1.Constructing Support Vector Machine Ensembles for Cancer Classification Based on Proteomic Profiling
Mao YONG ; Zhou XIAO-BO ; Pi DAO-YING ; Sun YOU-XIAN
Genomics, Proteomics & Bioinformatics 2005;3(4):238-241
In this study, we present a constructive algorithm for training cooperative support vector machine ensembles (CSVMEs). CSVME combines ensemble architecture design with cooperative training for individual SVMs in ensembles. Unlike most previous studies on training ensembles, CSVME puts emphasis on both accuracy and collaboration among individual SVMs in an ensemble. A group of SVMs selected on the basis of recursive classifier elimination is used in CSVME, and the number of the individual SVMs selected to construct CSVME is determined by 10-fold cross-validation. This kind of SVME has been tested on two ovarian cancer datasets previously obtained by proteomic mass spectrometry. By combining several individual SVMs, the proposed method achieves better performance than the SVME of all base SVMs.
2.The expressions and clinical significance of programmed death 1/programmed death ligand 1 in children with acute lymphoblastic leukemia
Dao WANG ; Yanjie DING ; Ge ZHOU ; Jiao CHEN ; Hongliang YOU ; Huanhuan LI ; Bai LI ; Huixia WEI ; Yufeng LIU
Chinese Journal of Applied Clinical Pediatrics 2021;36(7):525-528
Objective:To investigate the mechanism of programmed death 1(PD-1)/ programmed death ligand 1(PD-L1) signaling pathway and its feasibility as a potential therapeutic target and prognostic predictor by detecting the expressions, of PD-1 and PD-L1 in bone marrow mononuclear cells of children with acute lymphoblastic leukemia (ALL), and to provide new ideas for the diagnosis and treatment of ALL as well.Methods:Bone marrow samples were collected from 59 children with ALL in the First Affiliated Hospital of Zhengzhou University from September 2018 to July 2019.Flow cytometry was applied to detect the expression of PD-1 and PD-L1 in bone marrow mononuclear cells in 59 ALL patients, including 47 newly-diagnosed ALL patients and 12 relapsed ALL patients, respectively, at initial diagnosis, after induction therapy and early intensive treatment.Their relevant clinical data were collected and compared with the bone marrow specimens of 12 children suffering from non-malignant blood diseases as the control group of the same hospital during the same period.Results:There was no significant difference in the expression of PD-1 in the bone marrow mononuclear cells of the primary diagnosis group, recurrence group and control group ( H=2.402, P>0.05). The expression of PD-L1 in the relapsed and refractory group [(7.32±3.60)%] and the newly diagnosed group [(3.18±2.37)%] was higher than that in the control group [(0.84±0.39)%], and the differences were statistically significant ( H= 28.048, P<0.05). In the initial treatment group, the expression of PD-L1 in the bone marrow mononuclear cells was the strongest expression before treatment ( B=1.293), followed by after induction treatment ( B=0.036) and after early intensive treatment ( B=0.000), suggesting that there was a downward trend as the continued treatment.The expression of PD-L1 was the weakest expression in the low-risk group ( B=-3.912) than in the medium-risk group ( B=-3.595) and high-risk group ( B=0.000), revealing that the expression of PD-L1 is related to the risk grades of ALL.The higher the risk rating is, the higher the PD-L1 protein expression is. Conclusions:The high expression of PD-L1 may be involved in the pathogenesis and be used as an adverse predictor of ALL childhood and an evaluation index of chemotherapy efficacy.PD-1 / PD-L1 signaling pathway may be a potential therapeutic target of ALL childhood.
3.Considerations on intervention goal and efficacy evaluation of traditional Chinese medicine in the treatment of neurological diseases.
Ren-ming XIE ; Bao-xin DU ; Yan HUANG ; Dao-you ZHOU ; Yong-yan WANG ; Pei-xin HUANG
Chinese journal of integrative medicine 2007;13(2):148-151
In the last several years, traditional Chinese medicine (TCM) has made much progress in the treatment of neurological diseases. The living space of TCM in neurological diseases lies in refractory diseases, aging and chronic diseases caused by multiple factors as well as sub-health state and chronic fatigue state. The effect model of TCM mainly consists of whole effect, self-organization, self-stable model, holographic effect and butterfly effect. The effective point of TCM in neurological diseases lies mainly in end-points and health-related events. Moreover, TCM has advantages in the evaluation of symptoms, syndrome and quality of life (QOL). Some key indexes should be included when evaluating the efficacy of TCM in neurological diseases. Meanwhile, the advantages of TCM such as end-points, health-related events and QOL should be highlighted. Multi-subject researching methods could be adopted to make a comprehensive evaluation of subjective and objective indexes. The clinical evidence on the TCM efficacy evaluation may come from RCTs, and other types of designs can also be considered.
Aging
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Humans
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Medicine, Chinese Traditional
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Nervous System Diseases
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drug therapy
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psychology
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Quality of Life
4.Construction of PTEN eukaryotic expression plasmid and its effects on breast carcinoma cell line MDA468.
Qing-yong CHEN ; Dao-da CHEN ; Chun-you WANG ; You-sheng ZHOU
Chinese Journal of Oncology 2005;27(4):216-219
OBJECTIVETo investigate the effects of exogenous wild PTEN gene stably transfection on growth of breast cancer cells in vitro.
METHODSAt first, a recombinant eukaryotic expression plasmid pcDNA3.1-PTEN was constructed. Human breast cancer cell line MDA468 was transfected with pcDNA3.1-PTEN or mock transfected plasmid pcDNA3.1(-) with lipofectamine. RT-PCR, immunohistochemical staining and Western blot were used to determine target gene expression. Cell viability was tested by MTT assay. Apoptosis was determined by flow cytometry with a double-staining method using FITC-conjugated annexin V and PI.
RESULTSThe PTEN stably transfected cells demonstrated the integration of the exogenous target gene and corresponding mRNA and protein over-expression. There was a significant decline in cell viability of pcDNA3.1-PTEN transfected MDA468 cells in comparison with the mock-transfected ones (P < 0.01). The PTEN-trasfected MDA468 cells also showed an increase in the rate of apoptosis, compared with parental and mock-trasfected cells (P < 0.001).
CONCLUSIONStable expression of exogenous PTEN can suppress the malignant phenotypes of the human breast cancer cell line MDA468.
Breast Neoplasms ; metabolism ; pathology ; Cell Line, Tumor ; Eukaryotic Cells ; metabolism ; Humans ; PTEN Phosphohydrolase ; biosynthesis ; genetics ; Phenotype ; Plasmids ; genetics ; Recombinant Proteins ; biosynthesis ; genetics ; Transfection
5.Parameters selection in gene selection using Gaussian kernel support vector machines by genetic algorithm.
Yong MAO ; Xiao-Bo ZHOU ; Dao-Ying PI ; You-Xian SUN ; Stephen T C WONG
Journal of Zhejiang University. Science. B 2005;6(10):961-973
In microarray-based cancer classification, gene selection is an important issue owing to the large number of variables and small number of samples as well as its non-linearity. It is difficult to get satisfying results by using conventional linear statistical methods. Recursive feature elimination based on support vector machine (SVM RFE) is an effective algorithm for gene selection and cancer classification, which are integrated into a consistent framework. In this paper, we propose a new method to select parameters of the aforementioned algorithm implemented with Gaussian kernel SVMs as better alternatives to the common practice of selecting the apparently best parameters by using a genetic algorithm to search for a couple of optimal parameter. Fast implementation issues for this method are also discussed for pragmatic reasons. The proposed method was tested on two representative hereditary breast cancer and acute leukaemia datasets. The experimental results indicate that the proposed method performs well in selecting genes and achieves high classification accuracies with these genes.
Algorithms
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Breast Neoplasms
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genetics
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Female
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Genes
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Humans
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Leukemia, Myeloid, Acute
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genetics
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Models, Genetic
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Oligonucleotide Array Sequence Analysis
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methods
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Predictive Value of Tests
6.Investigation of an outbreak of acute diarrhea caused by Human calicivirus.
Wen-zhang LI ; Hua-ping XIE ; Hai-yan WU ; Dao-yun ZHOU ; Li-shu ZHENG ; Yun-shan CAI ; You-ling KANG ; Xi JIANG ; Zhao-yin FANG
Chinese Journal of Experimental and Clinical Virology 2003;17(3):251-253
BACKGROUNDTo survey a diarrhea outbreak in Guangan city and analyze the cause of the disease.
METHODSThe population enrolled in the surveillance came from four different settings and was randomly sampled. Stool specimens collected from diarrhea patients were tested ordinarily for enteric bacteria and further examined for viral pathogens with PAGE, ELISA and RT-PCR.
RESULTSIn total, 4,567 persons were surveyed, among them 942 had acute diarrhea (prevalence 20.63%). The incidence was higher in rural area (28.6%) than in urban area (19.6%) (chi-square =22.29, P less than 0.005) with a peak in May 10 through 25 four human caliciviruses were detected from stool specimens by ELISA and RT-PCR in specimens from 4 and 1 patients, respectively.
CONCLUSIONHuman calicivirus probably was the cause of this diarrhea outbreak in Guangan city.
Acute Disease ; epidemiology ; Adolescent ; Adult ; Age Distribution ; Caliciviridae Infections ; epidemiology ; virology ; Child ; China ; epidemiology ; Diarrhea ; epidemiology ; virology ; Disease Outbreaks ; Feces ; virology ; Female ; Humans ; Male ; Middle Aged ; Norovirus ; isolation & purification ; Young Adult
7.Levels of PCDD/Fs, PCBs and PBDEs compounds in human placenta tissue.
Jian-qing ZHANG ; Xiao-kang SUN ; You-sheng JIANG ; Jian ZHOU ; Li-bin WANG ; Zhao-yi YE ; Dao-kui FANG ; Guo-bin WANG
Chinese Journal of Preventive Medicine 2008;42(12):911-918
OBJECTIVETo establish the methods of Polychlorinated Dibenzo-p-Dioxins and Dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) compounds determination by isotope dilution HRGC/HRMS simultaneously in human placenta tissue from mothers, and assess the human exposure risk to dioxins and PBDEs in study.
METHODSConcentrations of 17 PCDD/Fs and 12 dioxin-like PCBs as well as 7 PBDEs were measured in human placenta tissue samples by isotope dilution HRGC/HRMS. SigmaTEQ (PCDD + PCDFs + PCBs) concentration using WHO-TEF factor and PBDEs concentration was calculated respectively. Risk assessment of mother exposure to dioxins and PBDEs was evaluated.
RESULTSMedian of SigmaTEQ (PCDD + PCDFs + PCBs) concentration for six samples was 18.15 WHO-TEQ pg/g lipid, ranging from 5.14 - 67.01 WHO-TEQ pg/g lipid. Although the median of SigmaTEQ (PCDD + PCDFs + PCBs) was lower than that of human blood of EU and Japan, and close to that of Korea and Taiwan non-exposure as reported in the literatures, the highest SigmaTEQ (PCDD + PCDFs + PCBs) concentration of placenta sample exceeded the value of high dioxins exposure area subjects in Taiwan. The dominant contributor congener for WHO-TEQ were 2, 3, 4, 7, 8-PeCDF, 1, 2, 3, 7, 8-PeCDD, PCB126, totally accounted for 65 percent of SigmaWHO-TEQ. Median and average of PBDE concentration for six samples were 2.73 ng/g lipid and 7.17 ng/g lipid, respectively, ranging from 0.95 - 25.99 ng/g lipid. BDE47 was the dominant contributor congener for the total concentration, accounted for 35 percent.
CONCLUSIONThe methods of PCDD/Fs, PCBs and PBDEs compounds determined by isotope dilution HRGC/HRMS simultaneously in human placenta tissue from mothers were established successfully, and the human exposure risk to PCDD/Fs, PCBs and PBDEs should be surveyed for the donor with the highest SigmaTEQ (PCDD + PCDFs + PCBs) and PBDEs concentration of placenta sample in the future.
Benzofurans ; analysis ; Female ; Halogenated Diphenyl Ethers ; analysis ; Humans ; Maternal Exposure ; Placenta ; chemistry ; Polychlorinated Biphenyls ; analysis ; Polychlorinated Dibenzodioxins ; analogs & derivatives ; analysis ; Pregnancy
8.Renchangianin E: a new dibenzocyclooctadiene lignan from Kadsura renchangiana.
Shuang LIU ; You-Ping LUO ; Yi-Jie HU ; Li-Qing DENG ; Si-Yu ZHOU ; Zhi-Hua LIAO ; Dao-Feng CHEN ; Min CHEN
Acta Pharmaceutica Sinica 2014;49(10):1438-1441
A new dibenzocyclooctadiene lignan, renchangianin E (1) was isolated from the stems of Kadsura renchangiana. Its structure and stereochemistry were elucidated by spectroscopic methods, including 2D-NMR techniques.
Cyclooctanes
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chemistry
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Kadsura
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chemistry
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Lignans
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chemistry
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Magnetic Resonance Spectroscopy
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Molecular Structure
9.The relationship between adiponectin gene polymorphisms and the risk of the chronic periodontitis and diabetes mellitus
Jie ZHANG ; Ping HUANG ; Fan ZHANG ; You-Juan WANG ; Dao-Zhou LIU ; Hua ZHANG
Chinese Journal of Stomatology 2012;47(z1):21-25
Objective To study the relationship between adiponectin gene polymorphisms and the susceptibility of the chronic periodontitis and diabetes mellitus.Methods Two hundreds patients were selected and divided into four groups,according to their physical and periodontal status.The four group were as follows,the healthy group as control,the one with chronic periodontitis,the one with type Ⅱ diabetes mellitus,and the one suffered from the both.Then,DNA was extracted from buccal mucosa swabs,and the genotype of single nucleotide polymorphism (SNP) 276 as well as SNP 45 in adiponectin gene can be obtained using polymerase chain reaction (PCR) together with restrictive fragment length polymorphism analysis.The relationship between the adiponectin gene polymorphism and chronic periodontitis and diabetes mellitus was analyzed statistically.Results There was significant difference between the normal healthy group (GG:20,GT:26,TT:4) and the diabetes mellitus group (GG:16,GT:20,TT:14) at SNP 276 (P =0.034).But there is no statistically difference between the normal healthy group (GG:26,TG:21,TT:3) and the diabetes mellitus group (GG:27,TG:22,TT:1) at SNP 45 (P =0.856).Moreover,the distribution of SNP 276 shows no difference between the normal healthy group aud the group with chronic periodontitis (GG:14,GT:30,TT:6) (P =0.418).No significant difference was found from the adiponectin haplotype analysis of SNP 45 between the normal healthy group and the group with chronic periodontitis (GG:30,TG:18,TT:2) (P =0.699).According to Logistic regression,the OR of sex is 2.938 in the chronic periodontitis group with the mellitus diabetes(P =0.011).Conclusions These results suggest that SNP 276 in the ADIPOQ gene is associated with diabetes mellitus type 2,but not with chronic periodontitis.There was no association between the adiponectin gene 45 polymorphism and diabetes mellitus type 2.Besides,neither of SNP 276 and 45 has somethiug to do with chronic periodontitis.
10.Clinical Observation on Shuangye San in the Treatment of Type 2 Diabetes Mellitus Complicated with Non-alcoholic Fatty Liver Disease of Spleen Deficiency and Phlegm Stasis Type
Dao-Cheng ZHOU ; Gui-Ji RUAN ; You-You SHUAI ; Wen-Hua XU ; De-Liang LIU ; Heng-Xia ZHAO ; Hui-Lin LI
Journal of Guangzhou University of Traditional Chinese Medicine 2024;41(10):2687-2694
Objective To observe the clinical efficacy of Shuangye San(the prescription mainly composed of Mori Folium and Nelumbinis Folium)in the treatment of type 2 diabetes mellitus(T2DM)complicated with non-alcoholic fatty liver disease(NAFLD)of spleen deficiency and phlegm stasis type.Methods A total of 80 patients with T2DM complicated with NAFLD of spleen deficiency and phlegm stasis type were randomly divided into a treatment group and a control group,with 40 cases in each group.The control group was treated with conventional western medicine for lowering blood glucose and lipid,protecting liver and lowering enzymes.The treatment group was treated with the granules of Shuangye San orally on the basis of treatment for the control group.The course of treatment lasted for three months.The changes of traditional Chinese medicine(TCM)syndrome scores,homeostasis model assessment of insulin resistance(HOMA-IR),fasting insulin(FINS),fasting blood glucose(FBG),2-hour postprandial blood glucose(2hPG),glycosylated hemoglobin(HbA1C),total cholesterol(TC),triglyceride(TG),low-density lipoprotein cholesterol(LDL-C),high-density lipoprotein cholesterol(HDL-C),liver function indicators and B-ultrasound grading of fatty liver in the two groups were observed before and after treatment.After treatment,the clinical efficacy and safety of the two groups were evaluated.Results(1)After three months of treatment,the total effective rate of the treatment group was 85.00%(34/40),and that of the control group was 70.00%(28/40).The intergroup comparison(tested by chi-square test)showed that the efficacy of the treatment group was significantly superior to that of the control group(P<0.01).(2)After treatment,the scores of TCM symptoms of obese physique,heaviness and weakness in the limbs,shortness of breath and unwilling to talk,tightness and stabbing pain in the chest,abdominal distension and poor appetite in the two groups were decreased compared with those before treatment(P<0.05),and the decrease of TCM syndrome scores in the treatment group was significantly superior to that in the control group(P<0.05).(3)After treatment,the levels of glucose and lipid metabolism indicators of FINS,HOMA-IR,FBG,2hPG,HbA1C,TC,TG and LDL-C in the two groups were significantly decreased compared with those before treatment(P<0.05),and the level of HDL-C was significantly increased compared with that before treatment(P<0.05).The decrease of FINS,HOMA-IR,FBG,2hPG,HbA1C,TC,TG and LDL-C levels and the increase of HDL-C levels in the treatment group were significantly superior to those in the control group(P<0.05).(4)After treatment,the levels of liver function indicators of alanine aminotransferase(ALT),aspartate aminotransferase(AST)and gamma-glutamyl transpeptidase(GGT)in the two groups were significantly decreased compared with those before treatment(P<0.05),and the decrease of liver function indicators in the treatment group was significantly superior to that in the control group(P<0.05).(5)After treatment,the B-ultrasound grading of fatty liver of the two groups was significantly improved compared with that before treatment(P<0.05),and the improvement of fatty liver B-ultrasound grading in the treatment group was significantly superior to that in the control group,and the difference was statistically significant(P<0.05).(6)During the treatment,there were no adverse reactions such as impairment of liver and kidney function and abnormalities in routine blood,urine and stool test in the two groups.Conclusion Shuangye San exerts certain effect in the treatment of T2DM complicated with NAFLD of spleen deficiency and phlegm stasis type.It can alleviate the clinical symptoms of patients,correct the disorder of glucose and lipid metabolism,and improve liver function and fatty liver B-ultrasound grading.