1.In silico prediction of pK a values using explainable deep learning methods.
Chen YANG ; Changda GONG ; Zhixing ZHANG ; Jiaojiao FANG ; Weihua LI ; Guixia LIU ; Yun TANG
Journal of Pharmaceutical Analysis 2025;15(6):101174-101174
Negative logarithm of the acid dissociation constant (pK a) significantly influences the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of molecules and is a crucial indicator in drug research. Given the rapid and accurate characteristics of computational methods, their role in predicting drug properties is increasingly important. Although many pK a prediction models currently exist, they often focus on enhancing model precision while neglecting interpretability. In this study, we present GraFpK a, a pK a prediction model using graph neural networks (GNNs) and molecular fingerprints. The results show that our acidic and basic models achieved mean absolute errors (MAEs) of 0.621 and 0.402, respectively, on the test set, demonstrating good predictive performance. Notably, to improve interpretability, GraFpK a also incorporates Integrated Gradients (IGs), providing a clearer visual description of the atoms significantly affecting the pK a values. The high reliability and interpretability of GraFpK a ensure accurate pK a predictions while also facilitating a deeper understanding of the relationship between molecular structure and pK a values, making it a valuable tool in the field of pK a prediction.
2.KG-CNNDTI: a knowledge graph-enhanced prediction model for drug-target interactions and application in virtual screening of natural products against Alzheimer's disease.
Chengyuan YUE ; Baiyu CHEN ; Long CHEN ; Le XIONG ; Changda GONG ; Ze WANG ; Guixia LIU ; Weihua LI ; Rui WANG ; Yun TANG
Chinese Journal of Natural Medicines (English Ed.) 2025;23(11):1283-1292
Accurate prediction of drug-target interactions (DTIs) plays a pivotal role in drug discovery, facilitating optimization of lead compounds, drug repurposing and elucidation of drug side effects. However, traditional DTI prediction methods are often limited by incomplete biological data and insufficient representation of protein features. In this study, we proposed KG-CNNDTI, a novel knowledge graph-enhanced framework for DTI prediction, which integrates heterogeneous biological information to improve model generalizability and predictive performance. The proposed model utilized protein embeddings derived from a biomedical knowledge graph via the Node2Vec algorithm, which were further enriched with contextualized sequence representations obtained from ProteinBERT. For compound representation, multiple molecular fingerprint schemes alongside the Uni-Mol pre-trained model were evaluated. The fused representations served as inputs to both classical machine learning models and a convolutional neural network-based predictor. Experimental evaluations across benchmark datasets demonstrated that KG-CNNDTI achieved superior performance compared to state-of-the-art methods, particularly in terms of Precision, Recall, F1-Score and area under the precision-recall curve (AUPR). Ablation analysis highlighted the substantial contribution of knowledge graph-derived features. Moreover, KG-CNNDTI was employed for virtual screening of natural products against Alzheimer's disease, resulting in 40 candidate compounds. 5 were supported by literature evidence, among which 3 were further validated in vitro assays.
Alzheimer Disease/drug therapy*
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Biological Products/therapeutic use*
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Humans
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Neural Networks, Computer
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Machine Learning
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Drug Discovery/methods*
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Algorithms
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Drug Evaluation, Preclinical/methods*
3.Opinion on the development and research status of intelligent ophthalmology in China
Di GONG ; Wangting LI ; Xiaomeng LI ; Cheng WAN ; Yongjin ZHOU ; Yanwu XU ; Shaochong ZHANG ; Weihua YANG
International Eye Science 2024;24(3):448-452
This paper provides a comprehensive analysis of the current state of intelligent ophthalmology in China, including technological advancements, academic exchange platforms, policy support, future challenges, and potential solutions. Technologically, remarkable progress have been made in various areas of intelligent ophthalmology in China, including diabetic retinopathy, fundus image analysis, and crucial aspects such as quality assessment of medical artificial intelligence products, clinical research methods, technological evaluation, and industrial standards. Researchers are constantly improving the safety and standardization of intelligent ophthalmology technology by formulating clinical application guidelines and standards. Academic exchange platforms have been established to provide extensive collaboration opportunities for professionals across diverse fields, and various academic journals serve as publication platforms for intelligent ophthalmology research. Regarding public policy, the Chinese government has not only established a supportive policy environment for the advancement of intelligent ophthalmology through various documents and regulations, but provided a legal basis and management framework. However, there are still challenges to overcome, such as technological innovation, data privacy and security, outdated regulations, and talent shortages. To tackle these issues, there is a requirement for increased technological research and development, the establishment of regulatory frameworks, talent cultivation, and greater awareness and acceptance of new technologies among patients. By comprehensively addressing these challenges, intelligent ophthalmology in China is expected to continue leading the industry's global development, bringing more innovation and convenience to the field of ophthalmic healthcare.
4.Clinical and prognostic analysis of opsoclonus-myoclonus-ataxia syndrome in children
Ji ZHOU ; Xiuwei ZHUO ; Mei JIN ; Chao DUAN ; Weihua ZHANG ; Changhong REN ; Shuai GONG ; Xiaojuan TIAN ; Changhong DING ; Xiaotun REN ; Jiuwei LI
Chinese Journal of Pediatrics 2024;62(3):256-261
Objective:To summarize the clinical and prognostic features of children with opsoclonus-myoclonus-ataxia syndrome (OMAS).Methods:A total of 46 patients who met the diagnostic criteria of OMAS in the Department of Neurology, Beijing Children′s Hospital from June 2015 to June 2023 were retrospectively analyzed. Centralized online consultations or telephone visits were conducted between June and August 2023. The data of the children during hospitalization and follow-up were collected, including clinical manifestations, assistant examination, treatment and prognosis. According to the presence or absence of tumor, the patients were divided into two groups. The chi-square test or Mann-Whitney U test was used to compare the differences between the two groups. Univariate Logistic regression was used to analyze the factors related to OMAS recurrence and prognosis. Results:There were 46 patients, with 25 males and the onset age of 1.5 (1.2, 2.4) years. Twenty-six (57%) patients were diagnosed with neuroblastoma during the course of the disease, and no patients were categorized into the high-risk group. A total of 36 patients (78%) were followed up for≥6 months, and all of them were treated with first-line therapy with glucocorticoids, gammaglobulin and (or) adrenocorticotrophic hormone. Among the 36 patients, 9 patients (25%) were treated with second-line therapy for ≥3 months, including rituximab or cyclophosphamide, and 17 patients (47%) received chemotherapy related to neuroblastoma. At the follow-up time of 4.2 (2.2, 5.5) years, 10 patients (28%) had relapsed of OMAS. The Mitchell and Pike OMS rating scale score at the final follow-up was 0.5 (0, 2.0). Seven patients (19%) were mildly cognitively behind their peers and 6 patients (17%) were severely behind. Only 1 patient had tumor recurrence during follow-up. The history of vaccination or infection before onset was more common in the non-tumor group than in the tumor group (55%(11/20) vs. 23%(6/26), χ2=4.95, P=0.026). Myoclonus occurred more frequently in the non-tumor group (40%(8/20) vs. 4%(1/26), χ2=7.23, P=0.007) as the onset symptom. Univariate Logistic regression analysis showed that the tumor group had less recurrence ( OR=0.19 (0.04-0.93), P=0.041). The use of second-line therapy or chemotherapy within 6 months of the disease course had a better prognosis ( OR=11.64 (1.27-106.72), P=0.030). Conclusions:OMAS in children mostly starts in early childhood, and about half are combined with neuroblastoma. Neuroblastoma in combination with OMAS usually has a low risk classification and good prognosis. When comparing patients with OMAS with and without tumors, the latter have a more common infection or vaccination triggers, and myoclonus, as the onset symptom, is more common. Early addition of second-line therapy is associated with better prognosis in OMAS.
5.Clinical application of the new classification criteria in children with Miller Fisher syndrome and clinical characteristics analysis of different types of Miller Fisher syndrome
Xinying YANG ; Tongli HAN ; Xiuwei ZHUO ; Shuai GONG ; Jiuwei LI ; Shen ZHANG ; Weihua ZHANG
Chinese Journal of Applied Clinical Pediatrics 2022;37(3):178-181
Objective:To investigate the clinical application of the new classification criteria in children with Miller Fisher syndrome (MFS), and to analyze clinical characteristics of different types of MFS.Methods:Clinical data of MFS patients hospitalized in the Department of Neurology, Beijing Children′s Hospital, Capital Medical University from January 2015 to December 2019 were collected and analyzed retrospectively, including demographic characteristics, clinical symptoms, neurological examination findings, laboratory examination data, diagnosis and treatment, and prognosis.The counting data was described by percentage, and the measurement data was described by median.Results:A total of 23 patients were included in the research, including 14 males and 9 females, with a median age of 4 years and 8 months.There were 3 cases of pure MFS; 5 cases of incomplete MFS, including 1 case of acute ptosis and 4 cases of acute ataxia neuropathy; 15 cases of overlapping syndrome, including 13 cases of MFS/Guillain Barre syndrome (GBS), 1 case of MFS/pharyngocervical brachial variant GBS(PCB GBS)and 1 case of MFS/GBS/Bickertaff brainstem encephalitis (BBE). In addition to Ⅲ, Ⅳ and Ⅵ cranial nerve palsy, 11 cases had the involvement of other cra-nial nerves, including 2 cases in pure MFS, 8 cases in MFS/GBS and 1 case in MFS/GBS/BBE.Autonomic nervous dysfunction occurred in 6 cases.Respiratory muscle paralysis occurred in 6 cases, including 5 cases in MFS/GBS and 1 case in MFS/GBS/BBE.Graded by the Hughes scoring system (HG score), 3 cases with pure MFS were graded 4 points; 1 case with acute ptosis was graded 0; 3 cases with acute ataxia neuropathy were graded 2 points, and the other one was graded 3 points; 1 case with MFS/PCB GBS was graded 3 points; 10 cases with MFS/GBS were graded 4 points, 1 case was graded 3 points, and the other 2 cases were graded 2 points; 1 case with MFS/GBS/BBE was graded 4 points.Twenty-two patients were treated with intravenous immunoglobulin.The HG of all patients at discharge decreased at varying degree, which was graded 0 at 6 months of follow-up.Conclusions:The clinical application of the new diagnostic classification method is helpful to the accurate diagnosis of different types of MFS.More than half of MFS cases will develop into the overlapping syndrome.The overlapping of MFS and GBS or BBE is prone to the involvement of cranial nerves except for the external ophthalmic muscles, autonomic nerve dysfunction and respiratory muscle paralysis.The disease course of MFS varies, and its diagnosis should be comprehensively made.All cases of MFS in this study have a satisfactory prognosis.
6.The status quo, problems and challenge of chronic disease management system in Shanghai Hongkou district
Xiaojun MA ; Weihua GONG ; Meihong ZHU ; Yuncong HUANG ; Yonghua YANG ; Qing GU
Chinese Journal of General Practitioners 2021;20(7):781-785
From April to November 2019, 5 community health service centers in Shanghai Hongkou District were randomly selected for thematic group interviews to investigate the current status, problems and challenge for further development of chronic disease management. The community chronic disease management was mainly divided into growth period (typically hypertension and diabetes) and introduction period (cardiovascular and cerebrovascular diseases, respiratory diseases, dementia, osteoporosis). The management of hypertension and diabetes in the growing stage mainly faced difficulties such as refusal or non-cooperation of patients, loss of follow-up, incomplete quality control, not meeting quality control indicators, repeated management of comorbidities, insufficient information sharing, and discrepancy in assessment indicators of multiple parties. The management of cardiovascular and cerebrovascular diseases, respiratory diseases and other diseases in the introduction period mainly faced poor awareness rate of patients, loss of follow-up, difficulty in diagnosis, irregular medication, insufficient information sharing, lack of management plan, insufficient resource investment, and few variety of medicines in the community. The current management system should be refined to provide more effective and efficient chronic disease management in the community. Meanwhile, the awareness of residents, the information network and multi-center collaborative research also need to be strengthened.
7.Clinical imaging features and prognosis of 40 children with influenza associated encephalopathy
Xiuwei ZHUO ; Changhong DING ; Ming LIU ; Lifang DAI ; Shuai GONG ; Xiaojuan TIAN ; Ji ZHOU ; Jiuwei LI ; Weihua ZHANG
Chinese Journal of Applied Clinical Pediatrics 2021;36(24):1876-1881
Objective:To analyze the clinical and imaging features of influenza associated encephalopathy(IAE) in children, thus contributing to enhance the efficacy of early identification, timely treatment and prognosis.Methods:Clinical data, laboratory examination, imaging data, treatment and outcomes of 40 children with IAE diagnosed and treated in the Beijing Children′s Hospital, Capital Medical University from December 2016 to January 2020 were retrospectively analyzed.Clinical features were summarized and they were further classified according to clinical imaging features.The prognosis was compared and analyzed.Results:A total of 20 boys and 20 girls were recruited, with the age of attending hospital at (4.0±2.3) years (median, 3.2 years). There were 28 children with influenza A and 12 with influenza B. All children initially had fever, and the interval between fever and symptoms of neurological onset was 24 hours (0-120 hours). The most-common symptom of neurological onset was seizures(32 cases), among which 17 patients showed continuous seizures.All children presented encephalopathy at varying degrees, including 33 cases in coma and 7 in drowsiness or cognitive decline.Thirty cases developed central respiratory failure and received mechanical ventilation.Examination results showed 30 cases had elevated aspartate transaminase (AST), 18 cases had elevated alanine transaminase (ALT), 14 cases had elevated creatinine, 31 cases had elevated lactate dehydrogenase, 16 cases had elevated blood glucose and 1 case had significantly lowered blood glucose.Blood ammonia testing was performed in 38 children and 9 cases had elevated level.The whole exon sequencing in 6 cases showed de novo heterozygous mutation of the SCN1A gene in 1 case, and heterozygous mutation of the ATP1A2 gene inherited from the mother in another case.Lumbar puncture was performed in 35 cases, and all of them had a normal range of cerebrospinal fluid leukocyte counts, while 12 cases had elevated cerebrospinal fluid proteins.Abnormal image findings were examined in 33 cases and the acute necrotizing encephalopathy was the most common one (14 cases). All children received Peramivir or Oseltamivir after admission.A total of 28 cases were treated with glucocorticoids, and 29 cases were treated with immunoglobulin.Seventeen cases died, 9 cases had disability at varying degrees, and 14 cases recovered to the baseline.Patients were divided into good prognosis group and poor prognosis group.(1) Patients in good prognosis group presented significantly shorter interval between fever and first neurological symptoms[(22.7±12.2) h vs.(38.6± 30.9) h], higher Glasgow score on admission[(7.6±2.5) points vs.(4.5 ± 1.6) points], lower ALT [15.6 (9.0-1 631.5) U/L vs.140.2 (12.3-3 232.4) U/L] and lower AST [47.6 (25.4-1 721.3) U/L vs.251.8 (21.7-4 991.6) U/L] than those in poor prognosis group (all P<0.05). (2) Glucocorticoids were applied to 17 and 11 cases in good prognosis group and poor prognosis group, while immunoglobulins were applied to 17 and 12 cases, respectively ( P>0.05). (3) Patients were further classified into cytokine storm group, excitotoxicity group and unclassifiable group according to clinical imaging findings.The Glasgow score [ (4.6±1.7) points vs.(7.6±2.2) point vs.(7.3±2.8) points] and median modified Rankin Scale score (6.0 points vs.1.5 points vs.0) were significantly different among 3 groups (all P<0.01). Conclusions:Influenza associated encephalopathy is common in infants and young children.Fever, convulsions and rapidly progressing disturbance of consciousness are the most common clinical manifestations.Acute necrotizing encephalopathy is the most common subtype of clinical imaging syndrome.Acute onset and rapid progression predict the poor prognosis of influenza associated encephalopathy.
8.Clinical and genetic analysis of 5 pediatric patients with hemiplegic migraine presenting as acute encephalopathy
Xiuwei ZHUO ; Shuhong REN ; Shuai GONG ; Weihua ZHANG ; Jiuwei LI ; Yujuan ZHANG ; Changhong DING
Chinese Journal of Pediatrics 2021;59(4):316-321
Objective:To analyze the clinical and genetic characteristics, diagnosis and treatment of hemiplegic migraine (HM) manifested as acute encephalopathy in children, so as to improve the understanding of this disease.Methods:The clinical data of 5 children diagnosed with HM characterized by acute encephalopathy who were admitted to Beijing Children′s Hospital affiliated to Capital Medical University from August 2018 to June 2020 were retrospectively analyzed.Results:Among the 5 cases, 3 were males and 2 females with an age of 9.7 (3.9-12.7) years. The age of disease onset was 7.0(2.1-12.7) years. The peak symptoms of 5 children showed encephalopathy such as drowsiness and coma, as well as other clinical manifestations including headache, visual abnormality, hemiplegia, aphasia, convulsions, and fever, etc. The time to reach the peak was on the 2nd-6th day of the course of the disease. Before the onset of the disease 2 cases were found to have mild brain trauma and 2 cases had similar attacks in the past. Brain magnetic resonance imaging (MRI) showed hemispheric or partial cerebral cortex swelling and restricted diffusion of subcortical white matter in all cases, and cerebellar atrophy in 3 cases. All children received symptomatic treatment, and 2 of them were also treated with low-dose corticosteroids in the meantime. Finally all cases recovered clinically from the attack, but one had atrophic changes left in the affected area on brain MRI. Whole exon sequencing revealed variations of CACNA1A gene in all cases, among which 4 were de novo mutations and 1 case inherited from the mother who had migraine without aura. After the diagnosis, the 5 children were treated with long-term flunarizine and followed up for 22(7-29) months by telephone or in the outpatient clinic. Before the last follow-up, none of them showed weakness or encephalopathy, but one still had intermittent headaches and occasional transient right limb numbness.Conclusions:Hemipleg is often accompanied by impaired consciousness in addition to headache, hemiplegia, aphasia, visual abnormality, etc. Most patients recover completely after a short period, while a few recover slowly and may suffer sequelae such as brain atrophy and cognitive impairment and even death. CACNA1A gene variation is the most common genetic variation. Flunarizine could prevent recurrence of severe attack.
9.In vivo Kinematic Characteristics of the Elbow during Active Flexion-Extension Motion Using Dual Fluoroscopic Imaging System
Diyang ZOU ; Xiangjun HU ; Hai HU ; Weihua GONG ; Tsungyuan TSAI
Journal of Medical Biomechanics 2020;35(5):E622-E628
Objective To investigate the translation and rotation of healthy elbow joints during active flexion and extension, so as to provide references for the treatment of elbow instability and injuries. Methods Ten healthy subjects with no history of upper extremity trauma were recruited. Dual fluoroscopic imaging system (DFIS) was applied to quantify six-degree-of-freedom (6-DOF) kinematics of humeroulnar and humeroradial joint from full extension to maximum flexion in supination position. Correlation analysis was used to evaluate the relationship between the 6-DOF kinematics of the elbow joint. Results Valgus angle of humeroulnar joint gradually decreased from 15.2°±3.1° to 5.3°±2.3° with the flexion increasing. Valgus angle of humeroradical joint gradually decreased from 19.7°±4.2° to 8.2°±2.4° from full extension to maximum flexion. The valgus angle of humeroulnar and humeroradial joint was linearly related to the flexion angle during flexion and extension. The internal rotation of humeroulnar joint was quadratic nonlinearly related to the flexion angle during motion. The maximum internal rotation of the ulnar was 4.0°±4.9° at 110° flexion, and the maximum external rotation was 5.1°±4.2°. The internal rotation of humeroulnar joint gradually increased from 3.2°±16.0° to 27.2°±18.0°. Conclusions During normal flexion and extension of the elbow, the valgus angle of humeroulnar joint decreased linearly, while the internal and external rotation angle showed a nonlinear change, which first rotated internally and then rotated externally. The valgus angle of humeroradial joint decreased linearly and the internal rotation angle increased linearly. Therefore, humeroulnar joint is not a hinge joint during elbow flexion and extension. There is a kinematic difference between humeroulnar joint and humeroracial joint. For clinical treatment of complex elbow injuries, elbow instability and elbow replacement, different motion characteristics in joints should be considered to improve the outcome after surgery.
10.Clinical analysis of 13 cases with acute pandysautonomia
Xinying YANG ; Tongli HAN ; Changhong DING ; Junlan LYU ; Jiuwei LI ; Shen ZHANG ; Shuai GONG ; Weihua ZHANG ; Jin ZHOU ; Tingting LIU
Chinese Journal of Applied Clinical Pediatrics 2020;35(15):1166-1168
Objective:To summarize the clinical data of patients with acute pandysautonomia (APD) and discuss the treatment and prognosis of them.Methods:A total of 13 patients with APD in the Department of Neurology, Beijing Children′s Hospital, Capital Medical University, from January 2010 to December 2019, were investigated retrospectively.The general data, clinical symptoms, autonomic nerve examination and function test, laboratory examination, treatment and follow-up were collected and analyzed.Results:There were 4 males and 9 females in 13 patients with APD, with an average age was 8 years and 5 months (3 years and 8 months to 12 years and 5 months ). The average course of disease was 94.5 d (14-410 d). The common initial symptoms were gastrointestinal motility disorder (11 cases), dysuria (3 cases), and upright syncope/vertigo (3 cases). During the course of the disease, all the patients manifested with gastrointestinal motility disfunction and dyshidrosis, glands involvement and orthostatic hypotension in 12 cases, abnormal pupil in 9 case and urinary retention in 7 case.Other symptoms included fatigue in 9 cases, emotional disorder in 4 cases, limb weakness in 2 cases, and sensory disturbance in 2 cases.All the patients were treated with intravenous immunoglobulin (IVIG), and 3 cases combined with glucocorticoid.Six patients with severe gastrointestinal symptoms were treated with intravenous nutrition; 4 patients were fed with jejunum, 3 cases of whom returned to normal diet within 1-12 months, and 1 patient was followed up for 5 years and 2 months.Hyponatremia was found in 7 cases, which recovered in 2-30 d. Nine cases were followed up for 1 month to 9 years.Seven cases were normal in daily work and study, with satisfactory nutritional status, stable mood and no relapse.Conclusions:The clinical manifestations of APD are varied.The initial symptoms are gastrointestinal motility disorders, orthostatic hypotension, urinary retention and hyponatremia.Individualized multi-disciplinary comprehensive management for symptoms, especially the comprehensive treatment of gastrointestinal motility disorders, management of postural hypotension, and the urinary system diagnosis and individualized treatment of can shorten the length of hospital stay and improve the prognosis effectively.

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