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.Effect of melatonin in alleviating ovarian granulosa cell apoptosis induced by chronic hypoxia
Yinling XIU ; Ying LIU ; Kaixuan SUN ; Panpan ZHAO ; Shufang TANG ; Jing ZHOU ; Yitong ZHANG ; Yuexin YU
Journal of China Medical University 2025;54(11):1017-1022
Objective To investigate the effect and mechanism of melatonin in alleviating hypoxia-induced apoptosis in ovarian gra-nulosa cells.Methods Rat ovarian granulosa cells were isolated and divided into normoxic,hypoxic,and melatonin groups.Hypoxia-induced injury models were established in the hypoxic and melatonin groups,and granulosa cells in the melatonin group were treated with melatonin.A total of 24 rats were randomized into the control,model,and intervention groups(n=8 per group).Rat models of declining ovarian function induced by long-term hypoxia were established in the model and intervention groups.The rats in the intervention group were intraperitoneally injected with melatonin.Cell proliferation was measured using a CCK-8 assay,and lactate secretion and HIF-1αprotein with a specific kit,respectively.The levels of estradiol and progesterone in the cell supernatant and rat serum were detected using ELISA.Granulosa cell apoptosis was detected by flow cytometry,ovarian morphology by HE staining,and Bax and caspase-3 expression by Western blotting.Results Compared with the normoxic group,the hypoxic group exhibited decreased granulosa cell proliferation,increased apoptosis,elevated lactate and HIF-1α levels,and reduced estradiol and progesterone levels(P<0.05).Compared with hypoxic group,these changes were significantly reversed in the molatonin group(P<0.05).Compared with the control group,the model group showed increased lactate,HIF-1α,Bax,and caspase-3 levels,decreased estradiol and progesterone levels,and reduced follicles.Compared with the model group,all the indicators were ameliorated in the intervention group(P<0.05).Conclusion Melatonin alleviated hypoxia-induced granulosa cell apoptosis and promoted the recovery of ovarian function.
3.Effect of melatonin in alleviating ovarian granulosa cell apoptosis induced by chronic hypoxia
Yinling XIU ; Ying LIU ; Kaixuan SUN ; Panpan ZHAO ; Shufang TANG ; Jing ZHOU ; Yitong ZHANG ; Yuexin YU
Journal of China Medical University 2025;54(11):1017-1022
Objective To investigate the effect and mechanism of melatonin in alleviating hypoxia-induced apoptosis in ovarian gra-nulosa cells.Methods Rat ovarian granulosa cells were isolated and divided into normoxic,hypoxic,and melatonin groups.Hypoxia-induced injury models were established in the hypoxic and melatonin groups,and granulosa cells in the melatonin group were treated with melatonin.A total of 24 rats were randomized into the control,model,and intervention groups(n=8 per group).Rat models of declining ovarian function induced by long-term hypoxia were established in the model and intervention groups.The rats in the intervention group were intraperitoneally injected with melatonin.Cell proliferation was measured using a CCK-8 assay,and lactate secretion and HIF-1αprotein with a specific kit,respectively.The levels of estradiol and progesterone in the cell supernatant and rat serum were detected using ELISA.Granulosa cell apoptosis was detected by flow cytometry,ovarian morphology by HE staining,and Bax and caspase-3 expression by Western blotting.Results Compared with the normoxic group,the hypoxic group exhibited decreased granulosa cell proliferation,increased apoptosis,elevated lactate and HIF-1α levels,and reduced estradiol and progesterone levels(P<0.05).Compared with hypoxic group,these changes were significantly reversed in the molatonin group(P<0.05).Compared with the control group,the model group showed increased lactate,HIF-1α,Bax,and caspase-3 levels,decreased estradiol and progesterone levels,and reduced follicles.Compared with the model group,all the indicators were ameliorated in the intervention group(P<0.05).Conclusion Melatonin alleviated hypoxia-induced granulosa cell apoptosis and promoted the recovery of ovarian function.
4.Effects of facial emotion recognition on prosocial behavior of medical students in mask-obscured scenes:mediating effect of state empathy
Zhenming ZHANG ; Yingcan ZHENG ; Yingdan TANG ; Xinjie TAN ; Feifei WANG ; Jia WANG ; Mengyin ZHU ; Yitong XUE ; Guoyu YANG
Journal of Army Medical University 2024;46(13):1585-1592
Objective To explore the mediating effect of facial emotion recognition on prosocial behavior of medical students in mask-obscured scenes.Methods Fifty-three medical students from a medical university in Chongqing were enrolled from July to September 2023 to complete the facial emotion recognition task,the dictator gaming task and the state empathy test.Spearman correlation analysis was used to examine the correlation between mask wearing and state empathy,trait empathy and prosocial behaviours,and the PROCESS procedure was used to test the mediation of state empathy and the moderating effect of mask wearing or not.Results ①mask wearing,state empathy and prosocial behaviour were significantly correlated(P<0.01);② State empathy exerted mediated effect between facial emotion recognition and prosocial behavior,with the largest effect size(47%)for the relative mediating effect of sadness;③The interaction terms of facial emotion recognition and mask wearing had a significant effect on state empathy(P<0.05).Conclusion Facial emotion recognition can influence prosocial behavior directly and also exert indirect effect on prosocial behavior through state empathy.Compared to the condition without mask wearing,mask wearing can significantly facilitate the effect of happy,sad and neutral emotions on state empathy.
5.CBCT study on the safe location of palatal microscrew implant anchorage nail between maxillary first and second molars
LI Xinghan ; LI Jun ; MENG Yitong ; TANG Yulong ; XU Jialin ; YANG Ying ; DONG Yinjuan ; ZHANG Xiaodong
Journal of Prevention and Treatment for Stomatological Diseases 2022;30(1):39-44
Objective:
Conebeam CT (CBCT) was used to measure the palatine between the maxillary first and second molars. The proximal and distal palatal widths of the maxillary first and second molar and the palatal mucosal thickness and bone tissue thickness when microscrew implant anchorage nail were implanted at different angles provided a reference for the clinical selection of microscrew implant placement.
Methods:
The image data of 90 adult patients were selected as the research object, and the jaw bone was reconstructed by scanning. In maxillary palatine, selection of distances at 12 mm, 14 mm, 16 mm, and 18 mm from the palatal apex of maxillary first molar between the maxillary first and second molar were used as measurement, measured the proximal and distal palatal widths of maxillary first and second molar and the palatal mucosal thickness and bone tissue thickness when microscrew implant anchorage nails were implanted at 30 °, 45 °, 60 °, and 90 °. SPSS 26.0 software was used for one-way ANOVA and LSD pair comparison.
Results:
The larger the angle of the microscrew implant anchorage nail was, the smaller the proximal and distal medial widths between the maxillary first and second molar, and the difference was statistically significant (P < 0.05). Compared with the 90° direction, the proximal and distal medial widths of the microscrew implant anchorage nail were larger in the 60° direction. The greater the angle of implantation, the smaller the mucosal thickness and the greater the bone tissue thickness, and the results showed a significant difference (P < 0.001). Compared with the direction of 30° and 45°, the mucosal thickness at the direction of 60° was smaller, and the bone tissue thickness was larger. The higher the position of the microscrew implant anchorage nail, the greater the width of the proximal and distal medial, and the difference was statistically significant (P < 0.05). Compared with the positions 12 and 14 mm from the palatal tip, the proximal and distal medial widths of the microscrew implant anchorage nail were larger. The higher the implant position was, the greater the mucosal thickness and the smaller the bone tissue thickness. The results showed a significant difference (P < 0.001). Compared with the position of 18 mm from the palatal tip of the maxillary first molar, the mucosal thickness was smaller and the bone tissue thickness was larger.
Conclusion
It is most appropriate to implant microscrew implant anchorage nail at least 10 mm in length in the direction of 60° at the palatal apex 16 mm from the maxillary first molar in palatine between the first and second molar.
6.A multicenter study on the clinical features and risk factors of poor prognosis in neonatal necrotizing enterocolitis
Yueju CAI ; Liuhong QU ; Wei LI ; Xue FENG ; Liya MA ; Bingyan YANG ; Ping WANG ; Juan TANG ; Weiming YUAN ; Yanbin LI ; Xiaowen CHEN ; Zhe ZHANG ; Ning ZHAO ; Xiaohong HUANG ; Li TAO ; Mou WEI ; Heng SU ; Weichi DENG ; Kangcheng HE ; Yitong WANG ; Jinxing FENG ; Di GAO ; Yan HUANG ; Wei ZHOU
Chinese Journal of Applied Clinical Pediatrics 2019;34(1):24-29
Objective To explore the clinical features and risk factors of poor prognosis in neonatal necrotizing enterocolitis(NEC).Methods A retrospective study was carried out in the infants with NEC admitted to 6 cooperative hospitals in Guangdong Province between January 2005 and December 2014.The clinical features and risk factors of poor prognosis in preterm and full-term infants diagnosed NEC,early onset and late onset NEC were analyzed.Results A total of 449 cases who met the criteria were admitted during the study time.The mortality was 23.6% (106/449 cases),of which the preterm group was 24.6% (58/238 cases) while the full-term group was 22.7% (48/211 cases),the early onset group was 22.1% (45/204 cases) while the late onset group was 24.3% (57/235 cases).The median number of NEC onset in preterm group was 11 d after birth while the number of the full-term group was 6 d.Full-term infants who diagnosed NEC were more likely to manifest themselves as abdominal distension (52.1% vs.42.0%,x2 =4.597,P =0.032),vomiting(36.5% vs.17.2%,x2 =21.428,P =0.000) and bloody stool(30.3% vs.21.4%,x2 =4.653,P =0.031);but in the onset of NEC,preterm infants more likely to have feeding intolerance (21.0% vs.12.8%,x2=5.309,P =0.021).The early onset group of full-term NEC was much common in twins or multiplets(9.4% vs.1.1%,x2 =6.226,P =0.013),which rate of surgical therapy was much higher (41.0% vs.27.0%,P =0.036) and the breast-feeding rate before NEC was lower than the late onset group(14.5% vs.32.6%,x2 =9.500,P =0.002),the differences were statistically significant.The gestational age and birth weight were bigger in the early onset group of preterm NEC[(33.8 ±2.5) weeks vs.(32.2 ±2.8) weeks,t =4.261,P =0.000;(2.1 ±0.5) kg vs.(1.7 ± 0.5) kg,t =4.735,P =0.000)],but length of stay was shorter than the late onset group (18.0 d vs.26.5 d,P =0.000).Logistic regression analysis showed that the risk factors of poor prognosis of full-term NEC were shock,peritonitis and sepsis;while risk factors of poor prognosis of preterm NEC were small for gestational age infant,pulmonary hemorrhage,shock,intestinal perforation and sepsis;the risk factors of poor prognosis of the early onset group of full-term NEC was shock;while those of the late onset group were shock and peritonitis;the risk factors of poor prognosis in the early onset group of preterm NEC were shock and sepsis,while those in the late onset group were pulmonary hemorrhage,shock,intestinal perforation and sepsis.Conclusions Compared to the preterm NEC,the onset time of full-term NEC was earlier and the clinical manifestations were more typical.Early identification and management of shock,peritonitis,intestinal perforation,sepsis and pulmonary hemorrhage can reduce the risk of poor prognosis of neonate NEC.
7.Research on ligase-ELISA method for detecting K-ras gene mutations
Na XIAO ; Yitong TANG ; Haizhong CUI ; Zhishan LI ; Jiuming ZOU
Chongqing Medicine 2018;47(2):217-219
Objective To research a simple and sensitive K-ras gene mutations detection method in order to be suitable for the routine mutation detection.Methods The corresponding detection locus oligonucleotide probe was designed.By the connection,amplification,labeling and ELISA reaction in probe,the mutation locus genotype was determined by the ELISA reaction detection value.With the six point mutations of G12S,G12R,G12C,G12D,G12A and G12V in 12 codons of K-ras gene as the detection objects,the plasma circulation DNA sample in 72 cases of lung cancer was detected,then the results were compared with those obtained by the direct sequencing.Results Three samples were identified as the G12S,G12R and G12A mutatins by the established method.But no K-ras mutations were detected in the samples by using the direct sequencing,indicating that the direct sequencing had lower sensitivity and was not suitable for the mutation detection of heterogeneous samples such as circulating DNA.Conclusion The simple and sensitive K-ras gene mutation detection method is established and can conduct the routine mutation detection for the heterogeneous samples.
8.Study for gene mutation detection of circulating DNA with ligase-ELISA reaction
Haizhong CUI ; Na XIAO ; Yongping ZHANG ; Dagui CHEN ; Yitong TANG
Tianjin Medical Journal 2015;43(5):533-536
Objective To establish a single nucleotide polymorphisms genotyping (SNP) method for a convenient, accurate, and routine analysis of clinical samples. Methods Based on the design of oligonucleotide probe, the assay was performed through three steps:the conjunction of the detection probe, universal amplification, labeling and ELISA reaction. The genotype of each SNP was revealed by reading signals of each set of reaction tubes. This assay was applied to detect sixty-two plasma samples of lung cancer for circulating DNA for three SNPs of EGFR, c.2573T>G(L858R), EGFR, c.2582T>G>T(G719C). Results were compared with those obtained by direct sequencing. Results The heterozygote mutation was identified for L858R by both methods, although no mutation was detected for L861Q and G719C. Six samples were identified as heterozygotes with the new method, and only two samples were unambiguously identified as heterozygotes by the direct sequencing. Two additional samples could not be identified as heterozygotes because the peak of mutant allele was very low compared with that of wild allele. Conclusion The developed method enabled accurate identification of SNP in a convenient manner, and which is adapted to routine analysis from heterogeneous samples unambiguously.
9.A rapid detection method for single nucleotide polymorphisms based on ligase-agarose gel electrophoresis
Haizhong CUI ; Na XIAO ; Yongping ZHANG ; Dagui CHEN ; Yitong TANG ; Xuehong ZHAO ; Jinhui SHAO
Chongqing Medicine 2015;(10):1370-1373,1377
Objective To establish a simple,rapid and sensitive nucleotide polymorphisms genotyping method in order to conduct the routine clinical detections under the simple laboratory condition by this method.Methods Based on the ligase-agarose gel electrophoresis,the oligonucleotide detection probes of mutational sites was designed.The detection underwent the detection probe connecting,purification and universal amplification,finally the mutation genotypes of detection sites were judged by the ap-peared bands in the agarose gel electrophoresis(AGE).With the 3 SNP sites EGFR,c.2573T>G(L858R),EGFR,c.2582T> A (L861Q)and EGFR,c.2155 G>T(G719C)in epidermal growth factor receptor(EGFR)gene as the detection objects,the plasmid template and plasma circulating DNA sample in lung cancer were performed the detection.Results The established method was easy to operate with higher specificity and sensitivity.After 20-30 cycles of PCR amplification,the genotype of detection sites was clearly estimated according to the amplification band.When detecting the mixed alleles in the heterogeneous sample,minimal 2.5%mutation alleles could be detected out.This method and the direct sequencing method could respectively detect 6 cases and 2 cases of heterozygotes mutation in the SNP site of L858R among 62 samples of lung cancer.Conclusion The established detection method for SNP genotyping is suitable to the routine mutation detection on the heterogeneous samples under the simple laboratory condi-tion.
10.Alterations in Soleus Nerve Conduction Velocities Induced by Hindlimb Immobilization in Rats
Xuehong ZHAO ; Yan GAO ; Xiaoli FAN ; Yitong TANG
Chinese Journal of Rehabilitation Theory and Practice 2014;(7):626-628
Objective To observe the alterations in soleus nerve conduction velocities induced by hindlimb immobilization. Methods 24 healthy Sprague-Dawley rats were randomly divided into control group, immobilization 7 days group and immobilization 14 days group with 8 cases in each group. The plaster cast was fixed as the method to induce a hindllimb immobilization model in rats. The afferent thin fibers conduction velocity and the latency of M wave were observed with electrophysiological technique. Results 7 days after immobilization,the conduction velocity of muscle spindle primary afferent fiber decreased (P<0.05), the latency of M wave significantly prolonged 14 days after immobilization (P<0.05). Conclusion The soleus nerve conduction velocities decrease significantly following hindlimb immobilization and the alterations in afferent fibers are more serious than that in efferent fibers.


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