1.Research on The Genealogical Inference Efficiency of High-density SNPs
Jing LI ; Yi-Jie SUN ; Wen-Ting ZHAO ; Zi-Chen TANG ; Jing LIU ; Cai-Xia LI
Progress in Biochemistry and Biophysics 2026;53(3):740-753
ObjectiveThis study aims to explore the potential of different orders of magnitude single-nucleotide polymorphism (SNP) locus combinations for predicting distant kinship relationships. A high-density SNP locus set was constructed, and a comprehensive assessment of its inference capability was conducted. MethodsFirstly, we selected three commercial chip panels, CGA (Chinese genotyping array, Illumina), GSA (Global screening array, Illumina), Affy (23MF_V2 high-density SNP array, Affymetrix) and merged them after quality control, forming a high-density SNP locus panel(1 180 k). Secondly, we selected 161 samples and collected their peripheral blood samples by using whole-genome sequencing technology. Within this sample population, the levels of kinship relationships fully covered the range from level 1 to level 9, and the number of kinship pairs at each level was consistently maintained at over 50 pairs. From 161 samples data of whole-genome sequencing, the 1 180 k locus set was extracted, which is referred to as the high-density SNP locus set in the following text. The kinship inference was conducted using the identity-by-descent (IBD) algorithm with the selected optimal parameters. To comprehensively evaluate the performance of the high-density SNP locus set in kinship inference, we compared it with the three commercial chip panels, the intersection of these three chip loci, and the control sets constructed by randomly reducing the number of the high-density SNP locus set. Based on the changes in the IBD lengths, as well as the dynamic trends in prediction accuracy, we conducted a scientific assessment of the kinship inference capability of the high-density SNP locus set. ResultsAfter screening, a set of 1 184 334 autosomal SNPs was obtained. During the process of screening the optimal IBD length threshold, the result revealed that 0 cM, 1 cM, and 2 cM all demonstrated good applicability. However, to avoid the issue of a large amount of redundant information caused by setting a too low IBD length threshold, this study ultimately selected 2 cM as the optimal threshold. Compared with the average results of three chip panels, the high-density SNP locus set increased the total IBD length and the average IBD length across levels 1-9; the accuracy of the confidence interval for level 8 was 70.97%, which represented a 3.50% improvement; the average confidence interval accuracy for levels 1-8 was 91.39%, representing a 1.00% increase; and the false negative rates at levels 8 and 9 were reduced by 2.42% and 6.76%, respectively. The system efficacy of the high-density SNP locus set for kinship inference of first to eighth degree relationships reached 98.91%. Through random reduction of the high-density SNP locus set results, it is found that increasing the number of SNPs with the panel, the detection efficiency of IBD length showed a significant upward trend. At the same time, the overall trend in the accuracy of kinship relationship prediction as well as the confidence interval accuracy also indicated that both metrics steadily increased with the addition of more loci. ConclusionThe results show that the high-density SNPs panel significantly enhances the efficacy of distant kinship inference, accurately covering kinship degrees, with the average confidence interval accuracy for first to eighth degree relationships stably above 90%. The study finds that increasing the number of SNPs panel can improve the ability to predict distant kinship.
2.Evaluation of a deep learning-driven centerline extraction algorithm for optimizing the diagnosis of the"gray zone"in noninvasive coronary fractional flow reserve
Zi-qiang GUO ; Xi WANG ; Zi-nuan LIU ; Yi-pu DING ; Ran XIN ; Dong-kai SHAN ; Jun GUO ; Yun-dai CHEN ; Jun-jie YANG
Chinese Journal of Interventional Cardiology 2025;33(6):312-318
Objective To evaluate the diagnostic performance of the minimum-cost-path-based CT angiography-derived fractional flow reserve(MCP-FFR)and the deep learning-driven CT angiography-derived fractional flow reserve(DeepCL-FFR),and to particularly explore the potential value of the DeepCL algorithm in improving diagnostic accuracy within the"gray zone."Methods A retrospective analysis was conducted on 151 coronary vessels from 109 patients with coronary artery disease,who were hospitalized at the General Hospital of the People's Liberation Army between January 2020 and June 2021.Pearson correlation and Bland-Altman plots were employed to assess the correlation and agreement of the two CT-FFR methods with invasive FFR.A CT-FFR range of 0.70-0.80 was defined as the diagnostic"gray zone."The accuracy,sensitivity,specificity,positive predictive value,and negative predictive value for detecting hemodynamic abnormalities were calculated and analyzed.The DeLong test was used to compare the areas under the receiver operating characteristic curves(AUC)between the two CT-FFR calculation methods.Results Both CT-FFR methods exhibited a positive correlation with invasive FFR(MCP-FFR:r=0.75,P<0.001;DeepCL-FFR:r=0.86,P<0.001)and showed good agreement(MCP-FFR:mean difference=0.010,P=0.351;DeepCL-FFR:mean difference=-0.003,P=0.772).Both DeepCL-FFR(AUC 0.97,95%CI 0.94-0.99)and MCP-FFR(AUC 0.92,95%CI 0.88-0.97)demonstrated favorable diagnostic performance for detecting hemodynamic abnormalities(P=0.122).In the"gray zone"for hemodynamic abnormality,the diagnostic accuracy of MCP-FFR was 68.8%,whereas DeepCL-FFR increased it to 89.7%.DeepCL-FFR also exhibited superior diagnostic performance(AUC 0.89,95%CI 0.73-0.99)within the"gray zone,"which was significantly higher than that of MCP-FFR(AUC 0.71,95%CI 0.54-0.87)(P<0.001).Conclusions The deep learning-driven coronary centerline extraction algorithm,DeepCL,demonstrates superior diagnostic performance in CT-FFR for detecting hemodynamic abnormalities,particularly by significantly improving diagnostic accuracy in the"gray zone."
3.Mechanism of emodin improving cardiac hypertrophy in mice based on p38/ERK pathway
Jia SHI ; Sai-Ge SUN ; Yi-Lin HE ; Li XU ; Long-Xing LIU ; Zi-Jie GE ; Xiao-Yi ZOU ; Yu MA ; Yao-Cheng DING ; Kai QIAN
Chinese Pharmacological Bulletin 2025;41(7):1245-1252
Aim Mouse model of myocardial hypertro-phy was established via intraperitoneal injection of iso-proterenol(ISO)in mice.This approach allows for an in-depth investigation into the pharmacological effects and mechanisms of action of emodin,offering novel in-sights and directions for the improvement of myocardial hypertrophy.Methods The mice were randomly di-vided into the following groups:control group(CON),emodin group(EMO),MAPK activator control group(EMO+Ani),model group(ISO),treatment group(ISO+EMO),and activator intervention group(ISO+EMO+Ani).After treatment with emodin and inter-vention with MAPK activator,the heart weight ratio and cardiac size of each group were observed.Hematoxy-lin-eosin(HE)staining was used to observe the patho-logical changes in cardiac tissue,and kits were utilized to measure the levels of GSH,LDH,and MDA in the serum.Western blot was employed to detect the protein expression levels of inflammatory and oxidative factors,as well as p-p38,p-ERK,p38,and ERK in cardiac tis-sue.Results Emodin can significantly inhibit the production of myocardial inflammatory and oxidative factors induced by ISO,thereby effectively alleviating the degree of myocardial hypertrophy and fibrosis.Af-ter the p38/ERK signaling pathway was specifically ac-tivated by farnesol,the improvement effect of emodin on myocardial hypertrophy was weakened.Further comparison revealed that,compared with the myocardi-al hypertrophy pathological model group,the pathologi-cal protein expression levels in the farnesol-treated group showed no significant difference,and were even higher in some indicators.Conclusion Emodin can effectively inhibit the release of inflammatory factors and improve the state of oxidative stress by modulating the p38/ERK signaling pathway,thereby exerting an ameliorative effect on myocardial hypertrophy.
4.Compound Chaijin Jieyu formula modulates TLR4/NLRP3 signaling pathway to suppress central oxidative stress and ameliorate hippocampal synaptic plasticity impairment in depression
Lian-mei XUE ; De-guo LIU ; Qing-ping ZHANG ; Zi-rong LI ; Qian LIU ; Yi SHU ; Xiu-wen HUANG ; Li-dan LAN
Chinese Pharmacological Bulletin 2025;41(10):1972-1981
Aim To explore the mechanism by which the compound Chaijin Jieyu formula(CCJJY)regulates the TLR4/NLRP3 signaling pathway to inhibit central oxidative stress and improve hippocampal synaptic plasticity damage in depression.Methods SD rats were randomly divided into the control group,chronic unpredictable mild stress group,sleep deprivation group,chronic unpredictable mild stress combined with sleep deprivation group,positive drug group(venlafax-ine+melatonin),low-dose group of CCJJY,medium dose group of CCJJY,and high-dose group of CCJJY,with nine rats in each group.Except for the control group,a rat model of depression complicated with in-somnia was established using chronic unpredictable mild stress combined with sleep deprivation.Depres-sion-like and sleep behaviors in rats were evaluated through weight,food intake,water maze,and pento-barbital sodium tests.ELisa was used to detect ROS,AANAT,and HPLC-EC was used to detect 5-HT con-tent,while Western blot/RT-PCR was used to detect the expression of IL-1β,TLR4,NLRP3,PSD-95,and SYN related proteins and mRNA.HE and Golgic stai-ning were used to observe the pathological changes in the third ventricle,hippocampus,and neuronal synap-ses.Results Compared with the control group,the depression-like behaviors of the model group rats were significant.The expression of IL-1β,TLR4,and NL-RP3 in the hippocampus increased,while the expres-sion of PSD-95 and SYN decreased.Activation of NL-RP3 inflammasomes led to "sleeve like" pathological changes in the third ventricle,with hippocampal neu-rons undergoing apoptosis and significant damage to neuronal synaptic plasticity.Compared with the model group,after intervention with CCJJY,the expression of ROS,IL-1β,TLR4,and NLRP3 decreased,while the expression of AANAT,5-HT,PSD-95,and SYN in-creased.Pathological damage to the third ventricle and hippocampal neurons was repaired.Conclusion The CCJJY improves hippocampal synaptic plasticity dam-age in depression by regulating the TLR4/NLRP3 sig-naling pathway to inhibit central oxidative stress.
5.Effects of Aqueous Extract of Corn Silk Combined with Training on Exercise Function and Glycolipid Metabolism in Mice with Metabolic Syndrome
Yi-lin LIU ; Zi-ling SONG ; Ting ZHOU ; Ji-ping CHEN ; Zi-han LIN ; Yu-xuan ZHANG ; Ji-qiang ZENG ; Shan-rong ZHANG ; Zhi-peng WU ; Chen LU ; Ying ZHU
Progress in Modern Biomedicine 2025;25(15):2411-2420
Objective:To investigate the effects of combination therapy with aqueous extract of corn silk(CS)and training on exercise capacity and glycolipid metabolism in mice with metabolic syndrome(MS).Methods:In this study,db/db mice were used as the animal model of MS.The mice were administered aqueous extract of CS via gavage and subjected to different intensities of training for 12 weeks(3 months).The specific experimental design was as follows:24 db/db mice were randomly divided into four groups on average:negative control group(NC),aqueous extract of CS group(CS),aqueous extract of CS+moderate-intensity training group(CS+MT),and CS aqueous extract of CS+high-intensity training group(CS+HT).The maximum running speed,forelimb grip strength,body weight and fasting blood glucose of mice were measured before and after treatment.After the intervention,oral glucose tolerance test(OGTT)and insulin tolerance test(ITT)were conducted to assess glucose metabolism,while serum triglyceride(TG),total cholesterol(TC),high-density lipoprotein cholesterol(HDL-C),and low-density lipoprotein cholesterol(LDL-C)levels were measured to evaluate lipid metabolism.Results:After 3 months of intervention,there were significant differences in the maximum running speed and forelimb grip strength among the four groups(P<0.05).The maximum running speed and forelimb grip strength of CS group,CS+MT group and CS+HT group were higher than those of NC group(P<0.05).The CS+MT group exhibited higher forelimb grip strength,and the CS+HT group showed higher maximum running speed and forelimb grip strength compared to the CS group(P<0.05),while no significant difference was found between the CS+MT and CS+HT groups(P>0.05).Significant differences in body weight were observed among the four groups after 3 months of intervention(P<0.05).Specifically,the CS+MT and CS+HT groups exhibited significantly lower body weight compared to both the NC and CS groups(P<0.05),with the CS+MT group having the lowest body weight(P<0.05).Fasting blood glucose levels also differed significantly among the groups after 2 and 3 months of intervention(P<0.05).The CS,CS+MT,and CS+HT groups had lower fasting blood glucose levels compared to the NC group(P<0.05),with the CS+MT and CS+HT groups showing the lowest levels(P<0.05).No significant difference was found between the CS+MT and CS+HT groups(P>0.05).After 3 months of intervention,significant differences in the area under the curve(AUC)of OGTT and ITT were observed among the four groups(P<0.05).The AUC of OGTT and ITT were significantly lower in the CS,CS+MT,and CS+HT groups compared to the NC group(P<0.05).The CS+MT and CS+HT groups exhibited the lowest AUC values for both OGTT and ITT(P<0.05),with the CS+MT group showing the lowest AUC for OGTT(P<0.05).Significant differences in serum lipid levels were observed among the four groups after 3 months of intervention(P<0.05).TG,TC,and LDL-C levels were significantly lower,while HDL-C levels were higher in the CS,CS+MT,and CS+HT groups compared to the NC group(P<0.05).The CS+MT group had the lowest TG levels and the highest HDL-C levels compared to the CS+HT group(P<0.05),with no significant differences in TC and LDL-C levels between these two groups(P>0.05).Conclusion:Aqueous extract of CS combined with different intensity training can significantly improve the exercise capacity and glycolipid metabolism of MS mice and reduce body weight,especially CS combined with MT treatment is more effective in improving lipid metabolism.In addition,when combined with HT,aqueous extract of CS can also play an auxiliary role in reducing the side effects of high-intensity exercise and improving the therapeutic effect.
6.PD-L1 inhibits and regulates liver CD8+IFN-γ+ T cells to damage liver function and participate in atherosclerosis
Xiao LIU ; Xin WU ; Zi-yi ZHEN ; Jia-ying ZHANG ; Qi LI ; Chang CHEN
Chinese Pharmacological Bulletin 2025;41(4):638-645
Aim To study the effect of anti-PD-L1 monoclonal antibody on high-fat diet-induced athero-sclerosis in ApoE-/-mice.Methods Twenty-four ApoE-/-mice were randomly divided into the normal group,high-fat group,and high-fat+anti-PD-L1 mAb group.After 70 days,the blood samples were harves-ted.Blood vessels(aortic root to abdominal aorta)and liver from each groups were stained with Oil Red O.Hematoxylin-eosin staining(HE)was employed to vis-ualize structural changes in liver.Enzyme-linked im-munosorbent assay(ELISA)was applied to detect the serum levels of total cholesterol(CHO),triglyceride(TG),high-density lipoprotein(HDL-c),low-density lipoprotein(LDL-c)and inflammatory factors(IFN-γ,TNF-α,IL-1 β).Flow cytometry was used to detect the proportion of lymphocytes(CD4 and CD8).RT-PCR was utilized to assess the expressions of IFN-γ,TNF-α,IL-1 β,CD4 and CD8 in liver.Results Compared with the high-fat group,the treatment with anti-PD-L1 monoclonal antibody promoted vascular wall and liver lipid accumulation,and also up-regulated serum and liver content of cholesterol(CHO),triglyceride(TG)and high-density lipoprotein(HDL-c).Treatment with anti-PD-L1 monoclonal antibody up-regulated the con-tent of alanine aminotransferase(GPT)and aspartate aminotransferase(GOT)in serum and liver,but not al-kaline phosphatase(AKP).ELISA test indicated that treatment with anti-PD-L1 monoclonal antibody stimu-lated the serum level of IFN-γ,TNF-α and IL-1 β.Fur-thermore,the mRNA level of IFN-γ,TNF-α and IL-1 βin liver was also up-regulated after treatment with anti-PD-L1 monoclonal antibody.With flow cytometry,we observed that treatment with anti-PD-L1 monoclonal antibody promoted hepatic CD8+T and CD8+IFN-γ+T cell activation,but had no effect on CD4+IFN-γ+T cell activation under high-fat feeding conditions.Con-clusions Anti-PD-L1 monoclonal antibody adminis-tered under high-fat feeding conditions can damage liv-er function and aggravate atherosclerosis by activating liver CD8+IFN-γ+T cells.
7.Comparative Experimental Study of Nd∶YAG Laser Ablation of Fresh Isolated Pig Liver
Ruo-yu LIU ; Mu YUAN ; Hao LI ; Zi-yi ZHU ; Yu-lin TAN
Progress in Modern Biomedicine 2025;25(10):1613-1619,1657
Objective:To compare the characteristics and temperature changes of single and double fiber Nd∶YAG laser in fresh isolated pig liver,and to provide reference for clinical ablation treatment.Methods:Single-needle single-point and double-needle double-point ablations were perf ormed on fresh isolated pig livers using a 5 W power laser,and the morphology,range,and surrounding temperature changes of the ablation lesions caused by the two in vitro liver tissues were observed.Results:The ablation lesions were divided into carbonized area,necrotic area and deformed area from inside to outside.The carbonized area in the center of the ablation lesion in the double-fiber group was larger and the cell necrosis was more thorough.The aspect ratio(LD/TD)of the laser ablation lesion in the single-fiber group was larger than that in the double fiber group(P<0.001).The transverse diameter(TD)and volume(V)of the ablation lesion in the double-fiber group were larger than those in the single-fiber group(P<0.001).There was no significant difference in the longitudinal diameter(LD)of the ablation lesion between the double-fiber group and the single-fiber group(P>0.05).There was no significant difference in the temperature of 20 s,40 s and 60 s at 5 mm and 10 mm beside the ablation center between the two groups(all P>0.05).Conclusion:Under the condition of 5 W,the temperature changes around the single and double fiber ablation are similar.The single fiber is suitable for small tumor ablation,and the double fiber ablation range is larger,which can be used for one-time full coverage ablation of larger cancer nodules.
8.Evaluation of a deep learning-driven centerline extraction algorithm for optimizing the diagnosis of the"gray zone"in noninvasive coronary fractional flow reserve
Zi-qiang GUO ; Xi WANG ; Zi-nuan LIU ; Yi-pu DING ; Ran XIN ; Dong-kai SHAN ; Jun GUO ; Yun-dai CHEN ; Jun-jie YANG
Chinese Journal of Interventional Cardiology 2025;33(6):312-318
Objective To evaluate the diagnostic performance of the minimum-cost-path-based CT angiography-derived fractional flow reserve(MCP-FFR)and the deep learning-driven CT angiography-derived fractional flow reserve(DeepCL-FFR),and to particularly explore the potential value of the DeepCL algorithm in improving diagnostic accuracy within the"gray zone."Methods A retrospective analysis was conducted on 151 coronary vessels from 109 patients with coronary artery disease,who were hospitalized at the General Hospital of the People's Liberation Army between January 2020 and June 2021.Pearson correlation and Bland-Altman plots were employed to assess the correlation and agreement of the two CT-FFR methods with invasive FFR.A CT-FFR range of 0.70-0.80 was defined as the diagnostic"gray zone."The accuracy,sensitivity,specificity,positive predictive value,and negative predictive value for detecting hemodynamic abnormalities were calculated and analyzed.The DeLong test was used to compare the areas under the receiver operating characteristic curves(AUC)between the two CT-FFR calculation methods.Results Both CT-FFR methods exhibited a positive correlation with invasive FFR(MCP-FFR:r=0.75,P<0.001;DeepCL-FFR:r=0.86,P<0.001)and showed good agreement(MCP-FFR:mean difference=0.010,P=0.351;DeepCL-FFR:mean difference=-0.003,P=0.772).Both DeepCL-FFR(AUC 0.97,95%CI 0.94-0.99)and MCP-FFR(AUC 0.92,95%CI 0.88-0.97)demonstrated favorable diagnostic performance for detecting hemodynamic abnormalities(P=0.122).In the"gray zone"for hemodynamic abnormality,the diagnostic accuracy of MCP-FFR was 68.8%,whereas DeepCL-FFR increased it to 89.7%.DeepCL-FFR also exhibited superior diagnostic performance(AUC 0.89,95%CI 0.73-0.99)within the"gray zone,"which was significantly higher than that of MCP-FFR(AUC 0.71,95%CI 0.54-0.87)(P<0.001).Conclusions The deep learning-driven coronary centerline extraction algorithm,DeepCL,demonstrates superior diagnostic performance in CT-FFR for detecting hemodynamic abnormalities,particularly by significantly improving diagnostic accuracy in the"gray zone."
9.Mechanism of emodin improving cardiac hypertrophy in mice based on p38/ERK pathway
Jia SHI ; Sai-Ge SUN ; Yi-Lin HE ; Li XU ; Long-Xing LIU ; Zi-Jie GE ; Xiao-Yi ZOU ; Yu MA ; Yao-Cheng DING ; Kai QIAN
Chinese Pharmacological Bulletin 2025;41(7):1245-1252
Aim Mouse model of myocardial hypertro-phy was established via intraperitoneal injection of iso-proterenol(ISO)in mice.This approach allows for an in-depth investigation into the pharmacological effects and mechanisms of action of emodin,offering novel in-sights and directions for the improvement of myocardial hypertrophy.Methods The mice were randomly di-vided into the following groups:control group(CON),emodin group(EMO),MAPK activator control group(EMO+Ani),model group(ISO),treatment group(ISO+EMO),and activator intervention group(ISO+EMO+Ani).After treatment with emodin and inter-vention with MAPK activator,the heart weight ratio and cardiac size of each group were observed.Hematoxy-lin-eosin(HE)staining was used to observe the patho-logical changes in cardiac tissue,and kits were utilized to measure the levels of GSH,LDH,and MDA in the serum.Western blot was employed to detect the protein expression levels of inflammatory and oxidative factors,as well as p-p38,p-ERK,p38,and ERK in cardiac tis-sue.Results Emodin can significantly inhibit the production of myocardial inflammatory and oxidative factors induced by ISO,thereby effectively alleviating the degree of myocardial hypertrophy and fibrosis.Af-ter the p38/ERK signaling pathway was specifically ac-tivated by farnesol,the improvement effect of emodin on myocardial hypertrophy was weakened.Further comparison revealed that,compared with the myocardi-al hypertrophy pathological model group,the pathologi-cal protein expression levels in the farnesol-treated group showed no significant difference,and were even higher in some indicators.Conclusion Emodin can effectively inhibit the release of inflammatory factors and improve the state of oxidative stress by modulating the p38/ERK signaling pathway,thereby exerting an ameliorative effect on myocardial hypertrophy.
10.Comparative Experimental Study of Nd∶YAG Laser Ablation of Fresh Isolated Pig Liver
Ruo-yu LIU ; Mu YUAN ; Hao LI ; Zi-yi ZHU ; Yu-lin TAN
Progress in Modern Biomedicine 2025;25(10):1613-1619,1657
Objective:To compare the characteristics and temperature changes of single and double fiber Nd∶YAG laser in fresh isolated pig liver,and to provide reference for clinical ablation treatment.Methods:Single-needle single-point and double-needle double-point ablations were perf ormed on fresh isolated pig livers using a 5 W power laser,and the morphology,range,and surrounding temperature changes of the ablation lesions caused by the two in vitro liver tissues were observed.Results:The ablation lesions were divided into carbonized area,necrotic area and deformed area from inside to outside.The carbonized area in the center of the ablation lesion in the double-fiber group was larger and the cell necrosis was more thorough.The aspect ratio(LD/TD)of the laser ablation lesion in the single-fiber group was larger than that in the double fiber group(P<0.001).The transverse diameter(TD)and volume(V)of the ablation lesion in the double-fiber group were larger than those in the single-fiber group(P<0.001).There was no significant difference in the longitudinal diameter(LD)of the ablation lesion between the double-fiber group and the single-fiber group(P>0.05).There was no significant difference in the temperature of 20 s,40 s and 60 s at 5 mm and 10 mm beside the ablation center between the two groups(all P>0.05).Conclusion:Under the condition of 5 W,the temperature changes around the single and double fiber ablation are similar.The single fiber is suitable for small tumor ablation,and the double fiber ablation range is larger,which can be used for one-time full coverage ablation of larger cancer nodules.

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