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  1. Article: Editorial: The Genetic Causes Underlying Immune Mediated Disease: A Focus on Autoimmunity and Cancer.

    Jiménez-Morales, Silvia / Ren, Xianwen / Dean, Michael

    Frontiers in genetics

    2022  Volume 13, Page(s) 889160

    Language English
    Publishing date 2022-03-25
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.889160
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  2. Article ; Online: Spatial transcriptomics deconvolution at single-cell resolution using Redeconve.

    Zhou, Zixiang / Zhong, Yunshan / Zhang, Zemin / Ren, Xianwen

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 7930

    Abstract: Computational deconvolution with single-cell RNA sequencing data as reference is pivotal to interpreting spatial transcriptomics data, but the current methods are limited to cell-type resolution. Here we present Redeconve, an algorithm to deconvolute ... ...

    Abstract Computational deconvolution with single-cell RNA sequencing data as reference is pivotal to interpreting spatial transcriptomics data, but the current methods are limited to cell-type resolution. Here we present Redeconve, an algorithm to deconvolute spatial transcriptomics data at single-cell resolution, enabling interpretation of spatial transcriptomics data with thousands of nuanced cell states. We benchmark Redeconve with the state-of-the-art algorithms on diverse spatial transcriptomics platforms and datasets and demonstrate the superiority of Redeconve in terms of accuracy, resolution, robustness, and speed. Application to a human pancreatic cancer dataset reveals cancer-clone-specific T cell infiltration, and application to lymph node samples identifies differential cytotoxic T cells between IgA+ and IgG+ spots, providing novel insights into tumor immunology and the regulatory mechanisms underlying antibody class switch.
    MeSH term(s) Humans ; Transcriptome/genetics ; Gene Expression Profiling ; Algorithms ; Benchmarking ; Immunoglobulin Isotypes ; Single-Cell Analysis
    Chemical Substances Immunoglobulin Isotypes
    Language English
    Publishing date 2023-12-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-43600-9
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  3. Article ; Online: Spatial transcriptomics deconvolution at single-cell resolution using Redeconve

    Zixiang Zhou / Yunshan Zhong / Zemin Zhang / Xianwen Ren

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 15

    Abstract: Abstract Computational deconvolution with single-cell RNA sequencing data as reference is pivotal to interpreting spatial transcriptomics data, but the current methods are limited to cell-type resolution. Here we present Redeconve, an algorithm to ... ...

    Abstract Abstract Computational deconvolution with single-cell RNA sequencing data as reference is pivotal to interpreting spatial transcriptomics data, but the current methods are limited to cell-type resolution. Here we present Redeconve, an algorithm to deconvolute spatial transcriptomics data at single-cell resolution, enabling interpretation of spatial transcriptomics data with thousands of nuanced cell states. We benchmark Redeconve with the state-of-the-art algorithms on diverse spatial transcriptomics platforms and datasets and demonstrate the superiority of Redeconve in terms of accuracy, resolution, robustness, and speed. Application to a human pancreatic cancer dataset reveals cancer-clone-specific T cell infiltration, and application to lymph node samples identifies differential cytotoxic T cells between IgA+ and IgG+ spots, providing novel insights into tumor immunology and the regulatory mechanisms underlying antibody class switch.
    Keywords Science ; Q
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Olfactory disorder in Parkinson's disease

    REN Peng, CHEN Yali, ZHANG Xianwen

    Jichu yixue yu linchuang, Vol 43, Iss 6, Pp 994-

    2023  Volume 997

    Abstract: Olfactory dysfunction is the most common early non-motor symptom of Parkinson's disease (PD), which is used as a marker for the diagnosis of PD. The mechanism of olfactory dysfunction is very complex, which is a challenge in the research. The ... ...

    Abstract Olfactory dysfunction is the most common early non-motor symptom of Parkinson's disease (PD), which is used as a marker for the diagnosis of PD. The mechanism of olfactory dysfunction is very complex, which is a challenge in the research. The neuromediator such as the accumulation of α-synuclein, dopamine (DA), acetylcholine (ACh), 5-hydroxytryptamine (5-HT) and inflammatory factors are implicated in the olfactory dysfunction in PD. To further study the mechanism of olfactory dysfunction in PD may provide new ideas and therapeutic targets for treatment.
    Keywords parkinson's disease|olfactory dysfunction|α-synuclein|inflammation response|neuromediator ; Medicine ; R
    Language Chinese
    Publishing date 2023-06-01T00:00:00Z
    Publisher Institute of Basic Medical Sciences and Peking Union Medical College Hospital, Chinese Academy of Medical Sciences / Peking Union Medical College.
    Document type Article ; Online
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  5. Article ; Online: Diversified Chemical Structures and Bioactivities of the Chemical Constituents Found in the Brown Algae Family Sargassaceae.

    Peng, Yan / Yang, Xianwen / Huang, Riming / Ren, Bin / Chen, Bin / Liu, Yonghong / Zhang, Hongjie

    Marine drugs

    2024  Volume 22, Issue 2

    Abstract: Sargassaceae, the most abundant family in Fucales, was recently formed through the merging of the two former families Sargassaceae and Cystoseiraceae. It is widely distributed in the world's oceans, notably in tropical coastal regions, with the exception ...

    Abstract Sargassaceae, the most abundant family in Fucales, was recently formed through the merging of the two former families Sargassaceae and Cystoseiraceae. It is widely distributed in the world's oceans, notably in tropical coastal regions, with the exception of the coasts of Antarctica and South America. Numerous bioactivities have been discovered through investigations of the chemical diversity of the Sargassaceae family. The secondary metabolites with unique structures found in this family have been classified as terpenoids, phlorotannins, and steroids, among others. These compounds have exhibited potent pharmacological activities. This review describes the new discovered compounds from Sargassaceae species and their associated bioactivities, citing 136 references covering from March 1975 to August 2023.
    MeSH term(s) Humans ; Phaeophyceae ; Oceans and Seas ; Antarctic Regions
    Language English
    Publishing date 2024-01-24
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2175190-0
    ISSN 1660-3397 ; 1660-3397
    ISSN (online) 1660-3397
    ISSN 1660-3397
    DOI 10.3390/md22020059
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  6. Article ; Online: Human Genetic Variants Associated with COVID-19 Severity are Enriched in Immune and Epithelium Regulatory Networks.

    Feng, Zhanying / Ren, Xianwen / Duren, Zhana / Wang, Yong

    Phenomics (Cham, Switzerland)

    2022  Volume 2, Issue 6, Page(s) 389–403

    Abstract: Human genetic variants can influence the severity of symptoms infected with SARS-COV-2. Several genome-wide association studies have identified human genomic risk single nucleotide polymorphisms (SNPs) associated with coronavirus disease 2019 (COVID-19) ... ...

    Abstract Human genetic variants can influence the severity of symptoms infected with SARS-COV-2. Several genome-wide association studies have identified human genomic risk single nucleotide polymorphisms (SNPs) associated with coronavirus disease 2019 (COVID-19) severity. However, the causal tissues or cell types underlying COVID-19 severity are uncertain. In addition, candidate genes associated with these risk SNPs were investigated based on genomic proximity instead of their functional cellular contexts. Here, we compiled regulatory networks of 77 human contexts and revealed those risk SNPs' enriched cellular contexts and associated risk SNPs with transcription factors, regulatory elements, and target genes. Twenty-one human contexts were identified and grouped into two categories: immune cells and epithelium cells. We further aggregated the regulatory networks of immune cells and epithelium cells. These two aggregated regulatory networks were investigated to reveal their association with risk SNPs' regulation. Two genomic clusters, the chemokine receptors cluster and the oligoadenylate synthetase (OAS) cluster, showed the strongest association with COVID-19 severity, and they had different regulatory programs in immune and epithelium contexts. Our findings were supported by analysis of both SNP array and whole genome sequencing-based genome wide association study (GWAS) summary statistics.
    Supplementary information: The online version contains supplementary material available at 10.1007/s43657-022-00066-x.
    Language English
    Publishing date 2022-08-13
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2730-5848
    ISSN (online) 2730-5848
    DOI 10.1007/s43657-022-00066-x
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  7. Article ; Online: Toward a more systematic understanding of bacterial virulence factors and establishing Koch postulates in silico.

    Ren, Xianwen

    Virulence

    2013  Volume 4, Issue 6, Page(s) 437–438

    MeSH term(s) Bacteria/pathogenicity ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Humans ; Virulence Factors/chemistry ; Virulence Factors/metabolism
    Chemical Substances Bacterial Proteins ; Virulence Factors
    Language English
    Publishing date 2013-08-17
    Publishing country United States
    Document type Editorial ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 2657572-3
    ISSN 2150-5608 ; 2150-5594
    ISSN (online) 2150-5608
    ISSN 2150-5594
    DOI 10.4161/viru.26211
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  8. Article ; Online: Structural-Activity Relationship of Rare Ginsenosides from Red Ginseng in the Treatment of Alzheimer's Disease.

    Ye, Xianwen / Zhang, Haixia / Li, Qian / Ren, Hongmin / Xu, Xinfang / Li, Xiangri

    International journal of molecular sciences

    2023  Volume 24, Issue 10

    Abstract: Rare ginsenosides are the major components of red ginseng. However, there has been little research into the relationship between the structure of ginsenosides and their anti-inflammatory activity. In this work, BV-2 cells induced by lipopolysaccharide ( ... ...

    Abstract Rare ginsenosides are the major components of red ginseng. However, there has been little research into the relationship between the structure of ginsenosides and their anti-inflammatory activity. In this work, BV-2 cells induced by lipopolysaccharide (LPS) or nigericin, the anti-inflammatory activity of eight rare ginsenosides, and the target proteins expression of AD were compared. In addition, the Morris water maze test, HE staining, thioflavins staining, and urine metabonomics were used to evaluate the effect of Rh4 on AD mice. Our results showed that their configuration influences the anti-inflammatory activity of ginsenosides. Ginsenosides Rk1, Rg5, Rk3, and Rh4 have significant anti-inflammatory activity compared to ginsenosides
    MeSH term(s) Mice ; Animals ; Ginsenosides/pharmacology ; Ginsenosides/therapeutic use ; Ginsenosides/chemistry ; Alzheimer Disease/drug therapy ; Stereoisomerism ; Panax/chemistry
    Chemical Substances ginsenoside Rh1 (63223-86-9) ; Ginsenosides
    Language English
    Publishing date 2023-05-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24108625
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  9. Article ; Online: Author Corrections: Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly.

    Ren, Xianwen / Zhong, Guojie / Zhang, Qiming / Zhang, Lei / Sun, Yujie / Zhang, Zemin

    Cell research

    2021  Volume 31, Issue 12, Page(s) 1319–1320

    Language English
    Publishing date 2021-07-18
    Publishing country England
    Document type Published Erratum
    ZDB-ID 1319303-x
    ISSN 1748-7838 ; 1001-0602
    ISSN (online) 1748-7838
    ISSN 1001-0602
    DOI 10.1038/s41422-021-00550-5
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    In stock of ZB MED Cologne/Königswinter

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  10. Article ; Online: Flame-Retardant and Washable Finishing of Lyocell/Cotton Blended Fabrics Using Eco-Friendly Creatinine O-Phosphate

    Xuan Yang / Yunbo Zheng / Xiaohui Liu / Yuanlin Ren / Xianwen Yang / Qiuyan Zhang

    Journal of Natural Fibers, Vol 20, Iss

    2023  Volume 1

    Abstract: Creatinine O-phosphate (COP) containing phosphorus and nitrogen elements was used as eco-friendly flame-retardant for lyocell/cotton blended fabric (L/C fabric). The flame retardant fabrics are prepared by a simple and effective dip-dry-cure method. ... ...

    Abstract Creatinine O-phosphate (COP) containing phosphorus and nitrogen elements was used as eco-friendly flame-retardant for lyocell/cotton blended fabric (L/C fabric). The flame retardant fabrics are prepared by a simple and effective dip-dry-cure method. Fourier infrared spectroscopy (FTIR), scanning electron microscope (SEM), and X-ray photoelectron spectroscopy (XPS) analyses certified that COP has been successfully grafted onto the surface of the L/C fabric and distributed evenly. Compared with the control fabric, the thermogravimetric analysis (TG) results showed that the char residue rate of the flame-retardant fabric at 800°C increased by 229% (air atmosphere), indicating that it has excellent char-forming ability. Besides, cone calorimetry results showed that the PHRR and THR values of the treated L/C fabric were reduced by 88.83% and 76.65%, respectively. The volatile pyrolysis products of the treated L/C fabric were determined by thermogravimetric analysis coupled with Fourier transform infrared analysis (TG-IR). In general, these results indicated that the L/C fabric treated with COP had high flame retardancy, excellent washing resistance and thermal stability.
    Keywords lyocell/cotton blended fabric ; flame retardant ; eco-friendly material ; creatinine o-phosphate ; thermal decomposition ; combustion behavior ; Science ; Q ; Textile bleaching ; dyeing ; printing ; etc ; TP890-933
    Subject code 660
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Taylor & Francis Group
    Document type Article ; Online
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