1.GPT2-ICC: A data-driven approach for accurate ion channel identification using pre-trained large language models.
Zihan ZHOU ; Yang YU ; Chengji YANG ; Leyan CAO ; Shaoying ZHANG ; Junnan LI ; Yingnan ZHANG ; Huayun HAN ; Guoliang SHI ; Qiansen ZHANG ; Juwen SHEN ; Huaiyu YANG
Journal of Pharmaceutical Analysis 2025;15(8):101302-101302
Current experimental and computational methods have limitations in accurately and efficiently classifying ion channels within vast protein spaces. Here we have developed a deep learning algorithm, GPT2 Ion Channel Classifier (GPT2-ICC), which effectively distinguishing ion channels from a test set containing approximately 239 times more non-ion-channel proteins. GPT2-ICC integrates representation learning with a large language model (LLM)-based classifier, enabling highly accurate identification of potential ion channels. Several potential ion channels were predicated from the unannotated human proteome, further demonstrating GPT2-ICC's generalization ability. This study marks a significant advancement in artificial-intelligence-driven ion channel research, highlighting the adaptability and effectiveness of combining representation learning with LLMs to address the challenges of imbalanced protein sequence data. Moreover, it provides a valuable computational tool for uncovering previously uncharacterized ion channels.
2.Analysis and clinical application of preimplantation genetic testing for monogenic disorders in a case with Spinal muscular atrophy "2+ 0" genotype
Shaoying LI ; Jianchun HE ; Wenzhi HE ; Jiajia XIAN ; Lingling HUANG ; Gengye ZHAO ; Xin ZHANG ; Renqian DU ; Liming CHU ; Yueqiang WANG ; Lingyin KONG ; Bo LIANG ; Qing LI
Chinese Journal of Medical Genetics 2024;41(3):294-299
Objective:To explore the clinical application of preimplantation genetic testing for monogenic disorders (PGT-M) in an unique case with Spinal muscular atrophy (SMA) type 2+ 0.Methods:A special SMA family presented at the Third Affiliated Hospital of Guangzhou Medical University on October 19, 2020 was selected as the study subject. Multiple ligation-dependent probe amplification (MLPA) and molecular tagging linkage analysis were carried out to identify the SMN1 genotype of the couple and their fetus. Subsequently, next-generation sequencing (NGS), molecular tagging linkage analysis, and chromosomal microarray analysis were employed to determine the haplotypes and validate the result of PGT-M on the 11 embryos derived for the couple. Results:The female partner was identified as a carrier of the rare SMN1[2+ 0] variant, and prenatal diagnosis confirmed the fetus to be affected by SMA. Ultimately, PGT-M has successfully selected four embryos free from the pathogenic SMN1 variants and X chromosome deletion. Conclusion:PGT-M can effectively prevent the transmission of rare genetic variants such as the SMA 2+ 0 subtype in the families. Above finding has provided guidance for genetic counseling and family planning for the couple.
3.The impact of the behavior and lifestyle of physical and mental workers on their depressive symptoms
Jianjiang ZHANG ; Shaoying WANG ; Leying LEI ; Chengwan SHEN
Chinese Journal of Industrial Hygiene and Occupational Diseases 2024;42(9):673-678
Objective:To analyze the depressive symptoms of physical and mental workers and the impact of their behavior and lifestyle on their depressive symptoms.Methods:In August 2022, a cross-sectional study design was adopted to select 553 workers as research subjects using cluster sampling. General demographic information, health-related behaviors and lifestyles were collected, and their depressive symptoms were evaluated using the Chinese version of the Patient Health Questionnaire 9 (PHQ-9). The differences in general demographic information, health-related behaviors and lifestyles between physical and mental workers were analyzed, and logistic regression was used to analyze the influencing factors of depressive symptoms in occupational populations.Results:Among the 553 subjects, 317 were physical workers (57.32%) and 236 were mental workers (42.68%). Statistically significant differences were observed between the two groups in terms of education level, monthly income, smoking rate, regular physical exercise rate and appropriate sleep time rate ( P<0.05). The score and the detection rate of depression symptoms among physical workers were (9.67±2.75) points and 20.82% (66/317), respectively, which were higher than those of mental workers [(8.34±2.18) points, 12.71% (30/236) ] ( t=6.13, χ 2=6.20, P<0.05). The results of logistic regression analysis showed that smoking, regular physical exercise, appropriate sleep time and mental work were influencing factors of depressive symptoms among the occupational population ( OR=1.592, 95% CI: 1.316-1.825; OR=0.659, 95% CI: 0.416-0.830; OR=0.502, 95% CI: 0.257-0.717; OR=0.839, 95% CI: 0.522-0.967; P<0.05) . Conclusion:The depressive symptoms of physical workers are more serious than those of mental workers. Low education level, not frequently participating in physical exercise, smoking and sleep disorder are potential risk factors that affect the depressive symptoms of the occupational population.
4.Research of medication rules and multi-pathway mechanism of action in the treatment of vitiligo by traditional Chinese medicine compound patent
Xiaoyi DONG ; Deyou JIANG ; Zeyun WANG ; Yuxi MENG ; Zongfu MIN ; Xuan ZHANG ; Shaoying WANG ; Yuanhong WANG
Chinese Journal of Pharmacoepidemiology 2024;33(9):993-1005
Objective To explore the medication rules and mechanism of action of traditional Chinese medicine compound patent formulas for vitiligo,and provide ideas for the development and the patent declaration work of new Chinese medicines for vitiligo.Methods China Patent Publication Bulletin website,National Knowledge Infrastructure Database,Patent Information Service Platform of China Intellectual Property Right Net(CNIPR),and Baiten Patent Platform were used to search for the patents of traditional Chinese medicine compound formulas for vitiligo from the establishment of the databases to 30th September,2023.Excel software and Traditional Chinese Medicine Inheritance Computing Platform(TCMICS V3.0)were used to establish a database of compound formulas,and carry out the statistics of frequency,association rules and clustering analysis of the formulas for internal and external prescriptions.The target and mechanism of action of the internal prescriptions of core high-frequency Traditional Chinese Medicine group for the treatment of vitiligo were further explored by Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP),Symptom Mapping(Symmap),The Human Gene Database(Genecards),UniversalProtein(UniProt),STRING,Pharmaceutical DataBase(PDB)and other databases as well as software such as R Studio 4.2.2 and Cytoscape 3.9.1,and AutoDock Vina was used for molecular docking validation.Results The internal formulas included 335 patents and the external formulas included 189 patents.The rules of internal and external use are similar.The high-frequency traditional Chinese medicines are Tribuli Fructus,Psoraleae Fructus,Angelicae sinensis,Radix Polygoni Multiflori,Carthami Flos,Angelica dahurica,etc.;the key efficacies of the medicines are based on tonifying the deficiency,activating blood circulation and removing blood stasis;and the properties of the Chinese medicines are the nature of warmth,coldness and flatness,sweetness,bitterness,pungency and attribution to the liver,the spleen,the heart and the kidneys.Commonly used oral medicine pairs are Chuanxiong rhizome-Angelica,Astragalus-Angelica,etc.,high-frequency pairs of external medicines are Fructus mume-Psoraleae fructus,cuscuta-Psoraleae fructus,etc.;internal and external clustering of the core drugs are Psoraleae fructus,Tribuli Fructus,Angelica,Polygonum multiflorum,Angelica dahurica,Safflower,and other high-frequency medicines.The key targets of internal patents for the treatment of vitiligo are genes such as albumin,protein kinase B1,cystatinase 3,etc.The main active ingredients of the internal grouping for the treatment of vitiligo may be quercetin,kaempferol,luteolin,etc.,and the therapeutic mechanism may be related to the end products of glycosylation/receptor for glycosylation end products,tumour necrosis factor signalling pathway,phosphatidylinositol 3-kinase/protein kinase B and other signalling pathways,and involved in the process of blood lipids and atherosclerosis,human cytomegalovirus infection.The molecular docking results confirmed the docking activity of the herbal components with key receptor proteins.Conclusion This study reveals the similarity between the internal and external patented formulas of vitiligo in terms of medication,flavour,and meridian,suggesting that the pathways and indexes such as albumin,interleukin,and tumour necrosis factor of vitiligo patients can be improved by tonifying the liver and kidney,activating blood circulation and removing blood stasis,which also provides a reference for the research and development of new medicines for vitiligo,patent protection,and the use of clinical prescriptions.
5.Clinical analysis of complete left bundle branch block after transcatheter closure of ventricular septal defect in 25 children
Bingyu MA ; Yifan LI ; Dongpo LIANG ; Ling SUN ; Xu HUANG ; Shaoying ZENG ; Shusheng WEN ; Shushui WANG ; Zhiwei ZHANG ; Yumei XIE
Chinese Journal of Applied Clinical Pediatrics 2024;39(10):743-749
Objective:To summarize the clinical treatment of complete left bundle branch block (CLBBB) after the transcatheter closure of ventricular septal defect (VSD).Methods:A case series study was conducted on the treatments and outcomes of 25 children with CLBBB after transcatheter VSD closure in Guangdong Provincial People′s Hospital from January 2010 to December 2023.Paired sample t test was used to evaluate the effect of occlude removal. Results:Among the 25 patients, 12 were males (48%), and 13 were females (52%).The age at surgery was 3.18 (2.51-3.86) years, the height before surgery was 95.0 (90.0-97.5) cm, and the weight before surgery was 13 (12-15) kg.Fourteen children were early-onset cases (≤ 1 month), while the other 11 were late-onset cases (> 1 month).The mean follow-up time was (6.63±3.93) years.Of the 14 early-onset cases, 6 children underwent occluder removal within 1 month and restored normal heart rhythm or incomplete right bundle branch block; 4 children underwent occluder removal after 1 month, of whom 2 recovered, 1 remained CLBBB, and 1 had complete atrioventricular block (CAVB); the other 4 children received drug treatment, of whom 2 had normal heart rhythm, 1 had left anterior fascicular block, and 1 died of cardiac shock and heart failure.All the 11 late-onset cases were first treated by drugs, of whom 3 recovered, and the other 8 remained CLBBB.One of the 8 cases received occluder removal at 8 months after surgery and recovered, 1 had CAVB, and the other 6 remained CLBBB.Conclusions:For patients with CLBBB after transcatheter closure of VSD, drug therapy is not always effective, and CLBBB is easy to recur.Therefore, occluder removal is recommended to be done immediately after CLBBB is discovered.Patients with persistent CLBBB should be followed up regularly, and pacemaker implantation may be performed if necessary.
6.The impact of the behavior and lifestyle of physical and mental workers on their depressive symptoms
Jianjiang ZHANG ; Shaoying WANG ; Leying LEI ; Chengwan SHEN
Chinese Journal of Industrial Hygiene and Occupational Diseases 2024;42(9):673-678
Objective:To analyze the depressive symptoms of physical and mental workers and the impact of their behavior and lifestyle on their depressive symptoms.Methods:In August 2022, a cross-sectional study design was adopted to select 553 workers as research subjects using cluster sampling. General demographic information, health-related behaviors and lifestyles were collected, and their depressive symptoms were evaluated using the Chinese version of the Patient Health Questionnaire 9 (PHQ-9). The differences in general demographic information, health-related behaviors and lifestyles between physical and mental workers were analyzed, and logistic regression was used to analyze the influencing factors of depressive symptoms in occupational populations.Results:Among the 553 subjects, 317 were physical workers (57.32%) and 236 were mental workers (42.68%). Statistically significant differences were observed between the two groups in terms of education level, monthly income, smoking rate, regular physical exercise rate and appropriate sleep time rate ( P<0.05). The score and the detection rate of depression symptoms among physical workers were (9.67±2.75) points and 20.82% (66/317), respectively, which were higher than those of mental workers [(8.34±2.18) points, 12.71% (30/236) ] ( t=6.13, χ 2=6.20, P<0.05). The results of logistic regression analysis showed that smoking, regular physical exercise, appropriate sleep time and mental work were influencing factors of depressive symptoms among the occupational population ( OR=1.592, 95% CI: 1.316-1.825; OR=0.659, 95% CI: 0.416-0.830; OR=0.502, 95% CI: 0.257-0.717; OR=0.839, 95% CI: 0.522-0.967; P<0.05) . Conclusion:The depressive symptoms of physical workers are more serious than those of mental workers. Low education level, not frequently participating in physical exercise, smoking and sleep disorder are potential risk factors that affect the depressive symptoms of the occupational population.
7.Clinical Diseases Responding Specifically to Traditional Chinese Medicine:Chronic Prostatitis
Zhan QIN ; Mei MO ; Chaoba HE ; Liguo GENG ; Bin WANG ; Jisheng WANG ; Kecheng LI ; Nianwen HUANG ; Zhiming HONG ; Shaoying YUAN ; Xiaoxiao ZHANG
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(24):152-158
Chronic prostatitis is a common and frequently occurring disease in male clinics. Due to the diverse symptoms, complex etiology, unclear mechanisms, and recurrent episodes of chronic prostatitis, Western medicine often faces the challenge of limited treatment options and unsatisfactory outcomes. In order to fully leverage the unique advantages of traditional Chinese medicine (TCM) in the treatment of chronic prostatitis, the China Association of Chinese Medicine organized a discussion among experts from the fields of TCM urology, Western urology, and related pharmacy. The experts focused on the advancements in the understanding of chronic prostatitis in modern medicine, various theories on the etiology, pathogenesis, and treatment of chronic prostatitis in TCM, entry points from interdisciplinary fields, the role and advantages of TCM in the comprehensive management of chronic prostatitis, and research into mechanisms related to chronic prostatitis. After discussions, the experts concluded that chronic prostatitis is one of the diseases where TCM has a distinct advantage. TCM can effectively improve the clinical syndromes of chronic prostatitis, including urinary issues, social psychology, organ specificity, infection, nervous system problems, pain and discomfort, sexual dysfunction, etc., and can enhance the quality of life. For patients with chronic prostatitis who cannot tolerate or may not accept the adverse effects of Western medicine, as well as for those with non-inflammatory chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS), those with pain as the primary symptom, those with urinary tract symptoms, those with coexisting anxiety and depression, and those with abnormal semen liquefaction, TCM-based treatment can be the main approach. Currently, the optimal diagnosis and treatment strategy for chronic prostatitis has not yet been established, and further research from perspectives such as clinical epidemiology, evidence-based medicine, and molecular biology is needed. Both TCM and Western medicine should integrate their respective strengths, clarify the role and advantages of TCM interventions based on mutual reference, and improve the diagnosis and treatment standards for chronic prostatitis in China.
8.Research on Multi-Hospital District Homogenization Management based on Three-Level Public Hospital Performance Appraisal System
Ning DING ; Dong XU ; Ming ZHANG ; Shaoying ZENG ; Yidan ZHANG ; Li WEI ; Wen CHEN ; Yixiang PENG
Chinese Hospital Management 2024;44(9):19-22
Objective To analyze the problems existing in the homogenization management of multi-branch hospitals based on the annual performance assessment data,and provide reference for promoting the high-quality development of public hospital branch districts.Methods Based on the Performance Assessment Operation Manual of National Tertiary Public Hospitals(2022 edition),10 indicators including the proportion of discharged patients undergoing surgery and the proportion of fourth-level surgery were screened,and the functional positioning,quality and safety,revenue and expenditure structure,and cost control of 4 hospitals of a certain medical institution from 2022 to 2023 were descriptively analyzed.Results The CMI value and the proportion of discharged surgery in the main hospital were significantly better than those in the branch hospitals,and there was no significant difference in the medical quality indicators of the four hospitals,and the operation efficiency of the branch hospital with outstanding specialty characteristics was better than that of other hospitals.Conclusion Public hospitals pay more attention to the"big specialty,small comprehensive"mode in the layout of branch districts,pay more attention to the quality control management at the specialty level in medical quality management,and strengthen the benefit analysis of different hospitals in the same specialty in operation management.
9.Research on Multi-Hospital District Homogenization Management based on Three-Level Public Hospital Performance Appraisal System
Ning DING ; Dong XU ; Ming ZHANG ; Shaoying ZENG ; Yidan ZHANG ; Li WEI ; Wen CHEN ; Yixiang PENG
Chinese Hospital Management 2024;44(9):19-22
Objective To analyze the problems existing in the homogenization management of multi-branch hospitals based on the annual performance assessment data,and provide reference for promoting the high-quality development of public hospital branch districts.Methods Based on the Performance Assessment Operation Manual of National Tertiary Public Hospitals(2022 edition),10 indicators including the proportion of discharged patients undergoing surgery and the proportion of fourth-level surgery were screened,and the functional positioning,quality and safety,revenue and expenditure structure,and cost control of 4 hospitals of a certain medical institution from 2022 to 2023 were descriptively analyzed.Results The CMI value and the proportion of discharged surgery in the main hospital were significantly better than those in the branch hospitals,and there was no significant difference in the medical quality indicators of the four hospitals,and the operation efficiency of the branch hospital with outstanding specialty characteristics was better than that of other hospitals.Conclusion Public hospitals pay more attention to the"big specialty,small comprehensive"mode in the layout of branch districts,pay more attention to the quality control management at the specialty level in medical quality management,and strengthen the benefit analysis of different hospitals in the same specialty in operation management.
10.Effect of spleen on the ability of hepatic macrophages to activate hepatic stellate cells in the progression of liver fibrosis
Shaoying ZHANG ; Dan WAN ; Xi DENG ; Xiao LIANG ; Fanfan LIANG ; Chongyu ZHANG ; Jiazhen ZHU ; Yang ZHAO ; Zongfang LI
Journal of Xi'an Jiaotong University(Medical Sciences) 2024;45(4):575-581
Objective To investigate the effect of spleen on hepatic macrophages mediated activation of hepatic stellate cells(HSCs)in mice with liver fibrosis.Methods Eighteen male C57BL/6 mice were randomly divided into three groups.Mice in Group A and Group B were injected intraperitoneally with CCl4 to establish liver fibrosis mouse model,while those in Group C were injected with corn oil as normal control.Four weeks later,mice with liver fibrosis received splenectomy(Spx)or sham operation(Sham),respectively.After continuous injection for 2 weeks,liver homogenates(L-Homo)were prepared and liver cells were isolated from the three groups.Expressions of IL-1β,IL-13,TGF-β,TNF-α,PDGF-β and VEGF in the liver homogenates of the three groups were detected by Luminex multifactor analysis.The expressions of these cytokines in liver macrophages(L-Mψ)and other non-parenchymal cells of Sham and Spx mice were analyzed by Real-time quantitative PCR(RT-qPCR)and flow cytometry.Macrophage cell line RAW264.7 or bone marrow-derived macrophages(BMDMs)were treated with liver homogenates from the Sham and Spx groups.Then the differently treated RAW264.7 cells were analyzed for mRNA expressions of cytokines and glutamine metabolism-related molecules by RT-qPCR,or transwell co-cultured with hepatic stellate cell line JS1.After co-culture,the survival and extracellular matrix expression of JS1 cells were analyzed.For comparison,Student's t test(between two groups)or one-way analysis of variance(among multiple groups)were used.Results Compared with normal control group,the concentrations of IL-1β,IL-13,TGF-β and TNF-α in the L-Homo of model group were significantly increased and showed higher levels in Sham group than in Spx group.Moreover,the hepatic macrophages were indicated as the major source of these cytokines.Consistently,macrophages treated with liver homogenate of Sham mice had increased expressions of IL-1β,TGF-β and TNF-α and glutaminase(GLS).After co-culture with macrophages treated with liver homogenate of Sham group rather than Spx group,JS1 expressed higher expressions of α-SMA and collagens.Conclusion The spleen is involved in regulating the secretion of cytokines by hepatic macrophages and enhancing their ability to activate hepatic stellate cells.

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