1.pLM4ACP: a model for predicting anticancer peptides based on machine learning and protein language models.
Yitong LIU ; Wenxin CHEN ; Juanjuan LI ; Xue CHI ; Xiang MA ; Yanqiong TANG ; Hong LI
Chinese Journal of Biotechnology 2025;41(8):3252-3261
Cancer is a serious global health problem and a major cause of human death. Conventional cancer treatments often run the risk of impairing vital organ functions. Anticancer peptides (ACPs) are considered to be one of the most promising therapeutic agents against common human cancers due to their small sizes, high specificity, and low toxicity. Since ACP recognition is highly limited to the laboratory, expensive, and time-consuming, we proposed pLM4ACP, a model for predicting ACPs based on machine learning and protein language models. In this model, the protein language model ProtT5 was used to extract the features of ACPs, and the extracted features were input into the support vector machine (SVM) classification algorithm for optimization and performance evaluation. The model showcased significantly higher accuracy than other methods, with the overall accuracy of 0.763, F1-score of 0.767, Matthews correlation coefficient of 0.527, and area under the curve of 0.827 on the independent test set. This study constructs an efficient anticancer peptide prediction model based on protein language models, further advancing the application of artificial intelligence in the biomedical field and promoting the development of precision medicine and computational biology.
Machine Learning
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Antineoplastic Agents/chemistry*
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Humans
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Peptides/chemistry*
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Support Vector Machine
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Algorithms
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Computational Biology/methods*
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Neoplasms/drug therapy*
2.Visualization analysis on research literature about Taohong Siwu Decoction based on CiteSpace
Shang LIU ; Yan CHEN ; Kanjana THANA ; Can WANG ; Ziqiong LONG ; Xingyue CHEN ; Xiaoxiao ZHANG ; Yitong HONG
International Journal of Traditional Chinese Medicine 2025;47(3):380-386
Objective:To understand the current research status, hot issues, and development trends of Taohong Siwu Decoction.Methods:Research literature about Taohong Siwu Decoction was retrieved from Wanfang Data, CBM, CNKI, and Chongqing VIP from January 1, 2014, to August 13, 2024. Excel 2024 software was used to analyze the annual number of publications, the source journals, literature types and the distribution of diseases and syndromes. CiteSpace 6.3.R3 software was used for visualization analysis on the authors, research institutions and key words.Results:A total of 2 519 articles were included, and the annual publication volume showed a fluctuating growth trend. There were 396 source journals, of which Medicine and Health published the most (80 articles); 208 authors were involved, and the core authors included Peng Daiyin of Anhui University of Chinese Medicine, Zhu Fuping of the First Affiliated Hospital of Hunan University of Chinese Medicine, Sun Shaoqiu of the Second Affiliated Hospital of Hunan University of Chinese Medicine and so on. The main research institutions in this field included Hunan University of Chinese Medicine and its affiliated hospitals. The high-frequency keywords included fracture, irregular menstruation, clinical efficacy, chloasma, Wuling Powder, experience of famous doctors, elderly, etc. Keywords could be clustered into 11 modules.Conclusions:The current research hotspots of Taohong Siwu Decoction mainly focus on the exploration of multi-system disease treatment, individualized syndrome differentiation and treatment, pharmacology and metabolic mechanism of Chinese materia medica, etc. Among them, the in-depth study of drug composition and metabolism, network pharmacology and mechanism is the research frontier in this field.
3.Construction of circular RNA vaccine against porcine reproductive and respiratory syndrome virus and optimization of circularization conditions
Chunhao TAO ; Ying HUANG ; Zhen WANG ; Yitong JIANG ; Hongfei ZHU ; Hong JIA
Chinese Journal of Veterinary Science 2025;45(5):896-904
In order to establish a highly efficient,convenient,and effective circular RNA(circRNA)vaccine preparation system,enhanced green fluorescent protein(EGFP)circRNA was constructed using permuted intron exon(PIE)strategy based on type Ⅰ introns.Then,circRNA circularization rates of RNA after in vitro transcription(IVT),primary circularization(IVC1),and secondary circularization(IVC2)were compared after purification.The constructed circRNA system was fur-ther applied to porcine reproductive and respiratory syndrome virus(PRRSV),and two circRNAs based on PRRSV GP5 protein were constructed and developed for in vitro expression.Results showed that circularization rates and protein expression effects of EGFP circRNA in IVC1 RNA and IVC2 RNA were similar,but both were significantly better than those of IVT RNA.Purity of EGFP circRNA reached 74%,and purities of two PRRSV GP5 protein circRNAs constructed using this preparation system were 71%and 64%,respectively.Western blot and indirect immunofluo-rescence assay(IFA)results indicated that both of the PRRSV GP5 protein circRNAs were suc-cessfully expressed.The results demonstrated that an easy-to-operate,low-cost circRNA prepara-tion system with high circularization rate was successfully constructed.Two PRRSV GP5 protein circRNA vaccines were successfully prepared using this system and expressed efficiently,which provides a reference for the development of animal circRNA vaccines and novel candidate vaccines against PRRSV.
4.Visual analysis of a nursing study of pelvic floor dysfunction disorders
Yitong HONG ; Xiaoxiao ZHANG ; Xingyue CHEN ; Ziqiong LONG ; Shang LIU ; Can WANG ; Yan CHEN
Chinese Journal of Practical Nursing 2025;41(32):2534-2541
Objective:To visually analyze the research hot-spots and development trends of pelvic floor dysfunction nursing, in order to provide a reference for the research of pelvic floor dysfunction nursing in China.Methods:The China National Knowledge Infrastructure (CNKI) and Web of Science core collection were used as the retrieval databases to retrieve the literature in the field of pelvic floor dysfunction nursing from the establishment of the database to January 31, 2025. CiteSpace 6.4.R1 software was used to visually analyze the included literature.Results:A total of 1 947 Chinese articles and 4 931 English articles were included. The number of English literature increased year by year, while Chinese literature showed a downward trend since 2019. There were more and stable core authors and core institutions in foreign research, while there was less cooperation among domestic authors and institutions. The research hotspots abroad mainly focused on improving the quality of nursing care and managing specific health problems. The future development trends were primarily randomized controlled trials, tension-free vaginal tape, postoperative care, and patient experience. The research hotspots in China mainly focused on nursing interventions. The future development trends were primarily patient quality of life and effectiveness evaluation.Conclusions:Due to different development stages, compared with foreign countries, there are still some deficiencies in evidence-based medicine, delicacy of nursing after tension-free vaginal tape, patient experience, innovation of nursing technology, and depth and breadth of nursing research in China. In the future, we should learn from foreign studies to promote the development of nursing research on pelvic floor dysfunction in China.
5.Construction of circular RNA vaccine against porcine reproductive and respiratory syndrome virus and optimization of circularization conditions
Chunhao TAO ; Ying HUANG ; Zhen WANG ; Yitong JIANG ; Hongfei ZHU ; Hong JIA
Chinese Journal of Veterinary Science 2025;45(5):896-904
In order to establish a highly efficient,convenient,and effective circular RNA(circRNA)vaccine preparation system,enhanced green fluorescent protein(EGFP)circRNA was constructed using permuted intron exon(PIE)strategy based on type Ⅰ introns.Then,circRNA circularization rates of RNA after in vitro transcription(IVT),primary circularization(IVC1),and secondary circularization(IVC2)were compared after purification.The constructed circRNA system was fur-ther applied to porcine reproductive and respiratory syndrome virus(PRRSV),and two circRNAs based on PRRSV GP5 protein were constructed and developed for in vitro expression.Results showed that circularization rates and protein expression effects of EGFP circRNA in IVC1 RNA and IVC2 RNA were similar,but both were significantly better than those of IVT RNA.Purity of EGFP circRNA reached 74%,and purities of two PRRSV GP5 protein circRNAs constructed using this preparation system were 71%and 64%,respectively.Western blot and indirect immunofluo-rescence assay(IFA)results indicated that both of the PRRSV GP5 protein circRNAs were suc-cessfully expressed.The results demonstrated that an easy-to-operate,low-cost circRNA prepara-tion system with high circularization rate was successfully constructed.Two PRRSV GP5 protein circRNA vaccines were successfully prepared using this system and expressed efficiently,which provides a reference for the development of animal circRNA vaccines and novel candidate vaccines against PRRSV.
6.Visual analysis of a nursing study of pelvic floor dysfunction disorders
Yitong HONG ; Xiaoxiao ZHANG ; Xingyue CHEN ; Ziqiong LONG ; Shang LIU ; Can WANG ; Yan CHEN
Chinese Journal of Practical Nursing 2025;41(32):2534-2541
Objective:To visually analyze the research hot-spots and development trends of pelvic floor dysfunction nursing, in order to provide a reference for the research of pelvic floor dysfunction nursing in China.Methods:The China National Knowledge Infrastructure (CNKI) and Web of Science core collection were used as the retrieval databases to retrieve the literature in the field of pelvic floor dysfunction nursing from the establishment of the database to January 31, 2025. CiteSpace 6.4.R1 software was used to visually analyze the included literature.Results:A total of 1 947 Chinese articles and 4 931 English articles were included. The number of English literature increased year by year, while Chinese literature showed a downward trend since 2019. There were more and stable core authors and core institutions in foreign research, while there was less cooperation among domestic authors and institutions. The research hotspots abroad mainly focused on improving the quality of nursing care and managing specific health problems. The future development trends were primarily randomized controlled trials, tension-free vaginal tape, postoperative care, and patient experience. The research hotspots in China mainly focused on nursing interventions. The future development trends were primarily patient quality of life and effectiveness evaluation.Conclusions:Due to different development stages, compared with foreign countries, there are still some deficiencies in evidence-based medicine, delicacy of nursing after tension-free vaginal tape, patient experience, innovation of nursing technology, and depth and breadth of nursing research in China. In the future, we should learn from foreign studies to promote the development of nursing research on pelvic floor dysfunction in China.
7.Temporal-spatial Generation of Astrocytes in the Developing Diencephalon.
Wentong HONG ; Pifang GONG ; Xinjie PAN ; Zhonggan REN ; Yitong LIU ; Guibo QI ; Jun-Liszt LI ; Wenzhi SUN ; Woo-Ping GE ; Chun-Li ZHANG ; Shumin DUAN ; Song QIN
Neuroscience Bulletin 2024;40(1):1-16
Astrocytes are the largest glial population in the mammalian brain. However, we have a minimal understanding of astrocyte development, especially fate specification in different regions of the brain. Through lineage tracing of the progenitors of the third ventricle (3V) wall via in-utero electroporation in the embryonic mouse brain, we show the fate specification and migration pattern of astrocytes derived from radial glia along the 3V wall. Unexpectedly, radial glia located in different regions along the 3V wall of the diencephalon produce distinct cell types: radial glia in the upper region produce astrocytes and those in the lower region produce neurons in the diencephalon. With genetic fate mapping analysis, we reveal that the first population of astrocytes appears along the zona incerta in the diencephalon. Astrogenesis occurs at an early time point in the dorsal region relative to that in the ventral region of the developing diencephalon. With transcriptomic analysis of the region-specific 3V wall and lateral ventricle (LV) wall, we identified cohorts of differentially-expressed genes in the dorsal 3V wall compared to the ventral 3V wall and LV wall that may regulate astrogenesis in the dorsal diencephalon. Together, these results demonstrate that the generation of astrocytes shows a spatiotemporal pattern in the developing mouse diencephalon.
Mice
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Animals
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Astrocytes
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Neuroglia/physiology*
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Diencephalon
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Brain
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Neurons
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Mammals
8.Predictive value of THR, MHR and NHR combined in assessing coronary artery stenosis severity and percutaneous coronary intervention
Cheng LIU ; Sen LIU ; Hong YANG ; Menglong JIN ; Ziyang LIU ; Zhenyan FU ; Yitong MA
Journal of Xi'an Jiaotong University(Medical Sciences) 2024;45(6):948-953
[Objective] To investigate the value of total cholesterol to high-density lipoprotein cholesterol ratio (THR), monocyte to high-density lipoprotein cholesterol ratio (MHR), and neutrophil to high-density lipoprotein cholesterol ratio (NHR) in predicting patients’ coronary artery stenosis severity and percutaneous coronary intervention (PCI). [Methods] A total of 6 281 patients who underwent coronary angiography at our hospital between June 2021 and June 2023 were retrospectively included in this study. These patients were divided into two groups: PCI group and non-PCI group. The clinical data, laboratory findings, and interventional treatment data of all patients were collected and analyzed. Pearson correlation analysis was employed to evaluate the correlation of THR, MHR and NHR with the degree of coronary artery stenosis. Binary Logistic stepwise regression and receiver operating characteristic (ROC) curve were utilized to assess the influencing factors and predictive value of THR, MHR and NHR single and combined indexes for coronary artery disease patients undergoing PCI. [Results] The PCI group was observed to be older, with a higher proportion of males, individuals with diabetes mellitus, and those who had undergone THR, MHR, NHR, and a Gensini score than the non-PCI group. Conversely, the proportion of previous stent implantation was less than that of the non-PCI group (P<0.05). The results of Pearson correlation analysis showed a significant and positive correlation of the Gensini score with THR (r=0.351, P<0.001), MHR (r=0.192, P<0.001), and NHR (r=0.236, P<0.001) levels, indicating that these variables had a significantly positive correlation with the degree of coronary artery stenosis. The results of multifactorial Logistic regression demonstrated that age >50 years, male sex, diabetes mellitus, THR, MHR, and NHR were independent risk factors for PCI in patients with coronary artery disease. Conversely, a history of previous stent implantation was identified as a protective factor for PCI in patients with coronary artery disease. Furthermore, the results of ROC curves indicated that the combined area under the curve (AUC) was the largest for THR, MHR, and NHR (AUC=0.809, 95%CI: 0.798-0.820). [Conclusion] THR, MHR and NHR correlate with the degree of coronary stenosis and have strong clinical applications in the assessment of coronary artery disease for PCI.
9.Advances in applications of neuroregulatory techniques in research on brain sciences
Mengnan LIU ; Xiaoyu TIAN ; Yitong LI ; Ning WU ; Jin LI ; Hong LI
Chinese Journal of Pharmacology and Toxicology 2024;38(2):128-136
Drugs and physical stimulation,including light,electricity,and magnetic fields,can be used to influence how neurons operate,among which chemogenetic and optogenetic technologies are most widely used.In recent years,magnetogenetic technology has also been developed that can acti-vate neurons in magnetic fields through magnetic sensitive actuators,leading to non-invasive and instanta-neous activation of specific brain regions.This article reviews the evolution of and problems with chemoge-netic and optogenetic techniques commonly used in brain science research.It also outlines the latest progress in magnetogenetic technologies,which are not full-fledged yet,as well as the role of transcra-nial electrical stimulation,transcranial magnetic stimulation,deep brain stimulation and transcranial ultra-sound stimulation technology in the functional regulation of brain diseases.Constant adjustment and improvement can make it possible for these technologies to be used more widely for the study of brain sciences and the treatment of brain diseases.
10.Study of correlation between Fli1 gene and prognosis and immunoinfiltration in patients with endometrial cancer
Wei LIAO ; Yitong LIU ; Toushen HONG ; Lan LI ; Lili SHEN
Immunological Journal 2024;40(7):593-600
Objective This study was to examine the association between the Fli1 gene and both prognosis and immune infiltration in patients with endometrial cancer.Methods Differential expression of the Fli1 gene was assessed utilizing the TIMER and GEPIA databases.The expression level of the FLI1 protein were evaluated through the Human Protein Atlas(HPA)database.The Kaplan-Meier Plotter database was employed to analyze the relationship between Fli1gene expression and patient prognosis in endometrial cancer.Additionally,the correlation between Fli1 gene expression and immune cell infiltration was investigated using the TIMER database.Results A significant underexpression of the Fli1gene in patients diagnosed with endometrial cancer(P<0.01).This was further corroborated by the Human Protein Atlas(HPA)database,which indicated a lower expression level of the FLI1 protein in tumor tissues compared to normal tissues.Furthermore,an analysis conducted using the Kaplan-Meier Plotter database demonstrated a correlation between low Fli1 gene expression and a poorer prognosis in endometrial cancer patients.TIMER database revealed a positive correlation between Fli1 expression and the infiltration of various immune cells,including B cells,CD4+T cells,and macrophages.The expression level of the Fli1 gene demonstrated a moderate to strong correlation with the marker genes of these immune cells(COR>0.4,P<0.05).Additionally,the expression of Fli1 gene was significantly positively correlated with multiple immune checkpoints.Conclusion The low expression of Fli1 is significantly associated with poor prognosis in patients with endometrial carcinoma,the higher infiltration of B cells,CD4+T cells,macrophages and other immune cells may play an important role.

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