted from the medicinal parts of 26 Gentiana scabra Bge. samples by using DNA kit extraction method. The ITS sequence was amplified through polymerase chain reaction (PCR), and then two-way sequencing was carried out. Other sources and outgroup sequences of the medicinal plant Gentiana scabra Bge. were downloaded from Genbank. After the sequencing results were spliced by using SeqMan 7.1.0 software, MEGA 7.0 software was used to analyze and compare the data, and calculate the genetic distance of K2P (Kimura 2-parameter). The phylogenetic tree was established by Neighbor-Joining (NJ) method for analysis. Results:According to the results of NJ cluster tree, all Gentiana scabra Bge. samples from different sources were clustered into one large branch, and Gentiana scabra Franch. and Gentiana triflora Pall. were clustered into one branch respectively, with obvious differences; Gentiana scabra and Gentiana manshurica Kitag. were clustered into one branch, and the genetic relationship was relatively close. In combination with the variation site and genetic distance, the base sequences of Gentiana scabra and Gentianamanshurica were very similar, and the interspecific differences were very small. Except for the intraspecific variation of only one sample collected in Liaoning Province, the base sequences of the other samples were the same, and there was no difference between " Gentiana scabra Bge. in Qingyuan" and Gentiana scabra Bge. samples from other regions in Liaoning Province. Conclusion:The DNA barcode technology of ITS sequence can be used to differentiate and identify medicinal plant Gentiana scabra Bge. and its original plants from different sources with a high success rate.
6.Study on DNA barcoding of Atractylodes chinensis (DC.) Koidz. herbs from Liaoning Province based on rbcL sequences
Ying YU ; Rong ZHAO ; Mingze GAO ; Jianing XUE ; Haibo YIN
International Journal of Traditional Chinese Medicine 2024;46(2):249-253
Objective:To use rbcL sequences to identify the rhizomes of the Liaoning collection of Atractylodes chinensis (DC.) Koidz.; To provide a basis for ensuring the feasibility of cultivation of the native herb in Liaoning Province. Methods:A total of 30 rhizomes of Atractylodes chinensis (DC.) Koidz. were collected from 10 regions cultivated in Liaoning Province, and the total DNA was extracted. DNA barcodes were screened by PCR, and the rbcL sequences of the samples were amplified and sequenced, and the amplification and sequencing success rates were calculated. Sequence alignment was performed using MEGA 7.0 software; a systematic clustering tree was constructed using the neighbour-joining method. Results:The success rates of DNA extraction from the rhizomes of Atractylodes chinensis (DC.) Koidz. were all 93.3%, and the success rates of PCR amplification and sequencing were all 100%. Among the 30 samples of Atractylodes chinensis (DC.) Koidz. in Liaoning Province, two samples had intraspecific variation, and the rest of the base sequences of Atractylodes chinensis (DC.) Koidz. were identical. Atractylodes chinensis (DC.) Koidz. was closer to the herbs of the genus Cangzhu, a relative species of Asteraceae, and was genetically more distant from the rest of Asteraceae. The NJ tree could distinguish Atractylodes chinensis (DC.) Koidz. and its relatives. Conclusion:The quality of Atractylodes chinensis (DC.) Koidz. cultivars in Liaoning Province is basically similar, and the rbcL sequence can be used as a valid sequence fragment for the identification of Atractylodes chinensis (DC.) Koidz. DNA barcode.
7.Experimental study on treatment of severe limb ischemia with Ad-hVEGF-hHGF gene
Rui ZHONG ; Jianing WANG ; Lei ZHANG ; Lingyun GUO ; Jianye YANG ; Fei ZHENG ; Yuwen YAN ; Danli YU ; Liguo TAN
The Journal of Practical Medicine 2024;40(5):639-645
Objective To explore the role and efficacy of VEGF and HGF gene adenovirus vector in promoting angiogenesis in ischemic tissue.Methods 84 Kunming mice were randomly divided into sham group,control group,VEGF group,HGF group and VEGF+HGF group,and the left lower limb ischemia model was established.The blood supply of ischemic tissue was observed by rheometer,and the expression levels of VEGF and HGF in each group were detected by Western Blot and ELISA.Immunohistochemical staining was used to detect angiogenesis(CD31,SMA)in ischemic tissues.Safety was assessed by side effects during treatment in mice.Results After the successful modeling,the blood flow velocity of the left lower limb in each group decreased significantly.On the 7th day after operation,the blood flow of the left lower limb in each group was significantly better than that on the 0th day after operation(P<0.05),and the blood flow of the left lower limb in Ad-VEGF-HGF group was significantly better than that in other groups(P<0.05).On the 28th day after operation,the blood flow of the left lower limb in Ad-VEGF-HGF group gradually stabilized,the blood flow in Ad-VEGF-HGF group was significantly better than that in other groups,and both VEGF group and HGF group were significantly better than the control group(P<0.05).On the 7th,14th,and 28th days following surgery,HGF and VEGF protein levels in the Ad-HGF,Ad-VEGF,and Ad-VEGF-HGF groups were substantially greater than those in the control group(P<0.05).The expression level in the Ad-VEGF-HGF group peaked on the 14th day(all P<0.001)and subsequently declined to preoperative levels on the 28th day after operation.Conclusion Ad-VEGF-HGF gene injection can effectively boost VEGF and HGF protein expression and rapidly reach the relative peak level,encour-aging angiogenesis after lower limb ischemia,increasing blood flow,and improving lower limb circulation.
8.Immunologic characterization of newly diagnosed multiple myeloma patients with renal impairment
WANG Rui ; YU Jianing ; ZHANG Liansheng ; LI Lijuan
Chinese Journal of Cancer Biotherapy 2024;31(6):607-612
[摘 要] 目的:探究伴有肾损害(RI)的多发性骨髓瘤(MM)患者与无RI患者间是否存在免疫学指标差异。方法:用2017年1月至2023年8月在兰州大学第二医院收治的134例首次确诊为MM的患者相关信息进行回顾性分析,研究对比RI组和非RI组及Durie⁃Salmon(DS)分期和危险分层两个亚组的10种免疫学指标和6个常规血液学参数的差异。结果:RI组外周血中性粒细胞/淋巴细胞比值(NLR)、外周血单核细胞/淋巴细胞比值(MLR)、CD8+ T细胞比例、IL-10均较非RI组高(均P<0.05),淋巴细胞绝对值、CD4/CD8比值均较非RI组低(均P<0.05)。DS-Ⅲ分期患者中,RI组NLR、MLR、CD8+ T细胞比例、IL-8、IL-10均较非RI组升高(均P<0.05),而DS-Ⅰ和DS-Ⅱ患者中,RI组和非RI组患者免疫指标无明显差异。高危MM患者RI组淋巴细胞数、NLR、IL-10均较非RI有明显差异(均P<0.05)。结论:伴RI的MM患者免疫相关指标异常更为明显,DS-Ⅲ分期和高危险度分层表现出明显的免疫指标异常,本研究结果对进一步阐明MM伴有RI患者预后较差的原因及个体化治疗提供参考依据。
9.Effect of sling exercise with Tuina therapy on kinesiophobia in old patients with lumbar disc herniation:a ran-domized controlled trial based on concept of brain-bone axis
Yuqin DAN ; Jianing SU ; Yi DING ; Xueyan WANG ; Danghan XU ; Jinghua WANG ; Yujing WU ; Mengyuan ZHANG ; Meng YIN ; Haifeng LU ; Gongchang YU ; Li LI
Chinese Journal of Rehabilitation Theory and Practice 2024;30(7):861-868
Objective To explore the effect of sling exercise with Tuina therapy on kinesiophobia in old patients with lumbar disc herniation,and analyze the mechanism based on brain-bone axis. Methods A total of 56 old patients with chronic lumbar disc herniation and kinesiophobia were selected from the Reha-bilitation Hospital of the Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine from September,2022 to December,2023;and randomly divided into control group(n=28)and experimental group(n=28).The control group accepted conventional exercise therapy,while the experimental group accepted sling exercise with Tuina therapy,for four weeks.They were assessed with simplified Chinese version of Tampa Scale of Kinesiophobia(TSK),Japanese Orthopaedic Association score(JOA)and Visual Analogue Scale for pain(VAS)before and after treatment,while the bone mineral density(BMD)was tested,the levels of osteoprote-gerin(OPG),norepinephrine(NE)and corticosteroids(Cor)in serum were measured,and the median frequency(MF)of weak-link erector spinae was detected with surface electromyography. Results Two cases dropped off in the control group,and one in the experimental group.The scores of all the assessment improved in both groups after treatment(|t|>14.168,P<0.001),as well as the serum levels of OPG,NE and Cor(|t|>2.103,P<0.05),BMD(|t|>2.726,P<0.05),and MF of erector spinae(|t|>14.736,P<0.001);all of them were better in the experimental group than in the control group(|t|>2.154,P<0.05). Conclusion Sling exercise with Tuina therapy can improve the pain and kinesiophobia of lumbar disc herniation in the old adults,which may promote the recovery of physical and mental function through regulating the levels of hor-mones and neurotransmitters related to the brain-bone axis.
10.Copper Deficiency Myeloneuropathy in a Patient With Wilson’s Disease
Yu WANG ; Zijun WEI ; Jianing MEI ; Xueyi HAN ; Hongping ZHAO ; Yulong ZHU ; Ping JIN ; Yunyun ZHANG
Journal of Movement Disorders 2024;17(1):123-126

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