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.Exploration of the Mechanism of Autophagy Induced by Morin in Non-small Cell Lung Cancer A549 Cells Based on mTOR/STAT3 Signaling Axis
Xinyue ZHAO ; Yingying TIAN ; Chuang LIU ; Yilin LI ; Yingnan LYU ; Shangyue YU ; Shiqiu TIAN ; Hailuan PEI ; Zeping ZUO ; Zhibin WANG
Traditional Chinese Drug Research & Clinical Pharmacology 2024;35(3):317-324
Objective To investigate the mechanism of morin-induced autophagy in non-small cell lung cancer A549 cells based on mTOR/STAT3 signaling axis.Methods A549 cells were divided into blank group and 30,60,90,120 and 150 μg·mL-1 of morin groups.After 24,48 and 72 hours of culture,the cell proliferation activity was detected by CCK-8 method,and the cell inhibition rate was calculated.A549 cells were divided into blank group and 30,90,150 μg·mL-1 morin groups.After 14 days of culture,the cell proliferation was detected by colony formation assay.After 24 hours of culture,the cell proliferation ability was detected by BeyoClickTM EdU-488.Apoptosis was detected by flow cytometry;acridine orange staining was used to detect cell autophagy;the formation of autophagosomes was observed by transmission electron microscopy.Western Blot was used to detect the expression levels of apoptosis,autophagy and mTOR/STAT3 signaling axis-related proteins in cells.A549 cells were divided into blank group,blank group + chloroquine(10 μg·mL-1)group,morin(30,150 μg·mL-1)group,morin(30,150 μg·mL-1)+ chloroquine(10 μg·mL-1)group.After 48 hours of intervention,the cell activity was detected by CCK-8 method,and the cell survival rate was calculated.Results Compared with the blank group,the inhibition rate of A549 cells in 60,90,120,150 μ g·mL-1 of morin group was significantly increased after 24 hours of intervention(P<0.05,P<0.001).The inhibition rates of A549 cells in 30,60,90,120 and 150 μg·mL-1 of morin groups were significantly increased after 48 and 72 hours of intervention(P<0.001).The number of A549 cell colonies and the number of green fluorescent proliferation positive cells in the 30,90,150 μg·mL-1 of morin groups were significantly decreased(P<0.01,P<0.001),the apoptosis rate was significantly increased(P<0.01,P<0.001),and the protein expression level of cleaved-PARP was significantly increased(P<0.001).The protein expression levels of p-P38/P38 MAPK in A549 cells of 90 and 150 μg·mL-1 of morin groups were significantly increased(P<0.01,P<0.001).Different degrees of orange fluorescence appeared in A549 cells of 30,90 and 150 μg·mL-1 of morin groups,and the orange fluorescence of 90 and 150 μg·mL-1 of morin groups was significant.Autophagosomes and autolysosomes appeared in the cytoplasm of A549 cells in 150 μg·mL-1 of morin group,respectively.The protein expression of LC3-Ⅱ in A549 cells of 150 μg·mL-1 of morin group was significantly up-regulated(P<0.05).The protein expression of Atg16L1-Ⅱ in A549 cells of 90,150 μg·mL-1 of morin group was significantly up-regulated(P<0.001),and the protein expressions of p-mTOR/mTOR and p-STAT3/STAT3 were significantly down-regulated(P<0.001).Compared with the morin(150 μg·mL-1)group,the survival rate of A549 cells in the morin(150 μg·mL-1)+chloroquine(10 μg·mL-1)group was significantly increased(P<0.05).Conclusion Morin can promote the apoptosis of A549 cells and induce autophagy in A549 cells,and the mechanism may be related to mTOR/STAT3 axis.
3.Association between family screen environment and screen content for preschool children in Shanghai
SUN Yi, YU Tao, PENG Yajun, CHEN Hao, LUO Sha, JIA Yingnan
Chinese Journal of School Health 2024;45(8):1144-1147
Objective:
To investigate the current status of screen exposure among preschool children in Shanghai and its association with family screen environment, so as to provide a scientific basis for family screen management.
Methods:
Using a convenient sampling method, a total of 349 preschool children aged 4-6 years were selected from 36 kindergarten classes in Xuhui District and Pudong New Area in Shanghai during April to June in 2023. Demographic characteristics and family screen environment were surveyed through an online questionnaire. Screen exposure of children was assessed using a diary method, with parents recording the activities over a 7day period. Multiple Logistic regression analysis was employed to identify factors influencing childrens screen content.
Results:
The average daily screen exposure time for children was (61.2±40.2) minutes, with an average of (12.4±17.6) minutes spent on educational screen content, 80.8% predominantly watched noneducational screen content. The percentages of time spent on educational screen content for 4yearold boys, 4yearold girls, 5yearold boys, 5yearold girls, 6yearold boys, and 6yearold girls were 20.1%, 14.7%, 21.3%, 21.9%, 20.6%, and 26.9%, respectively. Multivariate Logistic regression showed that children aged 5yearold (OR=0.49, 95%CI=0.25-0.96) and 6yearold (OR=0.45, 95%CI=0.21-0.95) were negatively associated with more noneducational screen content (P<0.05). However, occasional (OR=2.02, 95%CI=1.09-3.75) and sometimes (OR=4.50, 95%CI=1.70-11.90) using electronic devices to calm young child when crying, as well as children using electronic devices without adult supervision (OR=1.81, 95%CI=1.01-3.24) were positively associated with more noneducational screen content (P<0.05).
Conclusions
Preschool children in Shanghai exhibit high exposure to noneducational screen content, and family screen environment and parentchild interaction are associated with noneducational screen exposure. Strategies for family screen management should be developed to regulate childrens screen exposure behaviors, allowing electronic devices to play a positive role in their developmental process.
4.Quantitative assessment for bone resorption following cranial remodeling in children and adolescent congenital cranial deformity cases
Yingnan GENG ; Zheyuan YU ; Liang XU ; Huichuan DUAN ; Min WEI ; Jie YUAN
Chinese Journal of Plastic Surgery 2021;37(2):158-161
Objective:To quantitatively assess the degree of bone resorption following cranial bone remodeling for children and adolescent congenital cranial deformity cases in Crouzon syndrome.Methods:A total of 14 congenital cranial deformity patients (mean age 7.7 years) who underwent cranial bone remodeling between Mar. 2014 and Dec. 2018 were selected from Shanghai Ninth People’s Hospital, and retrospectively reviewed. They were treated with modified monobloc osteotomy and distraction osteogenesis. Craniectomy and cranial bone remodeling were performed, and the follow-up period was one week(t1) and one year(t2). The patients were scanned by spiral CT at the two following time points. Then data were imported into Mimics to acquire the three-dimensional model of skull. Bone volume was measured with Mimics Research 18.0 after three-dimensional CT reconstruction. The resorption rate was calculated as (V t1-V t2)/V t1×100%(V t1 represented bone volume before distraction osteogenesis, V t2 represented bone volume after distraction osteogenesis), followed by statistical analysis. Results:Among the 14 patients, bone resorption occurred in 11 patients and the resorption rate after 1 year was 3.482%. There was no significant difference between bone volumes at 1 week and 1 year after surgery( t=0.851, P=0.410). Conclusions:Bone resorption following cranial bone remodeling for children and adolescents with congenital cranial deformity did exist, however, it was acceptable. Therefore, the surgical treatment of cranial remodeling and distraction osteogenesis is advisable for children and youth with congenital cranial deformities over 1 year old.
5.Quantitative analysis of five compounds in gallnut lotion by UPLC-MS/MS
Qun ZHANG ; Yu CHEN ; Xiaowei ZHI ; Qiuping XU ; Yingnan YANG ; Liang ZHAO ; Chengjian LI
Journal of Pharmaceutical Practice 2021;39(5):437-441
Objective To develop an ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method to simultaneously detect the contents of gallic acid, syringin, phellodendrine, aesculin and rhein in the gallnut lotion. Methods An UPLC- MS/MS method was established. Separation was performed on an Agilent Poroshell 120 EC-C18(2.1 mm×150 mm, 2.7 μm)with a gradient mobile phase system of 0.2% formic water-acetonitrile solution. The flow rate was 0.3 ml/min. The temperature of column was 30 ℃. The injection volume was 2 μl. The MS detection was in dynamic MRM mode. Results gallic acid, syringin, phellodendrine, aesculin and rhein were successfully separated using this method, with good linear relationship as the ranges of 153.8-15380、10.31-1031、5.265-526.5、50.70-5070、1.054-105.4 ng/ml, respectively. The precision, repeatability, stability and recovery were good. Conclusion This UPLC-MS/MS method is stable, rapid, and reproducible., It is suitable for detecting the contents of gallic acid, syringin, phellodendrine, esculetin and in the gallnut lotion.
6.Quantitative assessment for bone resorption following cranial remodeling in children and adolescent congenital cranial deformity cases
Yingnan GENG ; Zheyuan YU ; Liang XU ; Huichuan DUAN ; Min WEI ; Jie YUAN
Chinese Journal of Plastic Surgery 2021;37(2):158-161
Objective:To quantitatively assess the degree of bone resorption following cranial bone remodeling for children and adolescent congenital cranial deformity cases in Crouzon syndrome.Methods:A total of 14 congenital cranial deformity patients (mean age 7.7 years) who underwent cranial bone remodeling between Mar. 2014 and Dec. 2018 were selected from Shanghai Ninth People’s Hospital, and retrospectively reviewed. They were treated with modified monobloc osteotomy and distraction osteogenesis. Craniectomy and cranial bone remodeling were performed, and the follow-up period was one week(t1) and one year(t2). The patients were scanned by spiral CT at the two following time points. Then data were imported into Mimics to acquire the three-dimensional model of skull. Bone volume was measured with Mimics Research 18.0 after three-dimensional CT reconstruction. The resorption rate was calculated as (V t1-V t2)/V t1×100%(V t1 represented bone volume before distraction osteogenesis, V t2 represented bone volume after distraction osteogenesis), followed by statistical analysis. Results:Among the 14 patients, bone resorption occurred in 11 patients and the resorption rate after 1 year was 3.482%. There was no significant difference between bone volumes at 1 week and 1 year after surgery( t=0.851, P=0.410). Conclusions:Bone resorption following cranial bone remodeling for children and adolescents with congenital cranial deformity did exist, however, it was acceptable. Therefore, the surgical treatment of cranial remodeling and distraction osteogenesis is advisable for children and youth with congenital cranial deformities over 1 year old.
7.Infectious complications following chimeric antigen receptor T-cell therapy for a hematologic malignancy within 28 days
Yingnan LI ; Mengyi DU ; Chenggong LI ; Yinqiang ZHANG ; Wenjing LUO ; Haiming KOU ; Heng MEI ; Yu HU
Chinese Journal of Hematology 2021;42(9):739-746
Objective:To explore the incidence, clinical and microbiological characteristics and risk factors of infection in patients with acute lymphoblastic (ALL) , non-Hodgkin lymphoma (NHL) , and multiple myeloma (MM) within 28 days after CAR-T cell infusion. It provides data support for early identification of infection and the rational use of antibacterial drugs in these patients.Methods:We retrospectively analyzed the baseline data of 170 patients with ALL, NHL and MM who received chimeric antigen receptor-modified T (CAR-T) -cell treatment in the Department of Hematology of Wuhan Union Hospital from January 2016 to December 2020, and the clinical characteristics of infection within 28 days after infusion, including 72 patients with ALL, 56 patients with NHL, and 42 patients with MM; we used Poisson regression and Cox proportional hazard regression models to assess high-risk factors for infection before and after infusion, respectively.Results:Among 170 patients, 119 infections occurred in 99 patients within 28 days, with a cumulative infection rate of 58.2%. Seventy-eight patients had 98 bacterial infections and the cumulative incidence of bacterial infection was 45.9%. The infection density was 2.01, and the median time for the first infection was about 12 days after infusion. The adjusted baseline characteristic model showed that ALL patients, previous 30 days of infection history, refractory disease, absolute neutrophil count (ANC) <0.5×10 9/L before infusion and ≥4 prior antitumor treatment regimens had a higher infection density within 28 days; grade 3 or 4 CRS was the only high-risk factor related to infection after infusion in the multivariate analysis. Conclusion:Infection is a common complication of CAR-T cell therapy in patients with hematologic malignancy. Bacterial infections occur in most patients regardless of the type of disease. ALL patients, previous 30 days of infection history, refractory disease, ANC<0.5×10 9/L before infusion and grade 3 or 4 CRS are risk factors for infection. Chinese Clinical Trial Register::ChiCTR-OIC-17011180, ChiCTR1800018143
8.Experience of surgical treatment on craniometaphyseal dysplasia
Yingnan GENG ; Jie YUAN ; Zheyuan YU ; Liang XU ; Huichuan DUAN ; Min WEI
Chinese Journal of Plastic Surgery 2020;36(6):655-659
Objective:To retrospect the treatment and clinical effect of craniometaphyseal dysplasia(CMD), and summarize the experience of cranial reconstruction and nasal deformity correction in the management of this case.Methods:From June 2004 to June 2018, three male CMD patients of Shanghai Ninth People’s Hospital who received treatment. One patient was 1 year-old child who received drug therapy. A 5 year-old boy was treated with nasal cavity expansion and orbital hypertelorism for plastic and reconstructive surgery. The 7 year-old patient received cranial reconstruction and nasal deformity correction. Moreover, surgical treatments from 1967 to 2017 in the literatures on CMD were reviewed.Results:Indicators (Ca, ATP, PTH) in the laboratory of the first child returned to normal after medication treatment, and there was no obvious abnormality in the following 2 months. Nasal cavity of the second case was enlarged and function of the nose was improved, and interorbital distance was reduced by 16-17 mm. However, cranial facial deformation was not ameliorated obviously. For the third patient, scaphocephaly deformity was significantly improved. Skull thickness decreased from 3cm to 1-2 cm, the anteroposterior diameter of the skull was shortened up to 6 cm. The immediate review of dd dimer was 4.25 mg/L, FDP was 20.6 μg/ml, which was significantly higher than preoperative tests (dd dimer 0.98 mg/L, FDP 7.24 μg/ml). Two weeks after surgery, the patient received skull debridement due to ineffective anti-infective treatment. Ten months later, the child was admitted to the hospital because of infection. CT scan showed bone resorption, and we treated him with skull debridement and cranioplasty. Following 16 months, the patient was in a stable condition without complications until now.Conclusions:Drug therapy has a potential role in CMD treatment. However, surgery is the only effective management of it, although there will be a high risk and many complications, and the patients need repeated operations.
9.Experience of surgical treatment on craniometaphyseal dysplasia
Yingnan GENG ; Jie YUAN ; Zheyuan YU ; Liang XU ; Huichuan DUAN ; Min WEI
Chinese Journal of Plastic Surgery 2020;36(6):655-659
Objective:To retrospect the treatment and clinical effect of craniometaphyseal dysplasia(CMD), and summarize the experience of cranial reconstruction and nasal deformity correction in the management of this case.Methods:From June 2004 to June 2018, three male CMD patients of Shanghai Ninth People’s Hospital who received treatment. One patient was 1 year-old child who received drug therapy. A 5 year-old boy was treated with nasal cavity expansion and orbital hypertelorism for plastic and reconstructive surgery. The 7 year-old patient received cranial reconstruction and nasal deformity correction. Moreover, surgical treatments from 1967 to 2017 in the literatures on CMD were reviewed.Results:Indicators (Ca, ATP, PTH) in the laboratory of the first child returned to normal after medication treatment, and there was no obvious abnormality in the following 2 months. Nasal cavity of the second case was enlarged and function of the nose was improved, and interorbital distance was reduced by 16-17 mm. However, cranial facial deformation was not ameliorated obviously. For the third patient, scaphocephaly deformity was significantly improved. Skull thickness decreased from 3cm to 1-2 cm, the anteroposterior diameter of the skull was shortened up to 6 cm. The immediate review of dd dimer was 4.25 mg/L, FDP was 20.6 μg/ml, which was significantly higher than preoperative tests (dd dimer 0.98 mg/L, FDP 7.24 μg/ml). Two weeks after surgery, the patient received skull debridement due to ineffective anti-infective treatment. Ten months later, the child was admitted to the hospital because of infection. CT scan showed bone resorption, and we treated him with skull debridement and cranioplasty. Following 16 months, the patient was in a stable condition without complications until now.Conclusions:Drug therapy has a potential role in CMD treatment. However, surgery is the only effective management of it, although there will be a high risk and many complications, and the patients need repeated operations.
10. Lower wide pedicle frontal periosteum flap reduces bone absorption after cranioplasty: a mid-term clinic observation
Yingnan GENG ; Min WEI ; Miao XU ; Liang XU ; Jie YUAN ; Dejun CAO ; Zheyuan YU
Chinese Journal of Plastic Surgery 2019;35(2):112-116
Objective:
To observe the influence of lower wide pedicle frontal periosteum flap on frontal bone absorption rate after cranioplasty.
Methods:
From February 2016 to July 2017, the lower wide pedicle frontal periosteum flap was produced in 12 patients of Shanghai Ninth People′s Hospital (7 males/5 females, aged 5-9 years, 10 hypertelorism, 2 Crouzon syndrome), who accepted intro-cranio-route plastic surgery, to cover the frontal bone window. A spiral CT scans were applied one week (t1) and one year (t2) after surgery. DICOM data was imported into Mimics software to reconstruct the 3D model of skull. The bone window covered the frontal bone was selected and the bone volume was calculated. The absorption rate was calculated as (Vt1-Vt2)/Vt1×100%. As a control group, the CT data of 20 patients (from January 2010 to December 2015, 11 males/9 females, 7 hypertelorism, 12 Crouzon syndrome, 1 Pfeiffer syndrome) were analyzed retrospectively in the same way, and compared to the experimental group.
Results:
The average bone absorption rate in experimental group was 8.65%±2.56% (


Result Analysis
Print
Save
E-mail