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):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.
2.Feasibility and exploration of optimal communication models for robot-assisted urological telesurgery: a multicenter, single-arm, retrospective study
Ye WANG ; Taoping SHI ; Sheng TAI ; Sunyi YE ; Yubai ZHANG ; Bingzhang QIAO ; Chenfeng WANG ; Gen CHENG ; Zhi LI ; Qing AI ; Qingbo HUANG ; Baojun WANG ; Qing YUAN ; Junnan XU ; Guojun LIU ; Yu CHEN ; Wuyi ZHAO ; Jianle MAO ; Shiwei LI ; Shuo WANG ; Dan XIA ; Wanhai XU ; Chaozhao LIANG ; Hongzhao LI ; Xin MA ; Xu ZHANG
Chinese Journal of Urology 2025;46(5):331-336
Objective:To evaluate the efficacy and feasibility of a domestically developed robotic surgical system based on fiber-optic dedicated line communication in cross-regional urological telesurgery.Methods:This was multicenter,single-arm,retrospective case series study. The data of patients who underwent urological telesurgeries using the telesurgical system between January 2023 and December 2024 were analyzed. The cohort included 59 patients from seven hospitals across China. Among the patients,47 were male(79.7%)and 12 were female(20.3%),with a median age of 63.0(56.0,68.0)years and a body mass index of(24.7 ± 3.0)kg/m 2. Surgical procedures included 32 radical prostatectomies,24 partial nephrectomies,one radical nephrectomy,one adrenalectomy,and one ureteral reconstruction. The perioperative indicators,pathological results and postoperative complications were analyzed. The network monitoring data were collected,and the perioperative data of patients,remote system monitoring data and costs were compared between the two communication modes of optical transport network(OTN)and cloud-connect network(CCN). Results:All 59 remote surgeries were successfully completed,with a mean operative time of(138.0 ± 54.0)minutes,median intraoperative blood loss of 50.0(30.0,100.0)ml and a postoperative hospital stay of 5.0(4.0,6.0)days. No cases required reoperation,Clavien-Dindo grade ≥3 complications,or readmission. The geographical distance between the primary and remote surgical sites ranged from 450 to 2 800 km. Network monitoring revealed increased bidirectional latency with distance increasing:the shortest latency time(Hefei-Hangzhou,450 km)was(16.59 ± 0.80)ms,while the longest(Harbin-Hangzhou,2 200 km)latency time was(53.31 ± 0.31)ms. Average frame loss per procedure was 0?1.27 frames. The results of subgroup analysis comparing OTN and CCN communication modes showed no significant differences in operative time[(130.7 ± 70.5)minutes vs.(142.1 ± 42.9)minutes, P = 0.442],postoperative hospitalization[6.0(4.0,8.0)d vs. 5.0(4.0,6.0)d, P = 0.581],or readmission rates(0 vs. 0). However,CCN demonstrated significant cost advantages with 500 RMB per operation vs. 3 000 RMB per operation for OTN. Conclusions:Urological telesurgery using fiber-optic communication is feasible. The CCN mode,with its cost-effectiveness,excellent usability,and multi-point interconnection flexibility,is currently the preferred communication model for telesurgical applications.
3.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.
4.Feasibility and exploration of optimal communication models for robot-assisted urological telesurgery: a multicenter, single-arm, retrospective study
Ye WANG ; Taoping SHI ; Sheng TAI ; Sunyi YE ; Yubai ZHANG ; Bingzhang QIAO ; Chenfeng WANG ; Gen CHENG ; Zhi LI ; Qing AI ; Qingbo HUANG ; Baojun WANG ; Qing YUAN ; Junnan XU ; Guojun LIU ; Yu CHEN ; Wuyi ZHAO ; Jianle MAO ; Shiwei LI ; Shuo WANG ; Dan XIA ; Wanhai XU ; Chaozhao LIANG ; Hongzhao LI ; Xin MA ; Xu ZHANG
Chinese Journal of Urology 2025;46(5):331-336
Objective:To evaluate the efficacy and feasibility of a domestically developed robotic surgical system based on fiber-optic dedicated line communication in cross-regional urological telesurgery.Methods:This was multicenter,single-arm,retrospective case series study. The data of patients who underwent urological telesurgeries using the telesurgical system between January 2023 and December 2024 were analyzed. The cohort included 59 patients from seven hospitals across China. Among the patients,47 were male(79.7%)and 12 were female(20.3%),with a median age of 63.0(56.0,68.0)years and a body mass index of(24.7 ± 3.0)kg/m 2. Surgical procedures included 32 radical prostatectomies,24 partial nephrectomies,one radical nephrectomy,one adrenalectomy,and one ureteral reconstruction. The perioperative indicators,pathological results and postoperative complications were analyzed. The network monitoring data were collected,and the perioperative data of patients,remote system monitoring data and costs were compared between the two communication modes of optical transport network(OTN)and cloud-connect network(CCN). Results:All 59 remote surgeries were successfully completed,with a mean operative time of(138.0 ± 54.0)minutes,median intraoperative blood loss of 50.0(30.0,100.0)ml and a postoperative hospital stay of 5.0(4.0,6.0)days. No cases required reoperation,Clavien-Dindo grade ≥3 complications,or readmission. The geographical distance between the primary and remote surgical sites ranged from 450 to 2 800 km. Network monitoring revealed increased bidirectional latency with distance increasing:the shortest latency time(Hefei-Hangzhou,450 km)was(16.59 ± 0.80)ms,while the longest(Harbin-Hangzhou,2 200 km)latency time was(53.31 ± 0.31)ms. Average frame loss per procedure was 0?1.27 frames. The results of subgroup analysis comparing OTN and CCN communication modes showed no significant differences in operative time[(130.7 ± 70.5)minutes vs.(142.1 ± 42.9)minutes, P = 0.442],postoperative hospitalization[6.0(4.0,8.0)d vs. 5.0(4.0,6.0)d, P = 0.581],or readmission rates(0 vs. 0). However,CCN demonstrated significant cost advantages with 500 RMB per operation vs. 3 000 RMB per operation for OTN. Conclusions:Urological telesurgery using fiber-optic communication is feasible. The CCN mode,with its cost-effectiveness,excellent usability,and multi-point interconnection flexibility,is currently the preferred communication model for telesurgical applications.
6.Predictive value of cerebroplacental ratio for perinatal outcomes of induction of labor in prolonged pregnancy
Jianlin ZHAO ; E GONG ; Haijun SHI ; Lan ZHANG ; Xing WANG ; Hongli LIU ; Jie GAN ; Chiying CAO ; Shuai HUANG ; Junnan LI ; Hongbo QI
Chinese Journal of Perinatal Medicine 2021;24(3):209-213
Objective:To investigate the predictive value of cerebroplacental ratio (CPR) for adverse perinatal outcomes of induction of labor in prolonged pregnancy.Methods:This retrospective study recruited 315 singleton pregnant women who had induced labor due to prolonged pregnancy (≥41 gestational weeks) in the First Affiliated Hospital of Chongqing Medical University from January 1, 2019 to April 30, 2020. Based on the occurrence of adverse perinatal outcomes (emergency delivery due to persistent abnormal fetal heart rate monitoring, umbilical artery blood pH at birth <7.2, 5 min Apgar scores<7, transferring to neonatal intensive care unit after birth, chorioamnionitis and vaginal delivery converted to cesarean section), they were divided into two groups: case group ( n=76) and normal group ( n=239). Clinical features and umbilical artery blood flow, middle cerebral artery (MCA) flow and CPR measured in the last ultrasound scan before induction were compared between the two groups using student's t-test, Mann-Whitney U test and Chi-square test. Receiver operating characteristic (ROC) curve was used to analyze the predictive values of umbilical artery blood flow, MCA flow and CPR for the adverse perinatal outcomes. Multivariate logistic regression analysis was used to screen the meaningful predictors. Results:Compared with the normal group, the umbilical artery pulsatility index (PI) (0.9±0.1 vs 0.8±0.1, t=-5.458, P<0.001) and the percentage of abnormal CPR (<1.0) increased significantly [21.1%(16/76) vs 6.3%(15/239), χ2=14.190, P<0.001] in the case group, while the MCA-PI and CPR decreased significantly (1.1±0.2 vs 1.3±0.3, t=5.658, P<0.001; 1.2±0.3 vs 1.6±0.5, t=8.940, P<0.001). The areas under the ROC curves of umbilical artery PI, MCA-PI and CPR for predicting adverse perinatal outcomes were 0.71, 0.71 and 0.77, respectively. CPR had the highest sensitivity (0.74) compared with umbilical artery PI (0.68) and MCA-PI (0.71), but the specificity of them were similar (0.67, 0.66 and 0.66). Multivariate logistic regression analysis showed that only CPR was the independent risk factor for adverse perinatal outcomes ( OR=0.028, 95% CI: 0.010-0.080, P<0.001). Conclusions:As an indicator for early prediction of adverse perinatal outcomes of induction of labor in prolonged pregnancy, CPR was more sensitive but less specific.
7.Preliminary results of multicenter studies on ABO-incompatible kidney transplantation
Hongtao JIANG ; Tao LI ; Kun REN ; Xiaohua YU ; Yi WANG ; Shanbin ZHANG ; Desheng LI ; Huiling GAN ; Houqin LIU ; Liang XU ; Zhigang LUO ; Peigen GUI ; Xiangfang TAN ; Bingyi SHI ; Ming CAI ; Xiang LI ; Junnan XU ; Liang XU ; Tao LIN ; Xianding WANG ; Hongtao LIU ; Lexi ZHANG ; Jianyong WU ; Wenhua LEI ; Jiang QIU ; Guodong CHEN ; Jun LI ; Gang HUANG ; Chenglin WU ; Changxi WANG ; Lizhong CHEN ; Zheng CHEN ; Jiali FANG ; Xiaoming ZHANG ; Tongyi MEN ; Xianduo LI ; Chunbo MO ; Zhen WANG ; Xiaofeng SHI ; Guanghui PEI ; Jinpeng TU ; Xiaopeng HU ; Xiaodong ZHANG ; Ning LI ; Shaohua SHI ; Hua CHEN ; Zhenxing WANG ; Weiguo SUI ; Ying LI ; Qiang YAN ; Huaizhou CHEN ; Liusheng LAI ; Jinfeng LI ; Wenjun SHANG ; Guiwen FENG ; Gang CHEN ; Fanjun ZENG ; Lan ZHU ; Jun FANG ; Ruiming RONG ; Xuanchuan WANG ; Guisheng QI ; Qiang WANG ; Puxun TIAN ; Yang LI ; Xiaohui TIAN ; Heli XIANG ; Xiaoming PAN ; Xiaoming DING ; Wujun XUE ; Jiqiu WEN ; Xiaosong XU
Chinese Journal of Organ Transplantation 2020;41(5):259-264
Objective:To summarize the patient profiles and therapeutic efficacies of ABO-incompatible living-related kidney transplantations at 19 domestic transplant centers and provide rationales for clinical application of ABOi-KT.Methods:Clinical cases of ABO-incompatible/compatible kidney transplantation (ABOi-KT/ABOc-KT) from December 2006 to December 2009 were collected. Then, statistical analyses were conducted from the aspects of tissue matching, perioperative managements, complications and survival rates of renal allograft or recipients.Results:Clinical data of 342 ABOi-KT and 779 ABOc-KT indicated that (1) no inter-group differences existed in age, body mass index (BMI), donor-recipient relationship or waiting time of pre-operative dialysis; (2) ABO blood type: blood type O recipients had the longest waiting list and transplantations from blood type A to blood type O accounted for the largest proportion; (3) HLA matching: no statistical significance existed in mismatch rate or positive rate of PRA I/II between two types of surgery; (4) CD20 should be properly used on the basis of different phrases; (5) hemorrhage was a common complication during an early postoperative period and microthrombosis appeared later; (6) no difference existed in postoperative incidence of complications or survival rate of renal allograft and recipients at 1/3/5/10 years between ABOi-KT and ABOc-KT. The acute rejection rate and serum creatinine levels of ABOi-KT recipients were comparable to those of ABOc-KT recipients within 1 year.Conclusions:ABOi-KT is both safe and effective so that it may be applied at all transplant centers as needed.
8.Application of intravascular ultrasound in analysis on influencing factors of prognosis in patients with different coronary artery in-stent restenosis
Yan CUI ; Yongfeng SHI ; Ziyuan GUO ; Bin LIU ; Jinpeng WANG ; Lei ZHAO ; Junnan WANG ; Jinhua PIAO
Journal of Jilin University(Medicine Edition) 2016;42(4):746-752
Objective:To collect the imaging data and related materials of the patients with in-stent restenosis (ISR)after coronary artery stent operation with intravascular ultrasound (IVUS),and to analyze the risk factors of ISR,and to propose the reasonable intervention strategies.Methods:Fifty patients with ISR were divided into ISR ≤ 50% drug group (n = 14 )and ISR > 50% drug group (n = 36),including drug-coated balloon therapy group (n=16)and stent treatment group (n=20);IVUS virtual organization technology was used to compare the plaque area,location,tissue composition,thrombus and other factors of the patients in various groups after treatment;the data changes after 6 months of follow-up were analyzed.Results:The IVUS results showed the plaque areas and plaque loads of the ISR patients treated with intervention were significantly reduced compared with before operation (P <0.05);the plaque compression degree of the patients in drug-coated balloon therapy group was lower than that in stent treatment group (P <0.05),but the differences were not found between drug-coated balloon therapy group and stent treatment group in fibrous tissue components and calcified tissue proportion (P >0.05).Conclusion:The ISR rate is higher in the patients with high degree of fiber components,plaque composition heterogeneity and distribution of diffuse tortuous and calcified lesions.ISR has no significant correlation with the plaque wall thickness and lipid content and plaque instability and necrotic tissue proportion.
9.Intraoperative autologous based blood conservation strategies in mitral valve replacement.
Linfeng QIAN ; Junnan ZHENG ; Liangwei CHEN ; Jianjie JIANG ; Yinglian CHEN ; Liping SHI ; Haige ZHAO ; Yiming NI
Chinese Journal of Surgery 2016;54(2):125-128
OBJECTIVETo evaluate whether intraoperative autologous donation (IAD) can reduce perioperative blood transfusion for patients underwent mitral valve replacement (MVR).
METHODSA total of 318 patients received implementation of IAD from January 2011 to December 2013 were analyzed retrospectively, and compared with 517 patients of the previous 36-month period (from January 2008 to December 2012). The method of small-volume retrograde autologous priming, strict blood transfusion standard along with IAD together constituted a progressive blood-saving strategy. Statistical methods including Students' t-test, Pearson's χ(2) test, Kruskal-Wallis analysis and multivariate Logistic regression model were used for comparisons of the data.
RESULTSThere were no significant difference between IAD group and non-IAD group considering preoperative patient demographics, characteristics and preoperative comorbidities. However, IAD group significantly reduced number of patients transfused with intra/post-operative packed red-blood cell (PRBC) (55(17.0%) vs. 215 (42.1%), χ(2)=53.0, P=0.000), and had significantly reduced postoperative chest tube output (150(380) ml vs. 700(660) ml, H=195.648, P=0.000), length of stay ((16±6) d vs. (20±8)d, t=9.60, P=0.000). But hematocrit were lower in IAD group (30%±5% vs.33%±4% at end of operation, t=7.76, P=0.000; 30%±4% vs. 32%±5% at discharge, P=0.000, t=3.86). Multivariate logistic aggression analysis revealed that age, IAD and smoking history were factors influencing the probability of intra or postoperative blood transfusion.
CONCLUSIONImplementation of blood conservation strategies based on intraoperative autologous donation in mitral valve replacement surgery can significantly reduce intra/postoperative blood transfusion as well as postoperative complications.
Blood Transfusion, Autologous ; Bloodless Medical and Surgical Procedures ; Cardiac Surgical Procedures ; methods ; Hematocrit ; Humans ; Logistic Models ; Mitral Valve ; surgery ; Postoperative Complications ; Retrospective Studies
10.Effects of tooth germ microenvironment in vitro on the differentiation of dental pulp stem cell and ectoblast mesenchyme stem cell.
Yijing WANG ; Xiaodong ZHANG ; Hua YU ; Yan JIN ; Junnan SHI
West China Journal of Stomatology 2012;30(6):579-583
OBJECTIVETo observe the differential ability of dental pulp stem cell (DPSC) and ectoblast mesenchyme stem cell (EMSC) that were cultured with tooth germ cell (TGC) as the tooth germ microenvironment.
METHODSThe TGC of 4-day old rat was used as the tooth germ microenvironment. The BrdU marked and determined DPSC and EMSC were cultured with the TGC respectively. The expression of cell surface antigen dentin sialoprotein (DSP) and alkaline phosphatase (ALP) activity were determined with double marker immunofluorescence. The differential ability of DPSC and EMSC were determined by the immunohistochemistry and image analysis in the tooth germ microenvironment.
RESULTSThe transformation efficiency of DSP positive cell in the EMSC co-culture group was higher than that in the DPSC co-culture group (P < 0.05). The transformation efficiency in the co-culture groups was higher than that in the non co-culture group after 7 days by the image analysis of immunohistochemistry (P < 0.05). The ALP activity in the co-culture groups increased after 3 and 7 days. The ALP activity in the EMSC co-culture group was higher than that in the DPSC co-culture group.
CONCLUSIONDPSC and EMSC cultured with TGC as the tooth germ microenvironment can be induced to differentiate into odontoblast. The ability of EMSC is higher than that of DPSC.
Animals ; Cell Differentiation ; Coculture Techniques ; Dental Pulp ; Epithelial Cells ; Extracellular Matrix Proteins ; In Vitro Techniques ; Mesenchymal Stromal Cells ; Mesoderm ; Phosphoproteins ; Rats ; Sialoglycoproteins ; Stem Cells ; Tooth ; Tooth Germ

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