1.Development of an Analytical Software for Forensic Proteomic SAP Typing
Feng HU ; Meng-Jiao WANG ; Jia-Lei WU ; Dong-Sheng DING ; Zhi-Yuan YANG ; An-Quan JI ; Lei FENG ; Jian YE
Progress in Biochemistry and Biophysics 2025;52(9):2406-2416
ObjectiveThe proteome of biological evidence contains rich genetic information, namely single amino acid polymorphisms (SAPs) in protein sequences. However, due to the lack of efficient and convenient analysis tools, the application of SAP in public security still faces many challenges. This paper aims to meet the application requirements of SAP analysis for forensic biological evidence’s proteome data. MethodsThe software is divided into three modules. First, based on a built-in database of common non-synonymous single nucleotide polymorphisms (nsSNPs) and SAPs in East Asian populations, the software integrates and annotates newly identified exonic nsSNPs as SAPs, thereby constructing a customized SAP protein sequence database. It then utilizes a pre-installed search engine—either pFind or MaxQuant—to perform analysis and output SAP typing results, identifying both reference and variant types, along with their corresponding imputed nsSNPs. Finally, SAPTyper compares the proteome-based typing results with the individual’s exome-derived nsSNP profile and outputs the comparison report. ResultsSAPTyper accepts proteomic DDA mass spectrometry raw data (DDA acquisition mode) and exome sequencing results of nsSNPs as input and outputs the report of SAPs result. The pFind and Maxquant search engines were used to test the proteome data of 2 hair shafts of2 individuals, and both obtained SAP results. It was found that the results of the Maxquant search engine were slightly less than those of pFind. This result shows that SAPTyper can achieve SAP fingding function. Moreover, the pFind search engine was used to test the proteome data of 3 hair shafts from 1 European person and 1 African person in the literature. Among the sites fully matched by the literature method, sites detected by SAPTyper are also included; for semi-matching sites, that is, nsSNPs are heterozygous, both literature method and SAPTyper method had the risk of missing detection for one type of the allele. Comparing the analysis results of SAPTyper with the SAP test results reported in the literature, it was found that some imputed nsSNP sites identified by the literature method but not detected by SAPTyper had a MAF of less than 0.1% in East Asian populations, and therefore they were not included in the common nsSNP database of East Asian populations constructed by this software. Since the database construction of this software is based on the genetic variation information of East Asian populations, it is currently unable to effectively identify representative unique common variation sites in European or African populations, but it can still identify SAP sites shared by these populations and East Asian populations. ConclusionAn automated SAP analysis algorithm was developed for East Asian populations, and the software named SAPTyper was developed. This software provides a convenient and efficient analysis tool for the research and application of forensic proteomic SAP and has important application prospects in individual identification and phenotypic inference based on SAP.
2.Analysis of the effect of fudosteine on induced sputum components in patients with stable neutrophil-dominated COPD
Zhanbo LI ; Kaifeng DU ; Zhilong JIANG ; Jiameng GAO ; Mengjie CHEN ; Yuan MA ; Zhihong CHEN
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(4):362-369
AIM:To observe the effect of fudostei-ne on induced sputum cell components and lung function in patients with stable neutrophil-dominat-ed COPD.METHODS:From October 2019 to Octo-ber 2022,53 patients with stable COPD were select-ed and divided into fudosteine group and placebo group.The placebo group was treated with routine treatment,and the fudosteine group was treated with fudosteine on the basis of routine treatment.The two groups were treated for 6 months.The clinical symptoms[Saint George's Respiratory Questionnaire(SGRQ),COPD Assessment Test(CAT)and Modified British Medical Research Council Dys-pnea scale(MMRC),Breathlessness,Cough,and Sputum Scale(BCSS)],lung function index,induced sputum cytology analysis and other related exami-nation results were recorded in detail before and after treatment.RESULTS:(1)Compared with the baseline,the forced expiratory volume in one sec-ond(FEV1),forced vital capacity(FVC),and the ra-tio of FEV1 to FVC(FEV1/FVC)of the two groups were improved after treatment,and the differenc-es were statistically significant(P<0.05).However,after treatment,there was no significant difference in pulmonary function between the two groups ex-cept for the percentage of carbon monoxide diffu-sion in the predicted value(DLCO%pre)(DLCO%pre in the fudosteine group was higher than that in the placebo group).(2)After treatment,the total num-ber of induced sputum cells and neutrophil counts in the fudosteine group were lower than those in the placebo group.Compared with the number of cells in each component at baseline,the total num-ber of induced sputum cells and neutrophil count in the fudosteine group were significantly lower(P<0.05).CONCLUSION:Fudosteine treatment in pa-tients with stable neutrophil-dominated COPD can improve lung function,reduce the total number of induced sputum cells and the total number of neu-trophils,thereby improving airway inflammation.
3. Analysis of the effect of fudosteine on induced sputum components in patients with stable neutrophil-dominated COPD
Zhanbo LI ; Kaifeng DU ; Zhilong JIANG ; Jiameng GAO ; Mengjie CHEN ; Yuan MA ; Zhihong CHEN ; Zhanbo LI ; Kaifeng DU
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(4):362-369
AIM: To observe the effect of fudosteine on induced sputum cell components and lung function in patients with stable neutrophil-dominated COPD. METHODS: From October 2019 to October 2022, 53 patients with stable COPD were selected and divided into fudosteine group and placebo group. The placebo group was treated with routine treatment, and the fudosteine group was treated with fudosteine on the basis of routine treatment. The two groups were treated for 6 months. The clinical symptoms [Saint George's Respiratory Questionnaire (SGRQ), COPD Assessment Test (CAT) and Modified British Medical Research Council Dyspnea scale (MMRC), Breathlessness, Cough, and Sputum Scale (BCSS)], lung function index, induced sputum cytology analysis and other related examination results were recorded in detail before and after treatment. RESULTS: (1) Compared with the baseline, the forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and the ratio of FEV1 to FVC (FEV1/FVC) of the two groups were improved after treatment, and the differences were statistically significant (P<0.05). However, after treatment, there was no significant difference in pulmonary function between the two groups except for the percentage of carbon monoxide diffusion in the predicted value (DLCO%pre) (DLCO%pre in the fudosteine group was higher than that in the placebo group). (2) After treatment, the total number of induced sputum cells and neutrophil counts in the fudosteine group were lower than those in the placebo group. Compared with the number of cells in each component at baseline, the total number of induced sputum cells and neutrophil count in the fudosteine group were significantly lower (P< 0.05). CONCLUSION: Fudosteine treatment in patients with stable neutrophil-dominated COPD can improve lung function, reduce the total number of induced sputum cells and the total number of neutrophils, thereby improving airway inflammation.
4.Analysis of the effect of fudosteine on induced sputum components in patients with stable neutrophil-dominated COPD
Zhanbo LI ; Kaifeng DU ; Zhilong JIANG ; Jiameng GAO ; Mengjie CHEN ; Yuan MA ; Zhihong CHEN
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(4):362-369
AIM:To observe the effect of fudostei-ne on induced sputum cell components and lung function in patients with stable neutrophil-dominat-ed COPD.METHODS:From October 2019 to Octo-ber 2022,53 patients with stable COPD were select-ed and divided into fudosteine group and placebo group.The placebo group was treated with routine treatment,and the fudosteine group was treated with fudosteine on the basis of routine treatment.The two groups were treated for 6 months.The clinical symptoms[Saint George's Respiratory Questionnaire(SGRQ),COPD Assessment Test(CAT)and Modified British Medical Research Council Dys-pnea scale(MMRC),Breathlessness,Cough,and Sputum Scale(BCSS)],lung function index,induced sputum cytology analysis and other related exami-nation results were recorded in detail before and after treatment.RESULTS:(1)Compared with the baseline,the forced expiratory volume in one sec-ond(FEV1),forced vital capacity(FVC),and the ra-tio of FEV1 to FVC(FEV1/FVC)of the two groups were improved after treatment,and the differenc-es were statistically significant(P<0.05).However,after treatment,there was no significant difference in pulmonary function between the two groups ex-cept for the percentage of carbon monoxide diffu-sion in the predicted value(DLCO%pre)(DLCO%pre in the fudosteine group was higher than that in the placebo group).(2)After treatment,the total num-ber of induced sputum cells and neutrophil counts in the fudosteine group were lower than those in the placebo group.Compared with the number of cells in each component at baseline,the total num-ber of induced sputum cells and neutrophil count in the fudosteine group were significantly lower(P<0.05).CONCLUSION:Fudosteine treatment in pa-tients with stable neutrophil-dominated COPD can improve lung function,reduce the total number of induced sputum cells and the total number of neu-trophils,thereby improving airway inflammation.
5.Analysis of the effect of fudosteine on induced sputum components in patients with stable neutrophil-dominated COPD
Zhanbo LI ; Kaifeng DU ; Zhilong JIANG ; Jiameng GAO ; Mengjie CHEN ; Yuan MA ; Zhihong CHEN
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(4):362-369
AIM:To observe the effect of fudostei-ne on induced sputum cell components and lung function in patients with stable neutrophil-dominat-ed COPD.METHODS:From October 2019 to Octo-ber 2022,53 patients with stable COPD were select-ed and divided into fudosteine group and placebo group.The placebo group was treated with routine treatment,and the fudosteine group was treated with fudosteine on the basis of routine treatment.The two groups were treated for 6 months.The clinical symptoms[Saint George's Respiratory Questionnaire(SGRQ),COPD Assessment Test(CAT)and Modified British Medical Research Council Dys-pnea scale(MMRC),Breathlessness,Cough,and Sputum Scale(BCSS)],lung function index,induced sputum cytology analysis and other related exami-nation results were recorded in detail before and after treatment.RESULTS:(1)Compared with the baseline,the forced expiratory volume in one sec-ond(FEV1),forced vital capacity(FVC),and the ra-tio of FEV1 to FVC(FEV1/FVC)of the two groups were improved after treatment,and the differenc-es were statistically significant(P<0.05).However,after treatment,there was no significant difference in pulmonary function between the two groups ex-cept for the percentage of carbon monoxide diffu-sion in the predicted value(DLCO%pre)(DLCO%pre in the fudosteine group was higher than that in the placebo group).(2)After treatment,the total num-ber of induced sputum cells and neutrophil counts in the fudosteine group were lower than those in the placebo group.Compared with the number of cells in each component at baseline,the total num-ber of induced sputum cells and neutrophil count in the fudosteine group were significantly lower(P<0.05).CONCLUSION:Fudosteine treatment in pa-tients with stable neutrophil-dominated COPD can improve lung function,reduce the total number of induced sputum cells and the total number of neu-trophils,thereby improving airway inflammation.
6.Analysis of the effect of fudosteine on induced sputum components in patients with stable neutrophil-dominated COPD
Zhanbo LI ; Kaifeng DU ; Zhilong JIANG ; Jiameng GAO ; Mengjie CHEN ; Yuan MA ; Zhihong CHEN
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(4):362-369
AIM:To observe the effect of fudostei-ne on induced sputum cell components and lung function in patients with stable neutrophil-dominat-ed COPD.METHODS:From October 2019 to Octo-ber 2022,53 patients with stable COPD were select-ed and divided into fudosteine group and placebo group.The placebo group was treated with routine treatment,and the fudosteine group was treated with fudosteine on the basis of routine treatment.The two groups were treated for 6 months.The clinical symptoms[Saint George's Respiratory Questionnaire(SGRQ),COPD Assessment Test(CAT)and Modified British Medical Research Council Dys-pnea scale(MMRC),Breathlessness,Cough,and Sputum Scale(BCSS)],lung function index,induced sputum cytology analysis and other related exami-nation results were recorded in detail before and after treatment.RESULTS:(1)Compared with the baseline,the forced expiratory volume in one sec-ond(FEV1),forced vital capacity(FVC),and the ra-tio of FEV1 to FVC(FEV1/FVC)of the two groups were improved after treatment,and the differenc-es were statistically significant(P<0.05).However,after treatment,there was no significant difference in pulmonary function between the two groups ex-cept for the percentage of carbon monoxide diffu-sion in the predicted value(DLCO%pre)(DLCO%pre in the fudosteine group was higher than that in the placebo group).(2)After treatment,the total num-ber of induced sputum cells and neutrophil counts in the fudosteine group were lower than those in the placebo group.Compared with the number of cells in each component at baseline,the total num-ber of induced sputum cells and neutrophil count in the fudosteine group were significantly lower(P<0.05).CONCLUSION:Fudosteine treatment in pa-tients with stable neutrophil-dominated COPD can improve lung function,reduce the total number of induced sputum cells and the total number of neu-trophils,thereby improving airway inflammation.
7.Analysis of the effect of fudosteine on induced sputum components in patients with stable neutrophil-dominated COPD
Zhanbo LI ; Kaifeng DU ; Zhilong JIANG ; Jiameng GAO ; Mengjie CHEN ; Yuan MA ; Zhihong CHEN
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(4):362-369
AIM:To observe the effect of fudostei-ne on induced sputum cell components and lung function in patients with stable neutrophil-dominat-ed COPD.METHODS:From October 2019 to Octo-ber 2022,53 patients with stable COPD were select-ed and divided into fudosteine group and placebo group.The placebo group was treated with routine treatment,and the fudosteine group was treated with fudosteine on the basis of routine treatment.The two groups were treated for 6 months.The clinical symptoms[Saint George's Respiratory Questionnaire(SGRQ),COPD Assessment Test(CAT)and Modified British Medical Research Council Dys-pnea scale(MMRC),Breathlessness,Cough,and Sputum Scale(BCSS)],lung function index,induced sputum cytology analysis and other related exami-nation results were recorded in detail before and after treatment.RESULTS:(1)Compared with the baseline,the forced expiratory volume in one sec-ond(FEV1),forced vital capacity(FVC),and the ra-tio of FEV1 to FVC(FEV1/FVC)of the two groups were improved after treatment,and the differenc-es were statistically significant(P<0.05).However,after treatment,there was no significant difference in pulmonary function between the two groups ex-cept for the percentage of carbon monoxide diffu-sion in the predicted value(DLCO%pre)(DLCO%pre in the fudosteine group was higher than that in the placebo group).(2)After treatment,the total num-ber of induced sputum cells and neutrophil counts in the fudosteine group were lower than those in the placebo group.Compared with the number of cells in each component at baseline,the total num-ber of induced sputum cells and neutrophil count in the fudosteine group were significantly lower(P<0.05).CONCLUSION:Fudosteine treatment in pa-tients with stable neutrophil-dominated COPD can improve lung function,reduce the total number of induced sputum cells and the total number of neu-trophils,thereby improving airway inflammation.
8.Analysis of the effect of fudosteine on induced sputum components in patients with stable neutrophil-dominated COPD
Zhanbo LI ; Kaifeng DU ; Zhilong JIANG ; Jiameng GAO ; Mengjie CHEN ; Yuan MA ; Zhihong CHEN
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(4):362-369
AIM:To observe the effect of fudostei-ne on induced sputum cell components and lung function in patients with stable neutrophil-dominat-ed COPD.METHODS:From October 2019 to Octo-ber 2022,53 patients with stable COPD were select-ed and divided into fudosteine group and placebo group.The placebo group was treated with routine treatment,and the fudosteine group was treated with fudosteine on the basis of routine treatment.The two groups were treated for 6 months.The clinical symptoms[Saint George's Respiratory Questionnaire(SGRQ),COPD Assessment Test(CAT)and Modified British Medical Research Council Dys-pnea scale(MMRC),Breathlessness,Cough,and Sputum Scale(BCSS)],lung function index,induced sputum cytology analysis and other related exami-nation results were recorded in detail before and after treatment.RESULTS:(1)Compared with the baseline,the forced expiratory volume in one sec-ond(FEV1),forced vital capacity(FVC),and the ra-tio of FEV1 to FVC(FEV1/FVC)of the two groups were improved after treatment,and the differenc-es were statistically significant(P<0.05).However,after treatment,there was no significant difference in pulmonary function between the two groups ex-cept for the percentage of carbon monoxide diffu-sion in the predicted value(DLCO%pre)(DLCO%pre in the fudosteine group was higher than that in the placebo group).(2)After treatment,the total num-ber of induced sputum cells and neutrophil counts in the fudosteine group were lower than those in the placebo group.Compared with the number of cells in each component at baseline,the total num-ber of induced sputum cells and neutrophil count in the fudosteine group were significantly lower(P<0.05).CONCLUSION:Fudosteine treatment in pa-tients with stable neutrophil-dominated COPD can improve lung function,reduce the total number of induced sputum cells and the total number of neu-trophils,thereby improving airway inflammation.
9.Analysis of the effect of fudosteine on induced sputum components in patients with stable neutrophil-dominated COPD
Zhanbo LI ; Kaifeng DU ; Zhilong JIANG ; Jiameng GAO ; Mengjie CHEN ; Yuan MA ; Zhihong CHEN
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(4):362-369
AIM:To observe the effect of fudostei-ne on induced sputum cell components and lung function in patients with stable neutrophil-dominat-ed COPD.METHODS:From October 2019 to Octo-ber 2022,53 patients with stable COPD were select-ed and divided into fudosteine group and placebo group.The placebo group was treated with routine treatment,and the fudosteine group was treated with fudosteine on the basis of routine treatment.The two groups were treated for 6 months.The clinical symptoms[Saint George's Respiratory Questionnaire(SGRQ),COPD Assessment Test(CAT)and Modified British Medical Research Council Dys-pnea scale(MMRC),Breathlessness,Cough,and Sputum Scale(BCSS)],lung function index,induced sputum cytology analysis and other related exami-nation results were recorded in detail before and after treatment.RESULTS:(1)Compared with the baseline,the forced expiratory volume in one sec-ond(FEV1),forced vital capacity(FVC),and the ra-tio of FEV1 to FVC(FEV1/FVC)of the two groups were improved after treatment,and the differenc-es were statistically significant(P<0.05).However,after treatment,there was no significant difference in pulmonary function between the two groups ex-cept for the percentage of carbon monoxide diffu-sion in the predicted value(DLCO%pre)(DLCO%pre in the fudosteine group was higher than that in the placebo group).(2)After treatment,the total num-ber of induced sputum cells and neutrophil counts in the fudosteine group were lower than those in the placebo group.Compared with the number of cells in each component at baseline,the total num-ber of induced sputum cells and neutrophil count in the fudosteine group were significantly lower(P<0.05).CONCLUSION:Fudosteine treatment in pa-tients with stable neutrophil-dominated COPD can improve lung function,reduce the total number of induced sputum cells and the total number of neu-trophils,thereby improving airway inflammation.
10.Analysis of the effect of fudosteine on induced sputum components in patients with stable neutrophil-dominated COPD
Zhanbo LI ; Kaifeng DU ; Zhilong JIANG ; Jiameng GAO ; Mengjie CHEN ; Yuan MA ; Zhihong CHEN
Chinese Journal of Clinical Pharmacology and Therapeutics 2024;29(4):362-369
AIM:To observe the effect of fudostei-ne on induced sputum cell components and lung function in patients with stable neutrophil-dominat-ed COPD.METHODS:From October 2019 to Octo-ber 2022,53 patients with stable COPD were select-ed and divided into fudosteine group and placebo group.The placebo group was treated with routine treatment,and the fudosteine group was treated with fudosteine on the basis of routine treatment.The two groups were treated for 6 months.The clinical symptoms[Saint George's Respiratory Questionnaire(SGRQ),COPD Assessment Test(CAT)and Modified British Medical Research Council Dys-pnea scale(MMRC),Breathlessness,Cough,and Sputum Scale(BCSS)],lung function index,induced sputum cytology analysis and other related exami-nation results were recorded in detail before and after treatment.RESULTS:(1)Compared with the baseline,the forced expiratory volume in one sec-ond(FEV1),forced vital capacity(FVC),and the ra-tio of FEV1 to FVC(FEV1/FVC)of the two groups were improved after treatment,and the differenc-es were statistically significant(P<0.05).However,after treatment,there was no significant difference in pulmonary function between the two groups ex-cept for the percentage of carbon monoxide diffu-sion in the predicted value(DLCO%pre)(DLCO%pre in the fudosteine group was higher than that in the placebo group).(2)After treatment,the total num-ber of induced sputum cells and neutrophil counts in the fudosteine group were lower than those in the placebo group.Compared with the number of cells in each component at baseline,the total num-ber of induced sputum cells and neutrophil count in the fudosteine group were significantly lower(P<0.05).CONCLUSION:Fudosteine treatment in pa-tients with stable neutrophil-dominated COPD can improve lung function,reduce the total number of induced sputum cells and the total number of neu-trophils,thereby improving airway inflammation.

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