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Article ; Online: Construction of an oxidative stress-associated genes signature in breast cancer by machine learning algorithms.

Hu, Daojun / Qin, Bing / Zhang, Li / Bu, Hanli

The Journal of international medical research

2024 Volume 52, Issue 3, Page(s) 3000605241232560

Abstract: Objective: To construct a prognostic model of a breast cancer-related oxidative stress-related gene (OSRG) signature using machine learning algorithms.: Methods: The OSRGs of breast cancer were constructed by least absolute shrinkage and selection ... ...

Abstract	Objective: To construct a prognostic model of a breast cancer-related oxidative stress-related gene (OSRG) signature using machine learning algorithms. Methods: The OSRGs of breast cancer were constructed by least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis. The Cancer Genome Atlas (TCGA) was used to analyse the gene expression and prognostic value. The Human Protein Atlas was used to analyse the protein expression of hub genes. Receiver operating characteristic analysis, calibration curve and decision curve analysis were used to predict the stability of this model. Results: The area under the curve of 1-, 3- and 5-year overall survival were 0.751, 0.707 and 0.645 in the TCGA training dataset; and 0.692, 0.678 and 0.602 in the TCGA testing dataset, respectively. Calibration plot showed good agreement between predicted probabilities and observed outcomes. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) pathway analysis indicated that multiple cancer-related pathways were highly enriched in the high-risk group. Immune infiltration analysis showed immune cells and their functions may play a key role in the development and mechanism of breast cancer. Conclusions: This new OSRG signature was associated with the immune infiltration and it might be useful in predicting the prognosis in patients with breast cancer.
MeSH term(s)	Humans ; Female ; Breast Neoplasms/genetics ; Oxidative Stress/genetics ; Breast ; Algorithms ; Machine Learning ; Prognosis
Language	English
Publishing date	2024-03-23
Publishing country	England
Document type	Journal Article
ZDB-ID	184023-x
ISSN	1473-2300 ; 0300-0605 ; 0142-2596
ISSN (online)	1473-2300
ISSN	0300-0605 ; 0142-2596
DOI	10.1177/03000605241232560
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Article ; Online: Identification of dominant taxa of sooty moulds and their impact on the leaf microbiome.

Lv, Zhiyuan / Hu, Chong / Hu, Yue / Wu, Daojun / Zhou, Hanyu / Tian, Lichao

Environmental microbiology

2023 Volume 25, Issue 4, Page(s) 853–866

Abstract: Sooty moulds are a widespread group of saprophytic ascomycetes that obtain nutrients from honeydew excreted by sap-feeding insects and coat plant tissue with mycelia. Research on sooty moulds has focused on fungal morphology and phylogeny-based taxonomy, ...

Abstract	Sooty moulds are a widespread group of saprophytic ascomycetes that obtain nutrients from honeydew excreted by sap-feeding insects and coat plant tissue with mycelia. Research on sooty moulds has focused on fungal morphology and phylogeny-based taxonomy, but little research has been conducted on the community structure. In this study, the PacBio sequencing platform was used to systematically analyse the fungal and bacterial diversity of the sooty mould community on camphor trees at two sampling sites. Six dominant sooty mould genera were identified, of which three genera of Dothideomycetes were enriched only in diseased samples, while three genera of Eurotiomycetes were present in both healthy and diseased samples. Bacterial diversity and co-occurrence network analysis indicated that the sooty moulds had an effect on the leaf surface bacterial communities but not on the endophyte communities. There was a close correlation between the six dominant pathogenic groups and bacteria in the soot layer. Transcriptomic data from Cinnamomum camphora samples showed that the sooty moulds that did not penetrate plant cells not only affected plant photosynthesis but also induced plant defence responses. This study systematically studied the microbial community of sooty moulds, indicating the close relationship between sooty moulds and the bacterial communities.
MeSH term(s)	Fungi/genetics ; Phylogeny ; Bacteria/genetics ; Microbiota/genetics ; Plant Leaves
Language	English
Publishing date	2023-01-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16321
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Article ; Online: Optimizing skin disease diagnosis: harnessing online community data with contrastive learning and clustering techniques.

Shen, Yue / Li, Huanyu / Sun, Can / Ji, Hongtao / Zhang, Daojun / Hu, Kun / Tang, Yiqi / Chen, Yu / Wei, Zikun / Lv, Junwei

NPJ digital medicine

2024 Volume 7, Issue 1, Page(s) 28

Abstract: Skin diseases pose significant challenges in China. Internet health forums offer a platform for millions of users to discuss skin diseases and share images for early intervention, leaving large amount of valuable dermatology images. However, data quality ...

Abstract	Skin diseases pose significant challenges in China. Internet health forums offer a platform for millions of users to discuss skin diseases and share images for early intervention, leaving large amount of valuable dermatology images. However, data quality and annotation challenges limit the potential of these resources for developing diagnostic models. In this study, we proposed a deep-learning model that utilized unannotated dermatology images from diverse online sources. We adopted a contrastive learning approach to learn general representations from unlabeled images and fine-tuned the model on coarsely annotated images from Internet forums. Our model classified 22 common skin diseases. To improve annotation quality, we used a clustering method with a small set of standardized validation images. We tested the model on images collected by 33 experienced dermatologists from 15 tertiary hospitals and achieved a 45.05% top-1 accuracy, outperforming the published baseline model by 3%. Accuracy increased with additional validation images, reaching 49.64% with 50 images per category. Our model also demonstrated transferability to new tasks, such as detecting monkeypox, with a 61.76% top-1 accuracy using only 50 additional images in the training process. We also tested our model on benchmark datasets to show the generalization ability. Our findings highlight the potential of unannotated images from online forums for future dermatology applications and demonstrate the effectiveness of our model for early diagnosis and potential outbreak mitigation.
Language	English
Publishing date	2024-02-08
Publishing country	England
Document type	Journal Article
ISSN	2398-6352
ISSN (online)	2398-6352
DOI	10.1038/s41746-024-01014-x
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Article ; Online: Polystyrene microplastics enhance microcystin-LR-induced cardiovascular toxicity and oxidative stress in zebrafish embryos.

Xiao, Yuchun / Hu, Liwen / Duan, Jiayao / Che, Huimin / Wang, Wenxin / Yuan, Yuan / Xu, Jiayi / Chen, Daojun / Zhao, Sujuan

Environmental pollution (Barking, Essex : 1987)

2024 , Page(s) 124022

Abstract: The health risks associated with combined exposure to microplastics (MPs) and cyanobacteria toxins have gained increasing attention due to the large-scale prevalence of cyanobacterial blooms and accumulation of MPs in aquatic environments. Therefore, we ... ...

Abstract	The health risks associated with combined exposure to microplastics (MPs) and cyanobacteria toxins have gained increasing attention due to the large-scale prevalence of cyanobacterial blooms and accumulation of MPs in aquatic environments. Therefore, we explored the cardiovascular toxic effects of microcystin-LR (MC-LR, 1, 10, 100 μg/L) in the presence of 5 μm polystyrene microplastics (PS-MPs, 100 μg/L) and 80 nm polystyrene nanoplastics (PS-NPs, 100μg/L) in zebrafish models. Embryos were exposed to certain PS-MPs and PS-NPs conditions in water between 3 h post-fertilization (hpf) and 168 hpf. Compared to MC-LR alone, a significant decrease in heart rate was observed as well as notable pericardial edema in the MC-LR+PS-MPs/NPs groups. At the same time, sinus venosus and bulbus arteriosus (SV-BA) distances were significantly increased. Furthermore, the addition of PS-MPs/NPs caused thrombosis in the caudal vein and more severe vascular damage in zebrafish larvae compared to MC-LR alone. Our findings revealed that combined exposure to PS-NPs and MC-LR could significantly decreased the expression of genes associated with cardiovascular development (myh6, nkx2.5, tnnt2a, and vegfaa), ATPase (atp1a3b, atp1b2b, atp2a1l, atp2b1a, and atp2b4), and the calcium channel (cacna1ab and ryr2a) compared to exposure to MC-LR alone. In addition, co-exposure with PS-MPs/NPs exacerbated the MC-LR-induced reactive oxygen species (ROS) production, as well as the ROS-stimulated apoptosis and heightened inflammation. We also discovered that astaxanthin (ASTA) treatment partially attenuated these cardiovascular toxic effects. Our findings confirm that exposure to MC-LR and PS-MPs/NPs affects cardiovascular development through calcium signaling interference and ROS-induced cardiovascular cell apoptosis. This study highlights the potential environmental risks of the co-existence of MC-LR and PS-MPs/NPs for fetal health, particularly cardiovascular development.
Language	English
Publishing date	2024-04-26
Publishing country	England
Document type	Journal Article
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2024.124022
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Zs.A 2599: Show issues

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Article ; Online: Association between Urinary Lead and Female Breast Cancer: A Population-Based Cross-Sectional Study.

Hu, Daojun / Zhang, Li / Qin, Bing / Wang, Ning / Li, Xingjun / Shi, Wenjie

Discovery medicine

2023 Volume 35, Issue 179, Page(s) 1177–1189

Abstract: Background: Previous studies have explored the relationship between serum lead levels and the risk of female breast cancer (FBC). However, it is still uncertain whether urinary lead levels are associated with FBC. This study aimed to investigate the ... ...

Abstract	Background: Previous studies have explored the relationship between serum lead levels and the risk of female breast cancer (FBC). However, it is still uncertain whether urinary lead levels are associated with FBC. This study aimed to investigate the potential association between urinary lead and FBC. Methods: A cross-sectional case-control study was conducted using the National Health and Nutrition Examination Survey (NHANES), which is a series of cross-sectional, nationally representative surveys of the United States population consisting of 10 survey waves from 1999 to 2018. This study analyzed a total of 2795 female participants (≥20 years), consisting of 210 participants with FBC and 2585 healthy controls. Urinary lead was detected using Inductively Coupled Plasma-Mass Spectrometry, which was divided into four levels by using quartiles-defining cut points. Multivariate logistic regression was used to analyze the association between urinary lead and FBC. Results: Multivariate logistic regression revealed that urinary lead was positively correlated with FBC (Odds ratio [OR], 2.16; 95% confidence interval [CI]: [1.18, 3.95], Conclusions: Urinary lead is likely positively associated with FBC in the US population.
MeSH term(s)	Humans ; Female ; United States/epidemiology ; Nutrition Surveys ; Cross-Sectional Studies ; Lead ; Breast Neoplasms/epidemiology ; Case-Control Studies
Chemical Substances	Lead (2P299V784P)
Language	English
Publishing date	2023-12-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2415544-5
ISSN	1944-7930 ; 1944-7930
ISSN (online)	1944-7930
ISSN	1944-7930
DOI	10.24976/Discov.Med.202335179.114
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Article ; Online: Identification of dominant taxa of sooty moulds and their impact on the leaf microbiome

Lv, Zhiyuan / Hu, Chong / Hu, Yue / Wu, Daojun / Zhou, Hanyu / Tian, Lichao

Environmental Microbiology. 2023 Apr., v. 25, no. 4 p.853-866

2023

Abstract: Sooty moulds are a widespread group of saprophytic ascomycetes that obtain nutrients from honeydew excreted by sap‐feeding insects and coat plant tissue with mycelia. Research on sooty moulds has focused on fungal morphology and phylogeny‐based taxonomy, ...

Abstract	Sooty moulds are a widespread group of saprophytic ascomycetes that obtain nutrients from honeydew excreted by sap‐feeding insects and coat plant tissue with mycelia. Research on sooty moulds has focused on fungal morphology and phylogeny‐based taxonomy, but little research has been conducted on the community structure. In this study, the PacBio sequencing platform was used to systematically analyse the fungal and bacterial diversity of the sooty mould community on camphor trees at two sampling sites. Six dominant sooty mould genera were identified, of which three genera of Dothideomycetes were enriched only in diseased samples, while three genera of Eurotiomycetes were present in both healthy and diseased samples. Bacterial diversity and co‐occurrence network analysis indicated that the sooty moulds had an effect on the leaf surface bacterial communities but not on the endophyte communities. There was a close correlation between the six dominant pathogenic groups and bacteria in the soot layer. Transcriptomic data from Cinnamomum camphora samples showed that the sooty moulds that did not penetrate plant cells not only affected plant photosynthesis but also induced plant defence responses. This study systematically studied the microbial community of sooty moulds, indicating the close relationship between sooty moulds and the bacterial communities.
Keywords	Cinnamomum camphora ; Dothideomycetes ; Eurotiomycetes ; camphor ; community structure ; endophytes ; fungal morphology ; fungi ; honeydew ; leaves ; microbial communities ; microbiome ; mycelium ; photosynthesis ; plant tissues ; saprophytes ; soot ; sooty molds ; taxonomy ; transcriptomics
Language	English
Dates of publication	2023-04
Size	p. 853-866.
Publishing place	John Wiley & Sons, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16321
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Less expression of CD4

Hu, Daojun / Li, Li / Shi, Wenjie / Zhang, Li

Clinica chimica acta; international journal of clinical chemistry

2020 Volume 510, Page(s) 1–4

Abstract: This study mainly focused on the very serious COVID-19 epidemic situation at present and provided a new insight for the treatment and monitor of patients with COVID-19. Through this meta-analysis, we could draw a conclusion that less expression of blood ... ...

Abstract	This study mainly focused on the very serious COVID-19 epidemic situation at present and provided a new insight for the treatment and monitor of patients with COVID-19. Through this meta-analysis, we could draw a conclusion that less expression of blood CD4
MeSH term(s)	Adult ; Aged ; CD4-Positive T-Lymphocytes/cytology ; CD8-Positive T-Lymphocytes/cytology ; COVID-19 ; Coronavirus Infections/diagnosis ; Coronavirus Infections/immunology ; Female ; Gene Expression Regulation ; Humans ; Male ; Middle Aged ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/immunology ; Prognosis
Keywords	covid19
Language	English
Publishing date	2020-06-27
Publishing country	Netherlands
Document type	Letter
ZDB-ID	80228-1
ISSN	1873-3492 ; 0009-8981
ISSN (online)	1873-3492
ISSN	0009-8981
DOI	10.1016/j.cca.2020.06.040
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Article: Background and roles: myosin in autoimmune diseases.

Fu, Longsheng / Zou, Yonghui / Yu, Boyang / Hong, Daojun / Guan, Teng / Hu, Jinfang / Xu, Yi / Wu, Yaoqi / Kou, Junping / Lv, Yanni

Frontiers in cell and developmental biology

2023 Volume 11, Page(s) 1220672

Abstract: The myosin superfamily is a group of molecular motors. Autoimmune diseases are characterized by dysregulation or deficiency of the immune tolerance mechanism, resulting in an immune response to the human body itself. The link between myosin and ... ...

Abstract	The myosin superfamily is a group of molecular motors. Autoimmune diseases are characterized by dysregulation or deficiency of the immune tolerance mechanism, resulting in an immune response to the human body itself. The link between myosin and autoimmune diseases is much more complex than scientists had hoped. Myosin itself immunization can induce experimental autoimmune diseases of animals, and myosins were abnormally expressed in a number of autoimmune diseases. Additionally, myosin takes part in the pathological process of multiple sclerosis, Alzheimer's disease, Parkinson's disease, autoimmune myocarditis, myositis, hemopathy, inclusion body diseases, etc. However, research on myosin and its involvement in the occurrence and development of diseases is still in its infancy, and the underlying pathological mechanisms are not well understood. We can reasonably predict that myosin might play a role in new treatments of autoimmune diseases.
Language	English
Publishing date	2023-08-23
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2023.1220672
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Article ; Online: Five-mRNA Signature for the Prognosis of Breast Cancer Based on the ceRNA Network

Wenjie Shi / Daojun Hu / Sen Lin / Rui Zhuo

BioMed Research International, Vol

2020 Volume 2020

Abstract: Background. The purpose of this study was to investigate the regulatory mechanisms of ceRNAs in breast cancer (BC) and construct a new five-mRNA prognostic signature. Methods. The ceRNA network was constructed by different RNAs screened by the edgeR ... ...

Abstract	Background. The purpose of this study was to investigate the regulatory mechanisms of ceRNAs in breast cancer (BC) and construct a new five-mRNA prognostic signature. Methods. The ceRNA network was constructed by different RNAs screened by the edgeR package. The BC prognostic signature was built based on the Cox regression analysis. The log-rank method was used to analyse the survival rate of BC patients with different risk scores. The expression of the 5 genes was verified by the GSE81540 dataset and CPTAC database. Results. A total of 41 BC-adjacent tissues and 473 BC tissues were included in this study. A total of 2,966 differentially expressed lncRNAs, 5,370 differentially expressed mRNAs, and 359 differentially expressed miRNAs were screened. The ceRNA network was constructed using 13 lncRNAs, 267 mRNAs, and 35 miRNAs. Kaplan-Meier (K-M) methods showed that two lncRNAs (AC037487.1 and MIR22HG) are related to prognosis. Five mRNAs (VPS28, COL17A1, HSF1, PUF60, and SMOC1) in the ceRNA network were used to establish a prognostic signature. Survival analysis showed that the prognosis of patients in the low-risk group was significantly better than that in the high-risk group (p=0.0022). ROC analysis showed that this signature has a good diagnostic ability (AUC=0.77). Compared with clinical features, this signature was also an independent prognostic factor (HR: 1.206, 95% CI 1.108−1.311; p<0.001). External verification results showed that the expression of the 5 mRNAs differed between the normal and tumour groups at the chip and protein levels (p<0.001). Conclusions. These ceRNAs may play a key role in the development of BC, and the new 5-mRNA prognostic signature can improve the prediction of survival for BC patients.
Keywords	Medicine ; R
Subject code	616
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Whole genome sequence of EC16, a bla

Huang, Junwei / Zhu, Jianjun / Gong, Daojun / Wu, Lin / Zhu, Yongze / Hu, Liqing

Journal of global antimicrobial resistance

2022 Volume 29, Page(s) 296–298

Abstract: Objectives: Escherichia coli sequence type 167 (ST167) is an international multiresistant high-risk clone associated with New Delhi metallo-beta-lactamase (NDM) carbapenemase. Here, we report the whole genome sequence of an ST167 clinical isolate (EC16), ...

Abstract	Objectives: Escherichia coli sequence type 167 (ST167) is an international multiresistant high-risk clone associated with New Delhi metallo-beta-lactamase (NDM) carbapenemase. Here, we report the whole genome sequence of an ST167 clinical isolate (EC16), obtained from a patient with abdominal infection in China, coharbouring the bla Methods: E. coli strain EC16 was subjected to antimicrobial susceptibility testing by the broth microdilution method. Whole-genome sequencing of E. coli EC16 was performed using both Oxford Nanopore PromethION and Illumina NovaSeq 6000 platforms. De novo hybrid assembly of short Illumina reads and long PromethION reads was performed using Unicycler. Genome annotation was performed using Prokka 1.14.6, and further whole-genome sequence data analyses were performed. Easyfig 2.2.3 was used to analyse the genetic surroundings of bla Results: The complete genome sequence of E. coli EC16 consists of six contigs comprising 5 317 797 bp, including one chromosome and five plasmids. Whole-genome sequencing and further bioinformatics analysis revealed that E. coli EC16 belonged to serotype O101:H9, fumC11 type, and ST167.bla Conclusion: In this study, we report a clinical E. coli ST167 strain carrying a novel IncFII-type bla
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli ; Escherichia coli Infections ; Humans ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2022-04-10
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2710046-7
ISSN	2213-7173 ; 2213-7173
ISSN (online)	2213-7173
ISSN	2213-7173
DOI	10.1016/j.jgar.2022.04.001
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