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Article: Comparative Evaluation of the Salivary and Buccal Mucosal Microbiota by 16S rRNA Sequencing for Forensic Investigations.

Wang, Shuangshuang / Song, Feng / Gu, Haoyu / Wei, Xiaowen / Zhang, Ke / Zhou, Yuxiang / Luo, Haibo

2022 Volume 13, Page(s) 777882

Abstract: The human microbiome has emerged as a new potential biomarker for forensic investigations with the development of high-throughput sequencing and bioinformatic analysis during the last decade. The oral cavity has many different microbial habitats, with ... ...

Abstract	The human microbiome has emerged as a new potential biomarker for forensic investigations with the development of high-throughput sequencing and bioinformatic analysis during the last decade. The oral cavity has many different microbial habitats, with each habit colonized by specific and individualized microbiota. As saliva and buccal mucosa are common biological evidence in forensic science, understanding the differences of microbial communities between the two is important for forensic original identification. Moreover, the oral microbiota is individualized, whereas there are few studies on the application of forensic personal identification that need to be supplemented. In this study,
Language	English
Publishing date	2022-03-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2022.777882
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Article ; Online: Resolving the recombination pattern of 38 X-STRs from Chinese Han three-generation pedigrees.

Song, Feng / Wei, Xiaowen / Zhou, Chengye / Wang, Shuangshuang / Deng, Chuncao / Liao, Miao / Luo, Haibo

Legal medicine (Tokyo, Japan)

2022 Volume 59, Page(s) 102135

Abstract: X-chromosomal markers have been proved as a useful tool for solving complex kinship cases due to its sex-linked inheriting feature. Among these markers, tightly linked X-STR clusters forming haplotypes are highly informative. The analysis of the ... ...

Abstract	X-chromosomal markers have been proved as a useful tool for solving complex kinship cases due to its sex-linked inheriting feature. Among these markers, tightly linked X-STR clusters forming haplotypes are highly informative. The analysis of the haplotypes requires determination of linkage disequilibrium. In this study, genetic linkage, recombination fractions and mutation rates of 38 X-STR loci in 177 three-generation pedigrees were investigated. Genetic linkage analysis and calculation of recombination fractions were performed within each pair of markers and clusters. Then mutation rates were calculated. The results showed that, a) 22 recombination events happened within the tightly linked X-STR clusters, which span<1.0 Mb; b) significantly linked marker pairs were observed with the LOD (logarithm of the odds) scores > 2.0 (2.0104 to 54.8316); c) the average mutation rate of the 38 X-STR loci was 1.32 × 10
MeSH term(s)	Humans ; Pedigree ; Microsatellite Repeats/genetics ; Chromosomes, Human, X/genetics ; Genetic Linkage/genetics ; China
Language	English
Publishing date	2022-08-22
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	2019555-2
ISSN	1873-4162 ; 1344-6223
ISSN (online)	1873-4162
ISSN	1344-6223
DOI	10.1016/j.legalmed.2022.102135
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Article ; Online: pH-Dependent Hydrogenotrophic Denitratation Based on Self-Alkalization.

Shi, Ling-Dong / Gao, Tian-Yu / Wei, Xiao-Wen / Shapleigh, James P / Zhao, He-Ping

Environmental science & technology

2022

Abstract: Producing stable nitrite is a necessity for anaerobic ammonium oxidation (anammox) but remains a huge challenge. Here, we describe the design and operation of a hydrogenotrophic denitratation system that stably reduced >90% nitrate to nitrite under self- ... ...

Abstract	Producing stable nitrite is a necessity for anaerobic ammonium oxidation (anammox) but remains a huge challenge. Here, we describe the design and operation of a hydrogenotrophic denitratation system that stably reduced >90% nitrate to nitrite under self-alkaline conditions of pH up to 10.80. Manually lowering the pH to a range of 9.00-10.00 dramatically decreased the nitrate-to-nitrite transformation ratio to <20%, showing a significant role of high pH in denitratation. Metagenomics combined with metatranscriptomics indicated that six microorganisms, including a
Language	English
Publishing date	2022-11-21
Publishing country	United States
Document type	Journal Article
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.2c05559
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Article ; Online: Developing a male-specific age predictive model based on Y-CpGs for forensic analysis.

Jiang, Lanrui / Zhang, Ke / Wei, Xiaowen / Li, Jiahang / Wang, Shuangshuang / Wang, Zefei / Zhou, Yuxiang / Zha, Lagabaiyila / Luo, Haibo / Song, Feng

Forensic science international

2023 Volume 343, Page(s) 111566

Abstract: In forensic work, predicting the age of the criminal suspect or victim could provide beneficial clues for investigation. Epigenetic age estimation based on age-correlated DNA methylation has been one of the most widely studied methods of age estimation. ... ...

Abstract	In forensic work, predicting the age of the criminal suspect or victim could provide beneficial clues for investigation. Epigenetic age estimation based on age-correlated DNA methylation has been one of the most widely studied methods of age estimation. However, almost all available epigenetic age prediction models are based on autosomal CpGs, which are only applicable to single-source DNA samples. In this study, we screened the available methylation data sets to identify loci with potential to meet the objectives of this study and then established a male-specific age prediction model based on 2 SNaPshot systems that contain 13 Y-CpGs and the mean absolute deviation (MAD) values were 4-6 years. The multiplex methylation SNaPshot systems and age-predictive model have been validated for sensitivity (the DNA input could be as low as 0.5 ng) and male specificity. They are supposed to have feasibility in forensic practice. In addition, it demonstrated that the method was also applicable to bloodstains, which were commonly found at crime scenes. The results showed good performance (the training set: R
MeSH term(s)	Male ; Humans ; Female ; Child, Preschool ; Child ; Forensic Genetics/methods ; CpG Islands ; DNA Methylation ; DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-01-11
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	424042-x
ISSN	1872-6283 ; 0379-0738
ISSN (online)	1872-6283
ISSN	0379-0738
DOI	10.1016/j.forsciint.2023.111566
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Article ; Online: Efficacy of varenicline or bupropion and its association with nicotine metabolite ratio among smokers with COPD.

Qin, Rui / Liu, Zhao / Cheng, An-Qi / Zhou, Xin-Mei / Su, Zheng / Cui, Zi-Yang / Li, Jin-Xuan / Wei, Xiao-Wen / Zhao, Liang / Chung, Kian Fan / Xiao, Dan / Wang, Chen

Respirology (Carlton, Vic.)

2024

Abstract: Background and objective: Nicotine metabolic ratio (NMR) has been associated with nicotine metabolism and smoking characteristics. However, there are few studies on the potential association between NMR and smoking cessation efficacy in smokers with ... ...

Abstract	Background and objective: Nicotine metabolic ratio (NMR) has been associated with nicotine metabolism and smoking characteristics. However, there are few studies on the potential association between NMR and smoking cessation efficacy in smokers with chronic obstructive pulmonary disease (COPD) in China or elsewhere. Methods: This study was a stratified block randomized controlled trial for smoking cessation in Chinese smokers with COPD. NMR was used as a stratification factor; slow metabolizers were defined as those with NMR <0.31, and normal metabolizers as those with NMR ≥0.31. Participants were randomly assigned to the varenicline or bupropion group. Follow-up visits were conducted at 1, 2, 4, 6, 9, 12 and 24 weeks. Results: Two hundred twenty-four participants were recruited and analysed from February 2019 to June 2022. In normal metabolizers, the 9-12 weeks continuous abstinence rate of varenicline (43.1%) was higher than in bupropion (23.5%) (OR = 2.47, 95% CI 1.05-5.78, p = 0.038). There was no significant difference in abstinence rates between treatment groups in slow metabolizers (54.1% vs. 45.9%, OR = 1.39, 95% CI 0.68-2.83, p = 0.366). For slow metabolizers, the total score of side effects in the varenicline group was significantly higher than the bupropion group (p = 0.048), while there was no significant difference in side effects between groups for normal metabolizers (p = 0.360). Conclusion: Varenicline showed better efficacy than bupropion in normal metabolizers, and bupropion showed equivalent efficacy in slow metabolizers with less side effects. According to our study, NMR provides a better justification for both scientific research and tailoring optimal pharmacotherapy for smoking cessation among smokers in COPD.
Language	English
Publishing date	2024-03-17
Publishing country	Australia
Document type	Journal Article
ZDB-ID	1435849-9
ISSN	1440-1843 ; 1323-7799
ISSN (online)	1440-1843
ISSN	1323-7799
DOI	10.1111/resp.14702
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Article: Research Progress on the Application of Human Oral Microbiome in Forensic Individual Identification.

Wang, Shuang-Shuang / Song, Feng / Wei, Xiao-Wen / Gu, Hao-Yu / Zhang, Ke / Zhou, Yu-Xiang / Jiang, Lan-Rui / Luo, Hai-Bo

Fa yi xue za zhi

2022 Volume 38, Issue 4, Page(s) 526–532

Abstract: The oral cavity is the second largest microbial bank in humans after the intestinal canal, colonizing a large number of microorganisms including viruses, bacteria, archaea, fungi and protozoa. The great number of microbial cells, good DNA stability, and ... ...

Abstract	The oral cavity is the second largest microbial bank in humans after the intestinal canal, colonizing a large number of microorganisms including viruses, bacteria, archaea, fungi and protozoa. The great number of microbial cells, good DNA stability, and individual has a unique microbial community, these characteristics make the human microbiome expected to become a new biomarker for forensic individual identification. This article describes the characteristics of human oral microorganisms and microbial molecular markers in detail, analyzes the potential application value of microorganisms in forensic individual identification, and reviews the research progress of human oral microorganisms in forensic individual identification.
MeSH term(s)	Humans ; Microbiota ; Forensic Medicine
Language	Chinese
Publishing date	2022-07-19
Publishing country	China
Document type	Journal Article
ISSN	1004-5619
ISSN	1004-5619
DOI	10.12116/j.issn.1004-5619.2021.510101
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Article ; Online: Large fragment Sanger sequencing identifies the newly encountered variant that caused null alleles in parentage testing.

Jiang, Lanrui / Song, Mengyuan / Wang, Zefei / Wei, Xiaowen / Zhou, Yuxiang / Wang, Shuangshuang / Zha, Lagabaiyila / Song, Feng / Luo, Haibo

International journal of legal medicine

2022

Abstract: Short tandem repeat (STR) is regarded as a crucial tool for personal identification as well as parentage testing. Thus, genotyping errors of STRs could have negative effects on the reliability of forensic identification. A null allele at the combined DNA ...

Abstract	Short tandem repeat (STR) is regarded as a crucial tool for personal identification as well as parentage testing. Thus, genotyping errors of STRs could have negative effects on the reliability of forensic identification. A null allele at the combined DNA index system (CODIS) core loci D2S1338 was found in a father-daughter pair with the AGCU Expressmarker 22 kit which was a commonly used commercial kit during our daily laboratory work. This null allele caused the father and daughter to not conform to the laws of inheritance, thus potentially generating erroneous conclusions that excluded parentage. To figure out the reason for this phenomenon, re-amplification with new primers and then large fragment Sanger sequencing was conducted. We found a G to G/T variation at the position which is fifty-nine bases away from the 3' end of the core repeat in both samples. This probably could be considered a novel variant at the primer binding region which had not been reported that resulted in the emergence of the null allele. We also found that there was more than one single-nucleotide polymorphism (SNP) with minor allele frequency (MAF) greater than 0.1 in the upstream and downstream sequences of D2S1338. When designing primers for amplification of D2S1338, the possible adverse results of these SNPs should be taken into account and avoided.
Language	English
Publishing date	2022-11-01
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1055109-8
ISSN	1437-1596 ; 0937-9827
ISSN (online)	1437-1596
ISSN	0937-9827
DOI	10.1007/s00414-022-02901-2
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Article ; Online: Prevalence of cigarette use and addiction among Chinese females by age and province: Findings from nationwide China Health Literacy Survey during 2018-19.

Xia, Xin / Li, Ying-Hua / Liu, Yi / Su, Zheng / Qin, Rui / Liu, Zhao / Xie, Ying / Huang, Zhen-Xiao / Zhou, Xin-Mei / Cheng, An-Qi / Li, Jin-Xuan / Wei, Xiao-Wen / Song, Qing-Qing / Zhao, Liang / Xiao, Dan / Wang, Chen

Drug and alcohol dependence

2024 Volume 258, Page(s) 111258

Abstract: Background: The prevalence of cigarette smoking among women is significantly different from that of men, however, cigarette use by women is little known. The study aims to describe cigarette use prevalence and patterns among Chinese females by age and ... ...

Abstract	Background: The prevalence of cigarette smoking among women is significantly different from that of men, however, cigarette use by women is little known. The study aims to describe cigarette use prevalence and patterns among Chinese females by age and province. Methods: This study was based on the 2018 China Health Literacy Survey (2018 CHLS), a nationally representative cross-sectional study, and our analysis included 43,319 female participants aged 20-69 with valid data. The prevalence of cigarette use was estimated overall by sociodemographic factors and weighted based on the census population data. The logistic regression model was conducted to estimate adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for the risk factors associated with cigarette use and dependency. Results: In China, the estimated female current cigarette use prevalence was 1.85%, with over half of the population suffering from tobacco dependence (7.34 million). Jilin Province has the highest cigarette prevalence among women (10.59%), while Fujian Province has the lowest (0.27%). Participants over 60 years old (aOR=1.61, 95%CI=1.20-2.14), single (aOR=1.54, 95%CI=1.07-2.21), with primary education (aOR=1.93, 95%CI=1.47-2.52) were more likely to smoke. The age of smoking initiation among women intergenerational advanced, and compared to the cigarette users without tobacco dependence, those who have tobacco dependence start smoking earlier in all age groups (25.69 years vs. 19.36 years, p<0.001). Conclusions: The cigarette use prevalence among Chinese women was 1.85%, and there are significant differences among provinces. We noted a trend of women initiating smoking at increasingly younger ages, particularly among those with tobacco dependence.
Language	English
Publishing date	2024-03-05
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	519918-9
ISSN	1879-0046 ; 0376-8716
ISSN (online)	1879-0046
ISSN	0376-8716
DOI	10.1016/j.drugalcdep.2024.111258
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Article: Evaluation of the AGCU Expressmarker 30 Kit composed of 31 loci for forensic application

Zhang, Ke / Song, Feng / Wang, Shuangshuang / Wei, Xiaowen / Gu, Haoyu / Xie, Mingkun / Zhou, Yuxiang / Luo, Haibo

Forensic science international. 2021 July, v. 324

2021

Abstract: With the widespread use of STR in identification of individuals, paternity testing, as well as population genetics, many commercially robust and validated STR multiplex kits were developed. The AGCU Expressmarker 30 Kit is a new autosomal STR system that ...

Abstract	With the widespread use of STR in identification of individuals, paternity testing, as well as population genetics, many commercially robust and validated STR multiplex kits were developed. The AGCU Expressmarker 30 Kit is a new autosomal STR system that contains 29 autosomal STR loci (D3S1358, vWA, D1S1656, CSF1PO, D8S1132, D19S253, D3S3045, D8S1179, D21S11, D16S539, TPOX, D6S477, Penta D, D2S441, D5S818, TH01, FGA, D15S659, D22S1045, D19S433, D13S317, D7S820, D6S1043, D10S1435, D10S1248, D2S1338, D18S51, D12S391, and Penta E), one insertion/deletion polymorphic marker on the Y chromosome (Y indel), and the amelogenin locus. A series of validation studies were performed in this context according to the guidelines of “Validation Guidelines for Forensic DNA Analysis Methods”. The sensitivity study showed that a full profile was observed with template DNA as low as 40 pg. In the stability study, all STR profiles were obtained at concentrations of humic acid up to 800 ng/μL, hematin up to 250 μM, and tannic acid up to 200 ng/μL. The mixture study demonstrated that all of the minor alleles could be called at ratios from 1:1–29:1 when the total DNA was 2 ng. In the population study, the total discrimination power for three population (Sichuan-Han, Gansu-Hui, and Guangxi-Zhuang) were above 0.9999999999999999999999999999999992, 0.999999999999999999999999999999998 and 0.999999999999999999999999999999994 as well as the cumulative probability of paternity exclusion were 0.999999999999953, 0.999999999999178, and 0.999999999999611 respectively. These results demonstrated that the AGCU Expressmarker 30 Kit is a useful tool for analyzing both forensic casework and database samples.
Keywords	DNA ; Y chromosome ; databases ; forensic sciences ; humic acids ; loci ; paternity ; population genetics ; probability ; tannins
Language	English
Dates of publication	2021-07
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	424042-x
ISSN	1872-6283 ; 0379-0738
ISSN (online)	1872-6283
ISSN	0379-0738
DOI	10.1016/j.forsciint.2021.110849
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: CLNode

Wei, Xiaowen / Gong, Xiuwen / Zhan, Yibing / Du, Bo / Luo, Yong / Hu, Wenbin

Curriculum Learning for Node Classification

2022

Abstract: Node classification is a fundamental graph-based task that aims to predict the classes of unlabeled nodes, for which Graph Neural Networks (GNNs) are the state-of-the-art methods. Current GNNs assume that nodes in the training set contribute equally ... ...

Abstract	Node classification is a fundamental graph-based task that aims to predict the classes of unlabeled nodes, for which Graph Neural Networks (GNNs) are the state-of-the-art methods. Current GNNs assume that nodes in the training set contribute equally during training. However, the quality of training nodes varies greatly, and the performance of GNNs could be harmed by two types of low-quality training nodes: (1) inter-class nodes situated near class boundaries that lack the typical characteristics of their corresponding classes. Because GNNs are data-driven approaches, training on these nodes could degrade the accuracy. (2) mislabeled nodes. In real-world graphs, nodes are often mislabeled, which can significantly degrade the robustness of GNNs. To mitigate the detrimental effect of the low-quality training nodes, we present CLNode, which employs a selective training strategy to train GNN based on the quality of nodes. Specifically, we first design a multi-perspective difficulty measurer to accurately measure the quality of training nodes. Then, based on the measured qualities, we employ a training scheduler that selects appropriate training nodes to train GNN in each epoch. To evaluate the effectiveness of CLNode, we conduct extensive experiments by incorporating it in six representative backbone GNNs. Experimental results on real-world networks demonstrate that CLNode is a general framework that can be combined with various GNNs to improve their accuracy and robustness.
Keywords	Computer Science - Machine Learning ; Computer Science - Social and Information Networks
Subject code	000 ; 006
Publishing date	2022-06-14
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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