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.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):1800-1809
Current experimental and computational methods have limitations in accurately and efficiently classi-fying 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 con-taining 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.
3.DHLX studied correlation between regulation of biliary flora and inflammatory factors on gallbladder stone formation
Yirong GAN ; Yuan YU ; Jinmei CHEN ; Chengji LI ; Wen YANG ; Jiaoan PANG ; Chunli LIU ; Lijun XIAO ; Jinhao TENG
Chinese Journal of Immunology 2025;41(3):644-649
Objective:By sequencing and analyzing the biliary flora by 16S rDNA high-throughput sequencing technology,to identify the main flora associated with gallbladder stone formation and the main flora regulated by the Dahuang lingxian(DHLX),pre-liminary investigation the effect of DHLX on the biliary flora.Methods:The 50 male guinea pigs were randomly divided into Normal group,Model group,DHLX group.There were 15 guinea pigs in the normal group and 20 guinea pigs in the DHLX group,and 20 guin-ea pigs in the model group:the guinea pig model of gallstone was replicated with high-fat lithogenic diet,which was simultaneously ad-ministrated by gavage.After continuous intervention for 8 weeks,bile and gallbladder tissue samples were collected,and the gallstone formation rate of guinea pigs in each group was calculated,the pathological morphological changes of gallbladder tissue were detected by HE,T-CHO,TBA,LPS,IL-6,TNF-α were detected by ELISA,and the changes of biliary flora were detected by 16S rDNA;the correlation between biliary flora and bile index was detected by Pearson statistical method.Results:The stone formation rate of guinea pigs in the normal group was 8.3%,the rate of model stone composition was 90.8%,and the stone composition rate of DHLX group was 36.4%,and the HE staining results showed that compared with the normal group,the mucous membrane of the guinea pig in the model group was thickened,the columnar epithelial cells were arranged in a large number of inflammatory cells,and the columnar epi-thelial cells of the gallbladder mucosa in the chinese medicine group were arranged neatly compared with the model group,the thick-ness of the mucosa was reduced compared with the model group,and some inflammatory cells were infiltrated;ELISA results showed that compared with the normal group,the expressions of T-CHO,LPS,IL-6 and TNF-α in the bile of guinea pigs in the model group were significantly increased(P<0.01),while the content of TBA was significantly reduced(P<0.01);compared with the model group,the expression of LPS and IL-6 in the bile of the DHLX group were significantly reduced(P<0.01).The results of 16S rDNA showed that compared with the normal group the Ace index and Chao1 index of the model group were significantly reduced(P<0.01),and the Chao1 index of the DHLX group was significantly higher than that of the model group(P<0.05);biliary flora at the genera level was mainly composed of Burkholderia,Sphingomycetes,Breghamus,Delfortella,Pseudomonas;correlation analysis showed that total cholesterol was negatively correlated with the abundance of Methyloversatilis(P<0.05),and total bile acids were positively corre-lated with the abundance of Burkholderia(P<0.05),and Pseudomonas erythrocytes,Rhizobia,the abundance of Phreatobacter was negatively correlated(P<0.01)and LPS was positively correlated with the abundance of Pseudomonas erythrocytes(P<0.01).Conclu-sion:Biliary microflora disorder exists in the formation of biliary stones,and biliary microflora may participate in the formation of stones by regulating cholesterol,bile acids and LPS.DHLX can regulate the changes in the abundance of the microflora,make the structure of the microflora become normal,reduce the inflammation of the gallbladder,and prevent the formation of gallstones.
4.Analysis of the infection status and clinical parameters of metapneumovirus in 2669 children with respiratory tract infections in Jianyang area
Ziyi ZHU ; Yulong LI ; Xiaoyue YANG ; La HE ; Chengji JI
Chinese Journal of Clinical Laboratory Science 2025;43(3):222-226
Objective To investigate the infection status and clinical parameters of human metapneumovirus(HMPV)in children with acute respiratory tract infections in Jianyang area.Methods A total of 2 669 hospitalized children with acute respiratory tract infec-tions at Jianyang People's Hospital from March 2023 to February 2024 were enrolled.Thirteen kinds of respiratory pathogens were de-tected using multiplex PCR and capillary electrophoresis.The clinical data of HMPV-infected children were collected and analyzed.Re-sults Out of 2 669 children with acute respiratory tract infections,209 were detected with HMPV,with a positive rate of 7.83%.HMPV-positive children were mainly concentrated in under 5 years old(73.21%),with cough,fever,wheezing,and shortness of breath as main clinical manifestations.The rate of single HMPV infection was 58.85%,and those of mixed bacterial infection and mixed viral infection were 26.69% and 13.88%,respectively.The levels of white blood cells(WBC),lymphocytes(LYM),platelets(PLT),C-reactive protein(CRP),alanine aminotransferase(ALT),aspartate aminotransferase(AST),lactate dehydrogenase(LDH),troponin I(cTn I),and procalcitonin(PCT)in the mixed infection group were significantly higher than those in the single HMPV infection group(P<0.05),while the levels of hemoglobin(Hb),total protein(TP),and creatinine(Cr)were significantly lower than those in the single HMPV infection group(P<0.05).Compared with the non-severe pneumonia group,the levels of WBC,Hb,PLT,and CRP in the severe pneumonia group were significantly increased(P<0.05).Multivariate Logistic regression analysis showed that age<3 years,co-infection,and CRP≥20 mg/L were risk factors for severe HMPV pneumonia(P<0.05).Conclusion HMPV is one of the important pathogens causing acute respiratory tract infections in children in Jianyang area.The elevated levels of some laboratory indicators are associated with the severity of infection.Early and comprehensive bacteriological testing and detection of inflammatory markers are beneficial for guiding clinical treatment.
5.Study on the correlation between gait disorder characteristics and serum uric acid levels in cerebral small vessel disease based on three-dimensional gait analysis
Yingying ZHENG ; Yuxuan LI ; Lingmin WANG ; Xingchen LIU ; Lu CHEN ; Chengji LIU ; Nan YANG
Chinese Journal of Nervous and Mental Diseases 2025;51(4):218-224
Objective The relationship between serum uric acid(UA)levels and gait kinematics characteristics in patients with cerebral small vessel disease(CSVD)was investigated.Methods Retrospective analysis was conducted on patients with CSVD from outparient clinics of the Neurology and Rehabilitation Department of Zhongshan Hospital affiliated with Guangzhou University of Chinese Medicine from January 2023 to December 2023.The general information of patients were collected and the gait of patients was analyzed using three-dimensional gait analysis.Patients were then divided into mild gait disorder group(0-1 points),moderate gait disorder group(2-3 points),and severe gait dysfunction group(4-5 points)based on gait results.The total burden of CSVD imaging and serum results such as UA were collected.The relationship between UA level and CSVD gait disorders was analyzed.Results This study recruited 105 CSVD patients.Patients were divided into different groups based on the severity of their gait disorder including 40 in the mild group,49 in the moderate group,and 16 in the severe group.The blood uric acid level in the moderate group(358.43±13.44)μmol/L was higher than that in the mild group(336.00±12.48)μmol/L,and the blood uric acid level in the severe group(289.94±11.88)μmol/L was lower than that in the mild and moderate groups(P<0.05).The MoCA score in the severe gait disorder group(21.38±0.13)was lower than that in the mild and moderate groups(28.05±0.09 vs.25.22±0.10)(P<0.05).The step width of the CSVD severe load group was(13.26±2.80)cm compared to the light and moderate load groups[(11.22±1.70)cm vs.(11.65±2.70)cm]increased(P<0.05),and the left swing phase in the severe group(35.90%)decreased compared to the mild and moderate groups(38.50%vs.37.20%)(P<0.05).Spearman correlation analysis showed a negative correlation between UA levels and CMB(r=-0.20,P=0.04).Hyperuricemia was negatively correlated with brain atrophy(r=-0.20,P=0.04).In patients with mild to moderate gait disorders,there was a positive correlation between hyperuricemia and the total burden of gait disorders(r=0.25,P=0.02),and hyperuricemia and right gait speed(r=-0.22,P=0.04),Right stride(r=-0.29,P<0.01),Left step speed(r=-0.32,P<0.01),Left step frequency(r=-0.29,P<0.01),The left stride was negatively correlated(r=-0.26,P=0.01).Conclusion In CSVD patients with mild to moderate gait disorders,the levels of uric acid and hyperuricemia are positively correlated with the total burden of gait disorders.The gait disorders are mainly characterized by reduced bilateral pace,bilateral stride,and left step frequency.
6.DHLX studied correlation between regulation of biliary flora and inflammatory factors on gallbladder stone formation
Yirong GAN ; Yuan YU ; Jinmei CHEN ; Chengji LI ; Wen YANG ; Jiaoan PANG ; Chunli LIU ; Lijun XIAO ; Jinhao TENG
Chinese Journal of Immunology 2025;41(3):644-649
Objective:By sequencing and analyzing the biliary flora by 16S rDNA high-throughput sequencing technology,to identify the main flora associated with gallbladder stone formation and the main flora regulated by the Dahuang lingxian(DHLX),pre-liminary investigation the effect of DHLX on the biliary flora.Methods:The 50 male guinea pigs were randomly divided into Normal group,Model group,DHLX group.There were 15 guinea pigs in the normal group and 20 guinea pigs in the DHLX group,and 20 guin-ea pigs in the model group:the guinea pig model of gallstone was replicated with high-fat lithogenic diet,which was simultaneously ad-ministrated by gavage.After continuous intervention for 8 weeks,bile and gallbladder tissue samples were collected,and the gallstone formation rate of guinea pigs in each group was calculated,the pathological morphological changes of gallbladder tissue were detected by HE,T-CHO,TBA,LPS,IL-6,TNF-α were detected by ELISA,and the changes of biliary flora were detected by 16S rDNA;the correlation between biliary flora and bile index was detected by Pearson statistical method.Results:The stone formation rate of guinea pigs in the normal group was 8.3%,the rate of model stone composition was 90.8%,and the stone composition rate of DHLX group was 36.4%,and the HE staining results showed that compared with the normal group,the mucous membrane of the guinea pig in the model group was thickened,the columnar epithelial cells were arranged in a large number of inflammatory cells,and the columnar epi-thelial cells of the gallbladder mucosa in the chinese medicine group were arranged neatly compared with the model group,the thick-ness of the mucosa was reduced compared with the model group,and some inflammatory cells were infiltrated;ELISA results showed that compared with the normal group,the expressions of T-CHO,LPS,IL-6 and TNF-α in the bile of guinea pigs in the model group were significantly increased(P<0.01),while the content of TBA was significantly reduced(P<0.01);compared with the model group,the expression of LPS and IL-6 in the bile of the DHLX group were significantly reduced(P<0.01).The results of 16S rDNA showed that compared with the normal group the Ace index and Chao1 index of the model group were significantly reduced(P<0.01),and the Chao1 index of the DHLX group was significantly higher than that of the model group(P<0.05);biliary flora at the genera level was mainly composed of Burkholderia,Sphingomycetes,Breghamus,Delfortella,Pseudomonas;correlation analysis showed that total cholesterol was negatively correlated with the abundance of Methyloversatilis(P<0.05),and total bile acids were positively corre-lated with the abundance of Burkholderia(P<0.05),and Pseudomonas erythrocytes,Rhizobia,the abundance of Phreatobacter was negatively correlated(P<0.01)and LPS was positively correlated with the abundance of Pseudomonas erythrocytes(P<0.01).Conclu-sion:Biliary microflora disorder exists in the formation of biliary stones,and biliary microflora may participate in the formation of stones by regulating cholesterol,bile acids and LPS.DHLX can regulate the changes in the abundance of the microflora,make the structure of the microflora become normal,reduce the inflammation of the gallbladder,and prevent the formation of gallstones.
7.Analysis of the infection status and clinical parameters of metapneumovirus in 2669 children with respiratory tract infections in Jianyang area
Ziyi ZHU ; Yulong LI ; Xiaoyue YANG ; La HE ; Chengji JI
Chinese Journal of Clinical Laboratory Science 2025;43(3):222-226
Objective To investigate the infection status and clinical parameters of human metapneumovirus(HMPV)in children with acute respiratory tract infections in Jianyang area.Methods A total of 2 669 hospitalized children with acute respiratory tract infec-tions at Jianyang People's Hospital from March 2023 to February 2024 were enrolled.Thirteen kinds of respiratory pathogens were de-tected using multiplex PCR and capillary electrophoresis.The clinical data of HMPV-infected children were collected and analyzed.Re-sults Out of 2 669 children with acute respiratory tract infections,209 were detected with HMPV,with a positive rate of 7.83%.HMPV-positive children were mainly concentrated in under 5 years old(73.21%),with cough,fever,wheezing,and shortness of breath as main clinical manifestations.The rate of single HMPV infection was 58.85%,and those of mixed bacterial infection and mixed viral infection were 26.69% and 13.88%,respectively.The levels of white blood cells(WBC),lymphocytes(LYM),platelets(PLT),C-reactive protein(CRP),alanine aminotransferase(ALT),aspartate aminotransferase(AST),lactate dehydrogenase(LDH),troponin I(cTn I),and procalcitonin(PCT)in the mixed infection group were significantly higher than those in the single HMPV infection group(P<0.05),while the levels of hemoglobin(Hb),total protein(TP),and creatinine(Cr)were significantly lower than those in the single HMPV infection group(P<0.05).Compared with the non-severe pneumonia group,the levels of WBC,Hb,PLT,and CRP in the severe pneumonia group were significantly increased(P<0.05).Multivariate Logistic regression analysis showed that age<3 years,co-infection,and CRP≥20 mg/L were risk factors for severe HMPV pneumonia(P<0.05).Conclusion HMPV is one of the important pathogens causing acute respiratory tract infections in children in Jianyang area.The elevated levels of some laboratory indicators are associated with the severity of infection.Early and comprehensive bacteriological testing and detection of inflammatory markers are beneficial for guiding clinical treatment.
8.Study on the correlation between gait disorder characteristics and serum uric acid levels in cerebral small vessel disease based on three-dimensional gait analysis
Yingying ZHENG ; Yuxuan LI ; Lingmin WANG ; Xingchen LIU ; Lu CHEN ; Chengji LIU ; Nan YANG
Chinese Journal of Nervous and Mental Diseases 2025;51(4):218-224
Objective The relationship between serum uric acid(UA)levels and gait kinematics characteristics in patients with cerebral small vessel disease(CSVD)was investigated.Methods Retrospective analysis was conducted on patients with CSVD from outparient clinics of the Neurology and Rehabilitation Department of Zhongshan Hospital affiliated with Guangzhou University of Chinese Medicine from January 2023 to December 2023.The general information of patients were collected and the gait of patients was analyzed using three-dimensional gait analysis.Patients were then divided into mild gait disorder group(0-1 points),moderate gait disorder group(2-3 points),and severe gait dysfunction group(4-5 points)based on gait results.The total burden of CSVD imaging and serum results such as UA were collected.The relationship between UA level and CSVD gait disorders was analyzed.Results This study recruited 105 CSVD patients.Patients were divided into different groups based on the severity of their gait disorder including 40 in the mild group,49 in the moderate group,and 16 in the severe group.The blood uric acid level in the moderate group(358.43±13.44)μmol/L was higher than that in the mild group(336.00±12.48)μmol/L,and the blood uric acid level in the severe group(289.94±11.88)μmol/L was lower than that in the mild and moderate groups(P<0.05).The MoCA score in the severe gait disorder group(21.38±0.13)was lower than that in the mild and moderate groups(28.05±0.09 vs.25.22±0.10)(P<0.05).The step width of the CSVD severe load group was(13.26±2.80)cm compared to the light and moderate load groups[(11.22±1.70)cm vs.(11.65±2.70)cm]increased(P<0.05),and the left swing phase in the severe group(35.90%)decreased compared to the mild and moderate groups(38.50%vs.37.20%)(P<0.05).Spearman correlation analysis showed a negative correlation between UA levels and CMB(r=-0.20,P=0.04).Hyperuricemia was negatively correlated with brain atrophy(r=-0.20,P=0.04).In patients with mild to moderate gait disorders,there was a positive correlation between hyperuricemia and the total burden of gait disorders(r=0.25,P=0.02),and hyperuricemia and right gait speed(r=-0.22,P=0.04),Right stride(r=-0.29,P<0.01),Left step speed(r=-0.32,P<0.01),Left step frequency(r=-0.29,P<0.01),The left stride was negatively correlated(r=-0.26,P=0.01).Conclusion In CSVD patients with mild to moderate gait disorders,the levels of uric acid and hyperuricemia are positively correlated with the total burden of gait disorders.The gait disorders are mainly characterized by reduced bilateral pace,bilateral stride,and left step frequency.
9.Construction of Dmd Gene Mutant Mice and Phenotype Verification in Muscle and Immune Systems
Min LIANG ; Yang GUO ; Jinjin WANG ; Mengyan ZHU ; Jun CHI ; Yanjuan CHEN ; Chengji WANG ; Zhilan YU ; Ruling SHEN
Laboratory Animal and Comparative Medicine 2024;44(1):42-51
Objective The aim is to utilize CRISPR/Cas9 gene editing technology to construct Dmd gene mutant mice with a point mutation in exon 23 of the Dmd gene. Subsequently, the phenotypic changes of the mice in muscles and immune systems are analyzed and verified, providing an evaluation model for Duchenne muscular dystrophy and other related diseases.MethodsBased on the sequence characteristics of exon 23 of the Dmd gene, small guide RNA (sgRNA) was designed and synthesized. Cas9 mRNA, sgRNA fragments, and oligo donor DNA were microinjected into fertilized eggs of C57BL/6J mice. After transferring the fertilized eggs to surrogate mice, F0 generation mice were born. After mating with F0 generation mice, offspring mice were obtained, and Dmd gene positive mutant (DmdMu/+) mice were obtained after genotype identification. Male hemizygous DmdMu/+(DmdMu/Y) mice were selected for phenotype validation. The body weight of live 3- and 9-month-old mice were recorded. Muscle tension was evaluated through the grid test. Hearts and semitendinosus muscles were collected, and the histopathological changes were observed using HE staining. Further, the expression of Dmd protein in muscle tissue of 9-month-old mice was analyzed by Western blotting.An acute inflammation model was established in DmdMu/Y mice using lipopolysaccharide induction. Peripheral blood from the submandibular vein was collected, and the changes in the proportion of neutrophils and monocytes were detected by flow cytometry.Results The results of genome sequencing and Western blotting confirmed the successful construction of Dmd gene point mutant mice (DmdMu/+ mice). Dmd protein expression was not detected in skeletal muscle and myocardium of DmdMu/+ mice, and it was significantly reduced compared to wild-type C57BL/6J mice (P<0.05). Compared with wild-type mice of the same background, DmdMu/Y mice at 3 and 9 months of age showed significant weight loss (P<0.01) and decreased muscle tension (P<0.05). 9-month-old DmdMu/Y mice exhibited significant pathological changes in skeletal muscle and myocardium, including widening of intermuscular space. Under normal condition, compared with wild-type mice, the proportion of neutrophils and monocytes in the peripheral blood of 3-month-old DmdMu/Y mice was significantly lower than that of wild-type mice (P<0.01). After lipopolysaccharide stimulation, the proportion of neutrophils in peripheral blood of 3-month-old DmdMu/Y mice remained significantly lower compared to that of wild-type mice (P<0.01). The proportion of neutrophils in peripheral blood of 9-month-old DmdMu/Y mice significantly decreased after lipopolysaccharide induction (P<0.01), with a trend of change observed in monocytes between groups.Conclusion The successful construction of the Dmd gene mutant mouse model has confirmed the vital function of Dmd gene in maintaining normal muscle tissue morphology and muscle tone. It preliminarily indicated that Dmd gene deletion could significantly reduce the proportion of neutrophils in peripheral blood, offering a new perspective for the study of immune system alterations in Duchenne muscular dystrophy patients.
10.A national multi-center prospective study on the perioperative practice of enhanced recovery after surgery for choledochal cysts in children
Ming YUE ; Jiexiong FENG ; Yan′an LI ; Yuanmei LIU ; Zhigang GAO ; Qi CHEN ; Hongwei XI ; Qiang YIN ; Chengji ZHAO ; Yuzuo BAI ; Wanfu LI ; Libin ZHU ; Weibing TANG ; Hongqiang BIAN ; Huizhong NIU ; Zhiheng GUO ; Heying YANG
Chinese Journal of General Surgery 2024;39(11):827-832
Objective:To evaluate the safety and efficacy of enhanced recovery after surgery(ERAS) in the perioperative period of congenital choledochal cysts in children.Methods:This is a multicenter prospective randomized controlled study. The clinical data of 273 pediatric congenital choledochal cysts(CCC) patients who underwent surgery at 14 medical centers with complete follow-up data were collected through the medical data analysis platform. Among them, 123 cases in ERAS group were managed perioperatively in strict accordance with ERAS mode, and 150 cases in conventional group were managed according to traditional mode. The length of hospital stay,time to first farting, time to complete feeding, the incidence of complications, cost and readmission rate within 30 days,stress indexes and liver function were compared between the two groups.Results:Compared with the conventional group, median time to start farting (2.0 d vs. 3.0 d, P<0.001), median time to complete feeding (5.0 d vs. 7.0 d, P<0.001), median postoperative hospitalization time (6.0 d vs. 9.0 d, P<0.001),the median total length of stay(13.0 d vs. 15.0 d, P<0.001) were shorter,the median hospitalization cost (37,000 yuan vs.43,000 yuan P<0.001) was lower, and stress indexes recovered quickly. The incidence of postoperative hospital stay and readimission rate within 30 d were not statistically different between the two groups. Conclusion:It is safe and feasible to implement ERAS for children with CCC in the perioperative period, which can reduce stress response, speed up recovery,and save medical costs.

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