1.DeepGCGR: an interpretable two-layer deep learning model for the discovery of GCGR-activating compounds.
Xinyu TANG ; Hongguo CHEN ; Guiyang ZHANG ; Huan LI ; Danni ZHAO ; Zenghao BI ; Peng WANG ; Jingwei ZHOU ; Shilin CHEN ; Zhaotong CONG ; Wei CHEN
Chinese Journal of Natural Medicines (English Ed.) 2025;23(11):1301-1309
The glucagon receptor (GCGR) is a critical target for the treatment of metabolic disorders such as Type 2 Diabetes Mellitus (T2DM) and obesity. Activation of GCGR enhances systemic insulin sensitivity through paracrine stimulation of insulin secretion, presenting a promising avenue for treatment. However, the discovery of effective GCGR agonists remains a challenging and resource-intensive process, often requiring time-consuming wet-lab experiments to synthesize and screen potential compounds. Recent advances in artificial intelligence technologies have demonstrated great potential in accelerating drug discovery by streamlining screening and efficiently predicting bioactivity. In the present work, we propose DeepGCGR, a two-layer deep learning model that leverages graph convolutional networks (GCN) integrated with a multiple attention mechanism to expedite the identification of GCGR agonists. In the first layer, the model predicts the bioactivity of various compounds against GCGR, efficiently filtering large chemical libraries to identify promising candidates. In the second layer, DeepGCGR classifies high bioactive compounds based on their functional effects on GCGR signaling, identifying those with potential agonistic or antagonistic effects. Moreover, DeepGCGR was specifically applied to identify novel GCGR-regulating compounds for the treatment of T2DM from natural products derived from traditional Chinese medicine (TCM). The proposed method will not only offer an effective strategy for discovering GCGR-targeting compounds with functional activation properties but also provide new insights into the development of T2DM therapeutics.
Deep Learning
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Drug Discovery/methods*
;
Humans
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Diabetes Mellitus, Type 2/metabolism*
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Medicine, Chinese Traditional
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Drugs, Chinese Herbal/pharmacology*
2.TCMKD: From ancient wisdom to modern insights-A comprehensive platform for traditional Chinese medicine knowledge discovery.
Wenke XIAO ; Mengqing ZHANG ; Danni ZHAO ; Fanbo MENG ; Qiang TANG ; Lianjiang HU ; Hongguo CHEN ; Yixi XU ; Qianqian TIAN ; Mingrui LI ; Guiyang ZHANG ; Liang LENG ; Shilin CHEN ; Chi SONG ; Wei CHEN
Journal of Pharmaceutical Analysis 2025;15(6):101297-101297
Traditional Chinese medicine (TCM) serves as a treasure trove of ancient knowledge, holding a crucial position in the medical field. However, the exploration of TCM's extensive information has been hindered by challenges related to data standardization, completeness, and accuracy, primarily due to the decentralized distribution of TCM resources. To address these issues, we developed a platform for TCM knowledge discovery (TCMKD, https://cbcb.cdutcm.edu.cn/TCMKD/). Seven types of data, including syndromes, formulas, Chinese patent drugs (CPDs), Chinese medicinal materials (CMMs), ingredients, targets, and diseases, were manually proofread and consolidated within TCMKD. To strengthen the integration of TCM with modern medicine, TCMKD employs analytical methods such as TCM data mining, enrichment analysis, and network localization and separation. These tools help elucidate the molecular-level commonalities between TCM and contemporary scientific insights. In addition to its analytical capabilities, a quick question and answer (Q&A) system is also embedded within TCMKD to query the database efficiently, thereby improving the interactivity of the platform. The platform also provides a TCM text annotation tool, offering a simple and efficient method for TCM text mining. Overall, TCMKD not only has the potential to become a pivotal repository for TCM, delving into the pharmacological foundations of TCM treatments, but its flexible embedded tools and algorithms can also be applied to the study of other traditional medical systems, extending beyond just TCM.
3.Hemodynamic effects of nalbuphine combined with etomidate or propofol for painless colonoscopy in elderly hypertensive patients
Danni LI ; Wei CHENG ; Lei WANG ; Pengfei GAO ; Yu CHEN
Chinese Journal of Clinical Medicine 2025;32(5):835-840
Objective To compare the effects of nalbuphine combined with etomidate and nalbuphine combined with propofol in painless colonoscopy for elderly patients with hypertension. Methods Elderly patients with hypertension who underwent painless colonoscopy in the Department of Anesthesiology of Affiliated Huaian No.1 People’s Hospital of Nanjing Medical University from August 2022 to February 2023 were selected and randomly divided into three groups: nalbuphine combined with etomidate group (E group), nalbuphine combined with propofol group (P group), and the nalbuphine combined with etomidate and propofol group (EP group). The primary endpoint was the incidence of hypotension during anesthesia. Secondary endpoints included mean arterial pressure (MAP), systolic blood pressure (SBP), diastolic blood pressure (DBP), and heart rate (HR) at five time points: before anesthesia (T0), before colonoscopy (T1), 5 minutes after colonoscopy (T2), at the end of the examination (T3), upon leaving the post-anesthesia care unit (PACU, T4). Additionally, examination time, awakening time, Ramsay score, and adverse reactions were compared among the three groups. Results A total of 180 patients were included in the analysis, with 60 cases in each group. The incidence of hypotension was 11.7%, 55.0%, and 33.3% in the E group, P group, and EP group, respectively. The incidence of hypotension in the E group was lower than that in the P and EP groups (P<0.05). At T1, T2, T3, and T4, MAP, SBP, and DBP in the E group were significantly higher than those in the P and EP groups (P<0.05). There were no statistically significant differences among the three groups in awakening time, Ramsay score, or incidence of adverse reactions. Conclusions Compared with nalbuphine combined with propofol, nalbuphine combined with etomidate for painless colonoscopy in elderly patients with hypertension resulted in a lower incidence of hypotension, less impact on hemodynamics, and higher safety.
4.Study on influencing factors for falls risks score in the elderly
Sihang FANG ; Dizhi LIU ; Chunyuan JIA ; Danni GAO ; Liang SUN ; Xiaoquan ZHU ; Qi ZHOU ; Ze YANG ; Wei XU ; Yuan LYU ; Guofang PANG ; Caiyou HU ; Huiping YUAN
Chinese Journal of Geriatrics 2024;43(11):1481-1485
Objective:To investigate the factors influencing fall risk scores in elderly individuals.Methods:A total of 4 419 individuals were randomly selected using the cluster sampling method from Beijing, Nanning(Guangxi), and Yinchuan(Ningxia).Data on demographic characteristics and fall-related incidents were gathered and analyzed for their correlation with fall risk scores.Results:The fall risk score showed significant associations with various factors, such as the history of falls within one year( β=-3.607, 95% CI: -3.881 to -3.332), care methods( β=2.442, 95% CI: 2.226 to 2.658), exercise( β=0.714, 95% CI: 0.443 to 0.986), retirement( β=-0.585, 95% CI: -0.819 to -0.351), age( β=0.173, 95% CI: 0.159 to 0.187), and use of walking aids( β=-3.737, 95% CI: -4.054 to -3.421). Conclusions:Fall risk scores in older adults are influenced by a variety of factors.Factors such as no history of falls within the past year, living independently, engaging in physical activity, and being employed may contribute to lower fall risk scores in older adults.
5.In silico cloning, expression and bioinformatics analysis of NtODB from common tobacco.
Tao CHEN ; Xinyi PENG ; Jianfeng QIN ; Xu QIN ; Mi WU ; Jinyuan HUANG ; Xianya HUANG ; Danni WEI ; Liping WANG ; Gang JIN
Chinese Journal of Biotechnology 2021;37(8):2836-2844
It has been reported that ODB genes play an important role in homologous recombination-directed DNA repair, suggesting their potential applications in plant breeding. To analyze the expression characteristics of tobacco NtODB gene, the cDNA sequence of NtODB was obtained using in silico cloning technique. The physicochemical properties, signal peptide, and advanced structures of the predicted protein were analyzed using bioinformatics tools. The results showed that the NtODB gene has a 579-bp open reading frame which encodes a protein with 192 amino acid residues. The protein NtODB is predicted to be alkaline and hydrophilic. Real-time quantitative PCR showed that NtODB was constitutively expressed in different tissues. Subcellular localization showed that NtODB was mainly expressed in cell membrane and chloroplast. These results may help us to better understand and elucidate the roles of ODB genes in the homologous recombination-directed DNA repair.
Amino Acid Sequence
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Base Sequence
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Cloning, Molecular
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Computational Biology
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Computer Simulation
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DNA, Complementary
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Phylogeny
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Plant Breeding
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Tobacco/genetics*
6.Theclinicopathologicalfeaturesand MRImanifestationsofuterinespecialleiomyoma
Botao HUANG ; Junxing OU ; Shuzhen HAN ; Danni CAI ; Wei CHEN ; Xin’an JIN
Journal of Practical Radiology 2019;35(7):1103-1106
Objective ToexploretheclinicopathologicalfeaturesandMRImanifestationsofseveralspecialtypesofuterineleiomyomato improvethediagnosticlevelofit.Methods TheclinicopathologicalfeaturesandMRImanifestationsof18caseswithuterineleiomyomathatwere verifiedbypathologicanalysiswereanalyzedretrospectively.Results Amongthe18cases,therewere11casesofcellularleiomyoma,5casesof fattyleiomyomaand2casesofintravenousleiomyoma.Thetumorswereroundorirregular,withaclearmarginandamaximumdiameterof3.2cm to12.5cm.CellularleiomyomashowedisointensityonT1WI,homogeneouslyorslightlyhyperintensityonT2WI,and mostofthem werehyperintenseonDWI,whileafewisointense.Thelesionshowedearlyobviousenhancementandcontinuedtostrengthen,higher thanthemyometriumofthesameperiod.Fattyleiomyomaconsistsofsmooth musclecellsandadipocytesindifferentproportions, smoothmuscletissueshowedisointensityonT1WI,andisointensityorslightlyhyperintensityonT2WI,whileadiposetissueshowed hyperintensityonT1WIandT2WI,hypointensityonfatsequence,lighttomoderateenhancementforsmooth muscletissueandadiposetissue ntravenousleiomyomashowedirregularcircuity,shuttlesolidlumpin myometriumorneartheuterus,whichshowedisointenseon T1WI,andunevenorhyperintensityonT2WI,moderateheterogeneousenhancement,multiplecircuityvesselswithinoraroundthelesions.Allthe threetypesofuterineleiomyomaabovehavecertainMRIfeaturesandareassociatedwithpathology.Conclusion TheMRIfindingsof thecell-richleiomyomashowthattheedgeofthetumorisclear,ofwhichshowhyperintensityonDWI,andearlyandcontinuousenhancement, whilethedegreeofenhancementishigherthanthatinthemyometriumofuterusatthesameperiod.MRIofuterineadiposeleiomyomashows"whirlpool"or "braided"distributionoffatsignalinthetumor,andnoenhancementinadiposetissue;MRIofvenousleiomyoma showsirregulartwistsandturnsbetweenthewallofuterusorbesidetheuterus,andmoderateorunevenintensificationafterenhancement. withoutI.
7. Isolation and epidemiological significance of Yersinia pestis phages in indicator animals from the house mouse plague foci of Yunnan Province
Youhong ZHONG ; Chao SU ; Biao DUAN ; Yibo DING ; Qingchun DU ; Cunjuan DUAN ; Danni ZHAO ; Wei LI ; Peng WANG ; Hesong WU
Chinese Journal of Endemiology 2019;38(11):861-867
Objective:
To investigate whether plague phages were present in the indicator animals of plague foci in Yunnan Province, and to explore their epidemiological significance.
Methods:
Anus swabs were collected from indicator animals (dogs or cats) of the 41 plague affected villages in 26 towns of 10 cities (counties, districts) of Yunnan plague foci from November of 2015 to March of 2018. The
8. Comparative study on composition regularities of Chinese materia medica formulas for four kinds of emmeniopathies by data-driven approach
Chinese Traditional and Herbal Drugs 2018;49(8):1939-1945
To study and compare the composition regularities of Chinese materia medica (CMM) formulas for four kinds of emmeniopathies, including irregular menstruation, dysmenorrhea, amenorrhea, and uterine bleeding, and contribute to the interpretation and prescription of composition mechanism for the optimization of CMM formulas by using a data-driven approach. A total of 1 761 CMM formulas from the Dictionary of Chinese Medicine Prescription for emmeniopathies were analyzed by the data mining method of Apriori algorithm with the indicators of support, confidence, and lift. The frequencies, composition regularities, and pivotal compositions of CMM were analyzed comparatively. Angelicae Sinensis Radix (ASR), Chuanxiong Rhizoma (CR), CR-ASR, Paeoniae Radix Alba (PRA)-ASR, and PRA-CR-ASR were higher commonly used CMM and CMM combinations for all the four emmeniopathies. Astragali Radix was the highest frequently used CMM for uterine bleeding. Persicae Semen (PS), Rhei Radix et Rhizoma, and PS-ASR were the frequently used CMM and CMM combinations for amenorrhea. Cyperi Rhizoma and Cyperi Rhizoma-ASR were the frequently used CMM and CMM combinations for dysmenorrhea. The latent association rules with significant lift included Hirudo→Tabanus and Olibanum→Myrrha for irregular menstruation, and Sappan Lignum→Carthami Flos and Tabanus→Hirudo for amenorrhea. Based on the CMM formulas from the Dictionary of Chinese Medicine Prescription, the data-driven approach revealed the similarities and differences in CMM compositions for the four emmeniopathies and uncovered the latent composition regularities and the pivotal CMM effectively.
9.Comparison of Methods for Automatic De-identification of Clinical Texts
Liting DU ; Wei LUO ; Lei LI ; Bin LIN ; Chenxi XIA ; Guoqing MA ; Danni XIONG ; Jingdong MA
Journal of Medical Informatics 2017;38(4):44-49
The paper introduces the common methods for automatic de-identification of clinical texts,including the method based on rules,machine learning method,comprehensive method,etc.,states the challenges for clinical texts practicability,system universality and scalability of clinical texts de-identification research,analyzes the further research direction,and provides reference for researchers of this field.
10.Clinical analysis of 66 cases of neonates born to mother with systemic lupus erythematosus
Chinese Journal of Neonatology 2017;32(3):205-208
Objective To investigate the influence of newborns born to mother with systemic lupus erythematosus (SLE).Method The clinical data of SLE mothers and their infants bern in the obstetric and were admitted to the neonatal ward ward of the First Affiliated Hospital of Guangxi Medical University from July 2012 to March 2015 were studied retrospectively.The infants were divided into active SLEactivity group and stable SLE group.The incidence of preterm birth,small for gestational age (SGA),cardiac conduction block,anemia,and thrombocytopenia were compared between the two groups of SLE mothers.Result A total of 66 infants were included in SLE mothers,including 14 cases (21.2%) of preterm infants and 18 cases of SGA (27.3%).14 cases belonged to the active SLE group while 52 cases belonged to the SLE stable group.When comparing the 2 groups,there were no differences found on the rates of preterm infant and small for gestational age (P > 0.05).The cardiac conduction block,anemia and thrombocytopenia happened separately in three cases of the active group,which had not seen in the SLE stable group.There was no statistically significant difference between the two groups (P > 0.05).Of the 66 cases,2 were diagnosed with neonatal lupus erythematosus (NLE) with an incidence of 3%.Conclusion SLE mothers with an active disease 10 days before delivery did not significantly increase the incidence of preterm infants and SGA,but were at risk of NLE.

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