1.Predicting Diabetic Retinopathy Using a Machine Learning Approach Informed by Whole-Exome Sequencing Studies.
Chong Yang SHE ; Wen Ying FAN ; Yun Yun LI ; Yong TAO ; Zu Fei LI
Biomedical and Environmental Sciences 2025;38(1):67-78
OBJECTIVE:
To establish and validate a novel diabetic retinopathy (DR) risk-prediction model using a whole-exome sequencing (WES)-based machine learning (ML) method.
METHODS:
WES was performed to identify potential single nucleotide polymorphism (SNP) or mutation sites in a DR pedigree comprising 10 members. A prediction model was established and validated in a cohort of 420 type 2 diabetic patients based on both genetic and demographic features. The contribution of each feature was assessed using Shapley Additive explanation analysis. The efficacies of the models with and without SNP were compared.
RESULTS:
WES revealed that seven SNPs/mutations ( rs116911833 in TRIM7, 1997T>C in LRBA, 1643T>C in PRMT10, rs117858678 in C9orf152, rs201922794 in CLDN25, rs146694895 in SH3GLB2, and rs201407189 in FANCC) were associated with DR. Notably, the model including rs146694895 and rs201407189 achieved better performance in predicting DR (accuracy: 80.2%; sensitivity: 83.3%; specificity: 76.7%; area under the receiver operating characteristic curve [AUC]: 80.0%) than the model without these SNPs (accuracy: 79.4%; sensitivity: 80.3%; specificity: 78.3%; AUC: 79.3%).
CONCLUSION
Novel SNP sites associated with DR were identified in the DR pedigree. Inclusion of rs146694895 and rs201407189 significantly enhanced the performance of the ML-based DR prediction model.
Diabetic Retinopathy/diagnosis*
;
Humans
;
Machine Learning
;
Male
;
Female
;
Polymorphism, Single Nucleotide
;
Middle Aged
;
Exome Sequencing
;
Aged
;
Adult
;
Pedigree
;
Diabetes Mellitus, Type 2/complications*
;
Genetic Predisposition to Disease
;
Mutation
2.Significance of echocardiography in distinguishing between two main subtypes of myocardial amyloidosis
Chong FAN ; Leilei PEI ; Chun YANG ; Tao ZHANG ; Wenjin ZHU ; Shun WANG
Journal of Xi'an Jiaotong University(Medical Sciences) 2024;45(5):789-793
Objective To explore the application value of echocardiography in the differential diagnosis of transthyretin cardiac amyloidosis(ATTR-CA)and immunoglobulin light chain cardiac amyloidosis(AL-CA).Methods We conducted a retrospective analysis of echocardiographic parameters of 50 confirmed CA patients diagnosed between November 2021 and January 2024 at The First Affiliated Hospital of Xi'an Jiaotong University,including 6 cases of ATTR and 44 cases of AL.Parameters that could potentially distinguish between the two subtypes were selected using t-tests and x2 tests,and the diagnostic capabilities of these parameters for the two subtypes were analyzed using receiver operating characteristic(ROC)curves.Results There were no statistically significant differences in general characteristics,global longitudinal strain(GLS),ratio of apical to basal strain,ejection fraction to GLS ratio(EFSR),maximum thickness of left ventricular myocardium,relative thickness of left ventricular wall,presence of thickened atrioventricular valves,or presence of enlarged atria between ATTR and AL groups(P>0.05).The interventricular septal thickness was greater than in ATTR group than in AL group(P<0.05),and the E/e'ratio(ratio of spectral Doppler early diastolic peak velocity to tissue Doppler early diastolic peak velocity)was greater in ATTR group than in AL group(P<0.05).ROC curve analysis showed that the areas under the curve for distinguishing between the two subtypes based on interventricular septal thickness and E/e'ratio were 0.891(95%CI:0.792-0.991)and 0.826(95%CI:0.698-0.955),respectively,with a sensitivity of 100.00%and specificity of 95.24%for combined diagnosis.Conclusion Echocardiographic parameters,including E/e'ratio and interventricular septal thickness,may have clinical significance in distinguishing between the two main subtypes of CA in patients.
3.Development of a High-throughput Sequencing Platform for Detection of Viral Encephalitis Pathogens Based on Amplicon Sequencing
Li Ya ZHANG ; Zhe Wen SU ; Chen Rui WANG ; Yan LI ; Feng Jun ZHANG ; Hui Sheng LIU ; He Dan HU ; Xiao Chong XU ; Yu Jia YIN ; Kai Qi YIN ; Ying HE ; Fan LI ; Hong Shi FU ; Kai NIE ; Dong Guo LIANG ; Yong TAO ; Tao Song XU ; Feng Chao MA ; Yu Huan WANG
Biomedical and Environmental Sciences 2024;37(3):294-302
Objective Viral encephalitis is an infectious disease severely affecting human health.It is caused by a wide variety of viral pathogens,including herpes viruses,flaviviruses,enteroviruses,and other viruses.The laboratory diagnosis of viral encephalitis is a worldwide challenge.Recently,high-throughput sequencing technology has provided new tools for diagnosing central nervous system infections.Thus,In this study,we established a multipathogen detection platform for viral encephalitis based on amplicon sequencing. Methods We designed nine pairs of specific polymerase chain reaction(PCR)primers for the 12 viruses by reviewing the relevant literature.The detection ability of the primers was verified by software simulation and the detection of known positive samples.Amplicon sequencing was used to validate the samples,and consistency was compared with Sanger sequencing. Results The results showed that the target sequences of various pathogens were obtained at a coverage depth level greater than 20×,and the sequence lengths were consistent with the sizes of the predicted amplicons.The sequences were verified using the National Center for Biotechnology Information BLAST,and all results were consistent with the results of Sanger sequencing. Conclusion Amplicon-based high-throughput sequencing technology is feasible as a supplementary method for the pathogenic detection of viral encephalitis.It is also a useful tool for the high-volume screening of clinical samples.
4.Associations of onset age, diabetes duration and glycated hemoglobin level with ischemic stroke risk in type 2 diabetes patients: a prospective cohort study
Xikang FAN ; Mengyao LI ; Yu QIN ; Chong SHEN ; Yan LU ; Zhongming SUN ; Jie YANG ; Ran TAO ; Jinyi ZHOU ; Dong HANG ; Jian SU
Chinese Journal of Epidemiology 2024;45(4):498-505
Objective:To investigate the associations of onset age, diabetes duration, and glycated hemoglobin (HbA1c) levels with ischemic stroke risk in type 2 diabetes patients.Methods:The participants were from Comprehensive Research on the Prevention and Control of the Diabetes in Jiangsu Province. The study used data from baseline survey from December 2013 to January 2014 and follow-up until December 31, 2021. After excluding the participants who had been diagnosed with stroke at baseline survey and those with incomplete information on onset age, diabetes duration, and HbA1c level, a total of 17 576 type 2 diabetes patients were included. Cox proportional hazard model was used to calculate the hazard ratio ( HR) and 95% CI of onset age, diabetes duration, and HbA1c level for ischemic stroke. Results:During the median follow-up time of 8.02 years, 2 622 ischemic stroke cases were registered. Multivariate Cox proportional risk regression model showed that a 5-year increase in type 2 diabetes onset age was significantly associated with a 5% decreased risk for ischemic stroke ( HR=0.95, 95% CI: 0.92-0.99). A 5-year increase in diabetes duration was associated with a 5% increased risk for ischemic stroke ( HR=1.05, 95% CI: 1.02-1.10). Higher HbA1c (per 1 standard deviation increase: HR=1.17, 95% CI: 1.13-1.21) was associated with an increased risk for ischemic stroke. Conclusion:The earlier onset age of diabetes, longer diabetes duration, and high levels of HbA1c are associated with an increased risk for ischemic stroke in type 2 diabetes patients.
5.Association of serum gamma-glutamyl transferase levels with cardiovascular disease risk in type 2 diabetes patients: a prospective cohort study
Mian WANG ; Xikang FAN ; Jian SU ; Yu QIN ; Chong SHEN ; Yan LU ; Zhongming SUN ; Jie YANG ; Ran TAO ; Jinyi ZHOU ; Ming WU
Chinese Journal of Epidemiology 2024;45(10):1339-1347
To investigate the associations of serum gamma-glutamyl transferase (GGT) levels with the risk of cardiovascular disease (CVD) and its subtypes in patients with type 2 diabetes mellitus (T2DM) in Jiangsu Province.Methods:The participants were enrolled in the Comprehensive Research project regarding 'Prevention and Control of Diabetes' in Jiangsu Province. The baseline survey was conducted from 2013 to 2014, and follow-up until December 31, 2021. After excluding the participants who self-reported with chronic liver disease/stroke/coronary heart disease at baseline survey and those with incomplete information on GGT, a total of 16 147 T2DM patients were included in the final analysis. Cox proportional hazard regression models were used to calculate the hazard ratio ( HR) and their 95% CI of GGT for CVD, myocardial infarction, and stroke. Restricted cubic spline models were applied to analyze the dose-response relationship between GGT and the risk of CVD and its subtypes. Results:During the median follow-up time of 8.02 years, 2 860 CVD cases were registered, including 196 cases of myocardial infarction and 2 730 cases of stroke. Multivariate Cox proportional risk regression model indicated that compared to the lowest serum GGT level group, the highest GGT level group had a 24% increased risk of CVD ( HR=1.24, 95% CI: 1.09-1.41) and a 23% increased risk of stroke ( HR=1.23, 95% CI: 1.08-1.40). The restricted cubic spline model showed a nonlinear dose-response relationship between GGT and the risk of CVD, myocardial infarction, and stroke in T2DM patients. Conclusions:High levels of GGT may be associated with an increased risk of cardiovascular disease in T2DM patients, which needs further exploration and validation in future clinical practice.
6.C-X3-C motif chemokine ligand 1/C-X3-C motif chemokine receptor 1 pathway in the recovery of memory function in hemorrhagic shock/resuscitation rats
Xiao-Jun WU ; Ri-Xing WANG ; Fang-Chong LIN ; You-Kai LÜ ; Qi-Tao FENG ; Tian-Qi YUN
Acta Anatomica Sinica 2024;55(2):158-166
Objective To investigate the effect of microglia activation regulated by C-X3-C motif chemokine ligand 1(CX3CL1)-C-X3-C motif chemokine receptor 1(CX3CR1)pathway on memory function in hemorrhagic shock/resuscitation rats.Methods The experiment was divided into two parts.In the first part,the rats were randomly divided into sham group,model-0.5 hour group,model-1.5 hour group,model-3 hour group,10 rats in each group.There were differences in the time of hemorrhagic shock among each group.In the second part,rats were randomly divided into control group and CX3CL1 group,10 rats in each group.The rats in CX3CL1 group were treated with CX3CL1 protein factor(intraventricular injection),and the rats in control group were treated with saline.All rats were trained in Morris water maze experiments before model construction,and tests of Morris water maze experiments were carried out after 4 days of model construction.After completion,the whole brains were taken for HE staining and immunohistochemical staining.Cerebrospinal fluid was taken for detection of inflammatory cytokines,and hippocampus tissues were taken for Real-time PCR detection and Western blotting detection.Results Compared with the sham group,the escape latency of rats in model group increased,the number of platform crossings and the resident time in the third quadrant decreased.The neuronal state was impaired in HE staining in model group.In addition,compared with the sham group,the expression of ionized calcium binding adaptor molecule-1(Iba1)in the brain of the rats in model group increased,the contents of tumor necrosis factor-α(TNF-α)and interleukin(IL)-6 in the cerebrospinal fluid increased,and the M1-type microglia markers CD16,TNF-α,IL-1β and inducible nitric oxide synthase(iNOS)mRNA content increased.At the same time,compared with the sham group,the expressions of CX3CL1 and CX3CR1 in the brain of model group decreased,and the expressions of phosphorylated nuclear factor-κB(p-NF-κB)and nucleotide binding oligomerization domain(NOD)-like receptor protein 3(NLRP3)increased.However,compared with the control group,rats in CX3CL1 group had reduced escape latency,increased platform crossing times and quadrantⅢresident time,and recovered neuronal states.In addition,the expression of Iba1 in the brain of CX3CL1 group decreased,the contents of TNF-α and IL-6 in the cerebrospinal fluid decreased,the mRNA contents of M1-type microglia markers like CD16,TNF-α,IL-1β and iNOS decreased,and the mRNA contents of markers of M2-type microglia glial like CD206,transforming growth factor-β(TGF-β),arginase-1(Arg1),Chitinase 3-like protein 1(Ym 1)increased.Conclusion CX3CL1 can help inhibit the excessive activation of microglia,induce the polarization of microglia to M2 type,inhibit the polarization of M1 type,reduce the release of inflammatory cytokines,and alleviate the memory function damage induced by hemorrhagic shock/resuscitation.
7.Development of a Prognostic Model for Overall Survival Adult Patients with Core Binding Factor Acute Myeloid Leukaemia
Lu-Yao SHI ; Ling-Ling LI ; Tao LI ; Ya-Fei LI ; Yan-Fang LIU ; Zhong-Xing JIANG ; Shu-Juan WANG ; Chong WANG
Journal of Experimental Hematology 2024;32(3):693-701
Objective:To analyze the factors affecting overall survival(OS)of adult patients with core-binding factor acute myeloid leukemia(CBF-AML)and establish a prediction model.Methods:A total of 216 newly diagnosed patients with CBF-AML in the First Affiliated Hospital of Zhengzhou University from May 2015 to July 2021 were retrospectively analyzed.The 216 CBF-AML patients were divided into the training and the validation cohort at 7:3 ratio.The Cox regression model was used to analyze the clinical factors affecting OS.Stepwise regression was used to establish the optimal model and the nomogram.Receiver operating characteristic(ROC)curve,calibration curve and decision curve analysis(DCA)were used to evaluate the model performance.Results:Age(≥ 55 years old),peripheral blood blast(≥80%),fusion gene(AML1-ETO),KIT mutations were identified as independent adverse factors for OS.The area under the ROC curve at 3-year was 0.772 and 0.722 in the training cohort and validation cohort,respectively.The predicted value of the calibration curve is in good agreement with the measured value.DCA shows that this model performs better than a single factor.Conclusion:This prediction model is simple and feasible,and can effectively predict the OS of CBF-AML,and provide a basis for treatment decision.
8.Spinal endoscopic technique in the surgical treatment of thoracic ossification of the ligamentum flavum
Xiangbin WANG ; Chong WANG ; Yong LI ; Tao LI ; Yubin LONG
Chinese Journal of Surgery 2024;62(8):793-797
Thoracic ossification of the ligamentum flavum (TOLF) is a pathological heterotopic ossification disease in which the fibrous tissue of the ligamentum flavum of the thoracic spine converts into bony tissue, often leading to thoracic spinal stenosis and compression of the thoracic spinal cord nerve. When TOLF patients present with symptoms of spinal cord nerve compression, surgical treatment is usually required, and traditional open surgery is more invasive and carries a higher risk of spinal cord nerve injury. In recent years, domestic and foreign researchers have tried to apply spinal endoscopic techniques such as microendoscopy, percutaneous foraminoscopy, and unilateral biportal endoscopy for the treatment of TOLF, which can maximize the preservation of normal bone while achieving adequate decompression of the spinal cord nerve, with less damage to spinal stability, and have the advantages of less surgical trauma, less bleeding, and faster postoperative recovery. Due to the special anatomical structure of the thoracic vertebra, spinal endoscopic techniques should focus on safety and it is recommended that they are performed in experienced centers, and surgical indications should be strictly controlled.
9.Development of a Traditional Chinese Medicine syndrome diagnosis scale for long-term simulated weightlessness experiments
Hongzhi SHI ; Chong XU ; Jiatuo XU ; Quanchun FAN ; Junlian LIU ; Liping TU ; Xiaojuan HU ; Chengpu ZHANG ; Shuang ZHAO ; Tao MI ; Yongzhi LI ; Yinghui LI
Space Medicine & Medical Engineering 2024;35(1):8-14
Objective To develop a Traditional Chinese Medicine(TCM)syndrome diagnosis scale suitable for evaluating the overall health status of participants in long-term simulated weightlessness experiments,and preliminarily evaluate its reliability and validity.Methods Based on the understanding of the pathogenesis of TCM in different stages of long-term manned spaceflight,a scale was developed through literature research and expert consultation.Test-retest reliability and internal consistency coefficient were used to test the reliability of the scale.Item analysis and factor principal component analysis were used to evaluate the validity of the scale,and a rotating component matrix was used to analyze the correlation between each item and dimension using 36 volunteers in a 90 days head down bed rest experiment as the research subjects.Results The scale contains eight dimensions and 57 items.The reliability analysis showed that the correlation coefficient of the total score of the scale for the first and second tests of 30 participants was 0.889,indicating high stability of the scale.The Cronbach coefficient of the scale was 0.934,indicating very good internal consistency.The split half reliability after correction was 0.858,indicating a high reliability of the scale.The validity analysis showed that the difference between the high score group and the low score one for each of the 57 items was statistically significant(P<0.01),and the Pearson correlation coefficient between each item and the total score of the scale was greater than 0.4(P<0.001).The cumulative contribution rate of 8 common factors extracted using principal component factor analysis was 55.293%,and the results of rotating component matrix analysis,after applying TCM theory and expert feedback,had a coincidence of up to 87.5%with the initial 8 dimensions,indicating good structural validity of the scale.Conclusion The scale has good reliability and validity,and can diagnose TCM syndromes.It is suitable for long-term simulated weightlessness experiment and provides an objective and quantitative new method for evaluating the subjective feelings of participants.
10.Bioequivalence study of pyrazinamide tablets in Chinese healthy subjects
Li-Bing YE ; Chong YAO ; Ying-Rong CHEN ; Lu-Yuan TONG ; Tao YANG ; Xiao LU ; Min XU ; Qiu-Yue JIN ; Shui-Xin YANG
The Chinese Journal of Clinical Pharmacology 2024;40(15):2236-2240
Objective To evaluate the bioequivalence and safety of two pyrazinamide tablets in healthy Chinese subjects.Methods An open,randomized,single-dose,two-sequence,two-cycle,double-cross trial design was used.All 48 healthy subjects(24 in fasting and 24 in fed trial)were randomized to receive a single oral dose of a 0.5 g pyrazinamide tablet(test or reference)per cycle.The plasma concentration of the drug was determined by liquid chromatography coupled to tandem mass spectrometry method.The pharmacokinetic parameters were calculated by WinNonlin v8.2,and the bioequivalence was evaluated by SAS 9.4.Results In the fasting group,the Cmax of the test and reference preparation of pyrazinamide tablets were(13.28±2.82)and(12.88±4.49)μg·mL-1,the AUC0-t were(139.17±26.58)and(138.63±28.92)h·μg·mL-1,the AUC0-∞ were(148.96±33.65)and(148.71±36.97)h·μg·mL-1 respectively.In the fed group,the Cmax of the test and reference preparation of pyrazinamide tablets were(11.89±1.96)and(11.99±1.92)μg·mL-1,the AUC0-t were(138.22±37.21)and(141.68±25.80)h·μg·mL-1,the AUC0-∞ were(152.20±32.41)and(151.04±28.05)h·μg·mL-,respectively.The 90%confidence intervals of Cmax,AUC0-t and AUC0-∞ geometric mean ratios of the test and reference preparation were all within 80.00%to 125.00%.The incidence of adverse events was 16.70%for both the test and reference preparation in the fasting group and 8.30%for both the test and reference preparation in the fed group,all of which were mild in severity.Conclusion The test and reference preparation of pyrazinamide tablets were bioequivalent,safe and well tolerated in healthy Chinese subjects under fasting and fed conditions.

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