1.Statistical methods for extremely unbalanced data in genome-wide association study (1)
Ning XIE ; Wenjian BI ; Zhongwen ZHANG ; Fang SHAO ; Yongyue WEI ; Yang ZHAO ; Ruyang ZHANG ; Feng CHEN
Chinese Journal of Epidemiology 2024;45(11):1582-1589
Extremely unbalanced data here refers to datasets where the values of independent or dependent variables exhibit severe unbalance in proportions, such as extremely unbalanced case-control ratio, very low incidence rate of disease, heavily censored time-to-event data, and low-frequency or rare variants. In such scenarios, the statistic derived from hypothesis test using the classical statistical method, e.g., logistic regression model and Cox proportional hazard regression model, might deviate from theoretical asymptotic distribution, resulting in inflation or deflation of type I error. With the increased availability and exploration of resources from large-scale population cohorts in genome-wide association study (GWAS), there is a growing demand for effective and accurate statistical approaches to handle extremely unbalanced data in independent and non-independent samples. Our study introduces classical statistical methods in genetic statistics firstly, then, summarizes the failure of classical statistical methods in dealing with extremely unbalanced data through simulation experiments to draw researchers' attention to the extremely unbalanced data in GWAS.
2.Chinese expert consensus on refined diagnosis,treatment,and management of advanced primary liver cancer(2023 edition)
Liu XIUFENG ; Xia FENG ; Chen YUE ; Sun HUICHUAN ; Yang ZHENGQIANG ; Chen BO ; Zhao MING ; Bi XINYU ; Peng TAO ; Ainiwaer AIZIER ; Luo ZHIWEN ; Wang FUSHENG ; Lu YINYING ; National Clinical Research Center for Infectious Diseases ; Society of Hepatology,Beijing Medical Association ; Translational Medicine Branch,China Association of Gerontology and Geriatrics
Liver Research 2024;8(2):61-71
Hepatocellular carcinoma(HCC),commonly known as primary liver cancer,is a major cause of malignant tumors and cancer-related deaths in China,accounting for approximately 85%of all cancer cases in the country.Several guidelines have been used to diagnose and treat liver cancer.However,these guidelines provide a broad definition for classifying advanced liver cancer,with an emphasis on a singular approach,without considering treatment options for individual patients.Therefore,it is necessary to establish a comprehensive and practical expert consensus,specifically for China,to enhance the diagnosis and treatment of HCC using the Delphi method.The classification criteria were refined for Chinese patients with HCC,and the corresponding optimal treatment regimen recommendations were developed.These recommendations took into account various factors,including tumor characteristics,vascular tumor thrombus grade,distant metastasis,liver function status,portal hypertension,and the hepatitis B virus replication status of patients with primary HCC,along with treatment prognosis.The findings and rec-ommendations provide detailed,scientific,and reasonable individualized diagnosis and treatment strategies for clinicians.
3.mfat-1 gene therapy prevents and ameliorates multiple sclerosis in mice
Min-Yi TANG ; Xin-Yun BI ; Shuai WANG ; Chao-Feng XING ; Xiao-Li WU ; Zi-Jian ZHAO ; Fang-Hong LI
Chinese Pharmacological Bulletin 2024;40(10):1930-1936
Aim To investigate the preventive and therapeutic effects of the mfat-1 gene therapy on exper-imental autoimmune encephalomyelitis in mice.Meth-ods mfat-1 gene therapy was used to render the host endogenous capability of producing ω-3 PUFAs,con-comitantly reduce the levels of ω-6 PUFAs,and change the proportion of ω-3/ω-6 PUFAs.Then,the levels of PUFAs in blood were analyzed by gas chromatography.The neurological deficits in mice were evaluated by neurological dysfunction score.HE staining and LFB staining of mouse spinal cord slices were used to ob-serve central nervous system inflammation infiltration and demyelinating lesions.Flow cytometry microsphere microarray technology was used to detect the content of cytokines in serum.Results The mfat-1 gene therapy could significantly raise the proportion of ω-3/ω-6 PU-FAs(P<0.05),markedly delay the incubation period and peak period and reduce neurological dysfunction scores(P<0.05),and improve inflammation and de-myelination of spinal cords(P<0.05).It could also greatly increase the levels of IL-2,IFN-γ,IL-4 and IL-17 in serum(P<0.05).Conclusion The pro-portion of ω-3/ω-6 PUFAs in blood circulation en-hanced by mfat-1 gene therapy can effectively prevent and treat experimental autoimmune encephalomyelitis in mice.
4.A new xanthone from hulls of Garcinia mangostana and its cytotoxic activity.
Feng-Ning ZHAO ; Qi NIU ; Die XIAO ; Hao-Nan XU ; Hao-Xin WANG ; Rong-Lu BI ; Hong-Ping HE ; Zhi-Yong JIANG
China Journal of Chinese Materia Medica 2023;48(21):5817-5821
Eight compounds were isolated from ethyl acetate fraction of 80% ethanol extract of the hulls of Garcinia mangostana by silica gel, Sephadex LH-20 column chromatography, as well as prep-HPLC methods. By HR-ESI-MS, MS, 1D and 2D NMR spectral analyses, the structures of the eight compounds were identified as 16-en mangostenone E(1), α-mangostin(2), 1,7-dihydroxy-2-(3-methy-lbut-2-enyl)-3-methoxyxanthone(3), cratoxyxanthone(4), 2,6-dimethoxy-para-benzoquinone(5), methyl orselinate(6), ficusol(7), and 4-(4-carboxy-2-methoxyphenoxy)-3,5-dimethoxybenzoic acid(8). Compound 1 was a new xanthone, and compound 4 was a xanthone dimer, compound 5 was a naphthoquinone. All compounds were isolated from this plant for the first time except compounds 2 and 3. Cytotoxic bioassay suggested that compounds 1, 2 and 4 possessed moderate cytotoxicity, suppressing HeLa cell line with IC_(50) va-lues of 24.3, 35.5 and 17.1 μmol·L~(-1), respectively. Compound 4 also could suppress K562 cells with an IC_(50) value of 39.8 μmol·L~(-1).
Humans
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Garcinia mangostana/chemistry*
;
HeLa Cells
;
Antineoplastic Agents
;
Magnetic Resonance Spectroscopy
;
Xanthones/pharmacology*
;
Garcinia/chemistry*
;
Plant Extracts/chemistry*
;
Molecular Structure
5.Expert consensus for the clinical application of autologous bone marrow enrichment technique for bone repair (version 2023)
Junchao XING ; Long BI ; Li CHEN ; Shiwu DONG ; Liangbin GAO ; Tianyong HOU ; Zhiyong HOU ; Wei HUANG ; Huiyong JIN ; Yan LI ; Zhonghai LI ; Peng LIU ; Ximing LIU ; Fei LUO ; Feng MA ; Jie SHEN ; Jinlin SONG ; Peifu TANG ; Xinbao WU ; Baoshan XU ; Jianzhong XU ; Yongqing XU ; Bin YAN ; Peng YANG ; Qing YE ; Guoyong YIN ; Tengbo YU ; Jiancheng ZENG ; Changqing ZHANG ; Yingze ZHANG ; Zehua ZHANG ; Feng ZHAO ; Yue ZHOU ; Yun ZHU ; Jun ZOU
Chinese Journal of Trauma 2023;39(1):10-22
Bone defects caused by different causes such as trauma, severe bone infection and other factors are common in clinic and difficult to treat. Usually, bone substitutes are required for repair. Current bone grafting materials used clinically include autologous bones, allogeneic bones, xenografts, and synthetic materials, etc. Other than autologous bones, the major hurdles of rest bone grafts have various degrees of poor biological activity and lack of active ingredients to provide osteogenic impetus. Bone marrow contains various components such as stem cells and bioactive factors, which are contributive to osteogenesis. In response, the technique of bone marrow enrichment, based on the efficient utilization of components within bone marrow, has been risen, aiming to extract osteogenic cells and factors from bone marrow of patients and incorporate them into 3D scaffolds for fabricating bone grafts with high osteoinductivity. However, the scientific guidance and application specification are lacked with regard to the clinical scope, approach, safety and effectiveness. In this context, under the organization of Chinese Orthopedic Association, the Expert consensus for the clinical application of autologous bone marrow enrichment technique for bone repair ( version 2023) is formulated based on the evidence-based medicine. The consensus covers the topics of the characteristics, range of application, safety and application notes of the technique of autologous bone marrow enrichment and proposes corresponding recommendations, hoping to provide better guidance for clinical practice of the technique.
6.Factors influencing bilirubin elevation and its correlation with UGT1A1 gene polymorphism in the early postoperative period of transjugular intrahepatic portosystemic shunt.
Bi Feng ZHANG ; Jian FANG ; Zhi Qiang ZHANG ; Xiu Lan AO ; Lei XIA ; Hai Cong WU ; Shi An ZHANG ; Zhi Xian WU ; Dong Liang LI
Chinese Journal of Hepatology 2023;31(5):524-531
Objective: To investigate the factors influencing total bilirubin elevation and its correlation with UGT1A1 gene polymorphism in the early postoperative period of transjugular intrahepatic portosystemic shunt (TIPS). Methods: 104 cases with portal hypertension and esophageal variceal hemorrhage (EVB) treated with elective TIPS treatment were selected as the study subjects and were divided into a bilirubin-elevated group and a normal bilirubin group according to the total bilirubin elevation level during the early postoperative period. Univariate analysis and logistic regression were used to analyze the factors influencing total bilirubin elevation in the early postoperative period. PCR amplification and first-generation sequencing technology were used to detect the polymorphic loci of the UGT1A1 gene promoter TATA box, enhancer c.-3279 T > G, c.211G > A, and c.686C > A. Logistic regression was used to analyze the correlation of four locus alleles and genotypes with elevated total bilirubin in the early postoperative period. Results: Among the 104 cases, 47 patients were in the bilirubin elevated group, including 35 males (74.5%) and 12 females (25.5%), aged (50.72 ± 12.56) years. There were 57 cases in the normal bilirubin group, including 42 males (73.7%) and 15 females (26.3%), aged (51.63 ± 11.10) years. There was no statistically significant difference in age (t = -0.391, P = 0.697) and gender (χ(2) = 0.008, P = 0.928) between the two groups of patients. Univariate analysis revealed that preoperative alanine transaminase (ALT) level (χ(2) = 5.954, P = 0.015), total bilirubin level (χ(2) = 16.638, P < 0.001), MELD score (χ(2) = 10.054, P = 0.018), Child-Pugh score (χ(2) = 6.844, P = 0.022), and postoperative portal vein branch development (χ(2) = 6.738, P = 0.034) were statistically significantly different between the two groups. Logistic regression analysis showed that preoperative ALT level, total bilirubin level, and portal vein branch development after TIPS were correlated with the elevated total bilirubin in the early postoperative period. The polymorphism of the c.211G > A locus of the UGT1A1 gene correlation had elevated total bilirubin in the early postoperative period of TIPS. The risk of elevated total bilirubin was increased in the population carrying allele A (P = 0.001, OR = 4.049) in the early postoperative period. Allelic polymorphisms in the TATA box promoter region and enhancer c.-3279 T > G and c.686C > A had no statistically significant difference between the bilirubin-elevated group and the normal bilirubin group. Conclusion: The preoperative ALT level, total bilirubin level, and portal vein branch development are correlated with the elevated total bilirubin in early postoperative patients. The polymorphisms of the UGT1A1 gene and enhancer c.211G > A are correlated with the occurrence of elevated total bilirubin in the early postoperative period of TIPS. Allele A carrier may have a higher risk of elevated total bilirubin in the early postoperative period.
Female
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Humans
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Male
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Bilirubin
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Esophageal and Gastric Varices
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Gastrointestinal Hemorrhage/surgery*
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Portasystemic Shunt, Transjugular Intrahepatic
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Postoperative Period
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Retrospective Studies
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Treatment Outcome
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Adult
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Middle Aged
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Glucuronosyltransferase/genetics*
7.Progress in research of long-term protective efficacy of human papillomavirus vaccine.
Xin Hua JIA ; Xue Feng KUANG ; Ya Han CHEN ; Yu Fei LI ; Zhao Feng BI ; Ting WU ; You Lin QIAO
Chinese Journal of Epidemiology 2023;44(5):851-854
The efficacy of HPV vaccine in preventing cervical cancer has been demonstrated in numerous clinical trials and clinical uses. The follow-up after clinical trials usually last for 5-6 years to evaluate the long-term efficacy, and a series of long-term follow-up studies have been conducted in some regions. The literature retrieval of HPV vaccine long term efficiency research both at home and abroad indicated that the protective efficacy of the vaccine against vaccine-type-related cervical intraepithelial neoplasia grade 2 and above is higher than 90%.
Humans
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Human Papillomavirus Viruses
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Biomedical Research
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Papillomavirus Vaccines
8.Evaluation of the effect of internet-based dietary self-management on blood pressure in high-risk population of hypertension in Haikou City community.
Li Min HE ; You Xuan YAN ; Chan Juan ZHAO ; Xue Li ZHU ; Bi Feng LIANG ; Guo Tian LIN ; Jun Cai CHEN ; Fan ZHANG
Chinese Journal of Preventive Medicine 2023;57(10):1581-1589
To explore the effect of Internet+diet self-management intervention technology on the blood pressure control of hypertension high-risk population through the intervention of hypertension high-risk population in Haikou City community, so as to provide scientific evidence for the prevention and treatment of cardiovascular diseases (CVD). The multi-stage cluster sampling method was used, and 295 hypertension high-risk participants were recruited from 15 communities in Haikou City from July to December 2021. The 15 communities were randomly divided into three groups: blank group, traditional group and Internet plus group by random number table method. The blank group referred to the group (99 participants) that did not take special intervention measures but the routine interventions in accordance with the "National Basic Public Health Service Standards (the Third Edition) Health Education Service Standards". On the basis of the blank group, the traditional group (95 participants) was intervened by giving additional traditional methods such as holding lectures and distributing popular science books. The Internet plus group (101 participants) was given additional Internet measures on the basis of the intervention of the traditional group. After 6 months, questionnaires, laboratory biochemical tests, and physical measurements were conducted. SPSS 25.0 software was applied for data analysis. Measurement data that followed normal distribution were statistically described by using mean±standard deviation, analysis of variance was used for inter group comparisons before intervention, analysis of covariance was used for inter group comparisons after intervention, and Bonferroni adjustment was used for pairwise comparisons between groups. Measurement data that did not follow the Normal distribution were represented by M (Q1, Q3). The rank sum test was used for inter group comparison. The k sample Kruskal Wallis single factor ANOVA was used to compare the distribution between different groups. Counting data were described by composition ratio or rate. Under the premise of balanced comparison between groups before intervention, Chi-squared test was used for inter group comparison after intervention, and Bonferroni adjustment method was used for pairwise comparison between groups. The results showed that a total of 295 participants were included, with males accounting for 35.6% (105) and females accounting for 64.4% (190). The age ranged from 55 to 74 years old, with an average age of (64.69±5.73) years. The number of married accounted for 95.6% (282 participants). There were no statistically significant differences in gender, age, family history, education level, occupation, marital status, drinking habits, regular exercise, dietary status, SBP (systolic blood pressure), DBP (diastolic blood pressure), pulse pressure difference, BMI (body mass index), folic acid, and 24-hour urine sodium among the three groups upon enrollment (P values>0.05). After the intervention, the drinking rate was as follows: Internet plus group (29, 28.7%)
Male
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Female
;
Humans
;
Middle Aged
;
Aged
;
Blood Pressure
;
Self-Management
;
Hypertension/prevention & control*
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Cardiovascular Diseases/prevention & control*
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Diet
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Sodium
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Internet
;
Folic Acid
9.Evaluation of the effect of internet-based dietary self-management on blood pressure in high-risk population of hypertension in Haikou City community.
Li Min HE ; You Xuan YAN ; Chan Juan ZHAO ; Xue Li ZHU ; Bi Feng LIANG ; Guo Tian LIN ; Jun Cai CHEN ; Fan ZHANG
Chinese Journal of Preventive Medicine 2023;57(10):1581-1589
To explore the effect of Internet+diet self-management intervention technology on the blood pressure control of hypertension high-risk population through the intervention of hypertension high-risk population in Haikou City community, so as to provide scientific evidence for the prevention and treatment of cardiovascular diseases (CVD). The multi-stage cluster sampling method was used, and 295 hypertension high-risk participants were recruited from 15 communities in Haikou City from July to December 2021. The 15 communities were randomly divided into three groups: blank group, traditional group and Internet plus group by random number table method. The blank group referred to the group (99 participants) that did not take special intervention measures but the routine interventions in accordance with the "National Basic Public Health Service Standards (the Third Edition) Health Education Service Standards". On the basis of the blank group, the traditional group (95 participants) was intervened by giving additional traditional methods such as holding lectures and distributing popular science books. The Internet plus group (101 participants) was given additional Internet measures on the basis of the intervention of the traditional group. After 6 months, questionnaires, laboratory biochemical tests, and physical measurements were conducted. SPSS 25.0 software was applied for data analysis. Measurement data that followed normal distribution were statistically described by using mean±standard deviation, analysis of variance was used for inter group comparisons before intervention, analysis of covariance was used for inter group comparisons after intervention, and Bonferroni adjustment was used for pairwise comparisons between groups. Measurement data that did not follow the Normal distribution were represented by M (Q1, Q3). The rank sum test was used for inter group comparison. The k sample Kruskal Wallis single factor ANOVA was used to compare the distribution between different groups. Counting data were described by composition ratio or rate. Under the premise of balanced comparison between groups before intervention, Chi-squared test was used for inter group comparison after intervention, and Bonferroni adjustment method was used for pairwise comparison between groups. The results showed that a total of 295 participants were included, with males accounting for 35.6% (105) and females accounting for 64.4% (190). The age ranged from 55 to 74 years old, with an average age of (64.69±5.73) years. The number of married accounted for 95.6% (282 participants). There were no statistically significant differences in gender, age, family history, education level, occupation, marital status, drinking habits, regular exercise, dietary status, SBP (systolic blood pressure), DBP (diastolic blood pressure), pulse pressure difference, BMI (body mass index), folic acid, and 24-hour urine sodium among the three groups upon enrollment (P values>0.05). After the intervention, the drinking rate was as follows: Internet plus group (29, 28.7%)
Male
;
Female
;
Humans
;
Middle Aged
;
Aged
;
Blood Pressure
;
Self-Management
;
Hypertension/prevention & control*
;
Cardiovascular Diseases/prevention & control*
;
Diet
;
Sodium
;
Internet
;
Folic Acid
10.LIN28 coordinately promotes nucleolar/ribosomal functions and represses the 2C-like transcriptional program in pluripotent stem cells.
Zhen SUN ; Hua YU ; Jing ZHAO ; Tianyu TAN ; Hongru PAN ; Yuqing ZHU ; Lang CHEN ; Cheng ZHANG ; Li ZHANG ; Anhua LEI ; Yuyan XU ; Xianju BI ; Xin HUANG ; Bo GAO ; Longfei WANG ; Cristina CORREIA ; Ming CHEN ; Qiming SUN ; Yu FENG ; Li SHEN ; Hao WU ; Jianlong WANG ; Xiaohua SHEN ; George Q DALEY ; Hu LI ; Jin ZHANG
Protein & Cell 2022;13(7):490-512
LIN28 is an RNA binding protein with important roles in early embryo development, stem cell differentiation/reprogramming, tumorigenesis and metabolism. Previous studies have focused mainly on its role in the cytosol where it interacts with Let-7 microRNA precursors or mRNAs, and few have addressed LIN28's role within the nucleus. Here, we show that LIN28 displays dynamic temporal and spatial expression during murine embryo development. Maternal LIN28 expression drops upon exit from the 2-cell stage, and zygotic LIN28 protein is induced at the forming nucleolus during 4-cell to blastocyst stage development, to become dominantly expressed in the cytosol after implantation. In cultured pluripotent stem cells (PSCs), loss of LIN28 led to nucleolar stress and activation of a 2-cell/4-cell-like transcriptional program characterized by the expression of endogenous retrovirus genes. Mechanistically, LIN28 binds to small nucleolar RNAs and rRNA to maintain nucleolar integrity, and its loss leads to nucleolar phase separation defects, ribosomal stress and activation of P53 which in turn binds to and activates 2C transcription factor Dux. LIN28 also resides in a complex containing the nucleolar factor Nucleolin (NCL) and the transcriptional repressor TRIM28, and LIN28 loss leads to reduced occupancy of the NCL/TRIM28 complex on the Dux and rDNA loci, and thus de-repressed Dux and reduced rRNA expression. Lin28 knockout cells with nucleolar stress are more likely to assume a slowly cycling, translationally inert and anabolically inactive state, which is a part of previously unappreciated 2C-like transcriptional program. These findings elucidate novel roles for nucleolar LIN28 in PSCs, and a new mechanism linking 2C program and nucleolar functions in PSCs and early embryo development.
Animals
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Cell Differentiation
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Embryo, Mammalian/metabolism*
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Embryonic Development
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Mice
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Pluripotent Stem Cells/metabolism*
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RNA, Messenger/genetics*
;
RNA, Ribosomal
;
RNA-Binding Proteins/metabolism*
;
Transcription Factors/metabolism*
;
Zygote/metabolism*

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