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  1. Book: Computational modeling of signaling networks

    Liu, Xuedong / Betterton, Meredith D.

    methods and protocols

    (Methods in molecular biology ; 880 ; Springer protocols)

    2012  

    Author's details ed. by Xuedong Liu ; Meredith D. Betterton
    Series title Methods in molecular biology ; 880
    Springer protocols
    Collection
    Language English
    Size XIV, 327 S. : Ill., graph. Darst.
    Publisher Humana Press
    Publishing place New York u.a.
    Publishing country United States
    Document type Book
    HBZ-ID HT017309846
    ISBN 978-1-61779-832-0 ; 1-61779-832-0 ; 9781617798337 ; 1617798339
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2012 A 2897 order for loan Magazin

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  2. Article ; Online: The complete mitochondrial genome of

    Wu, Xuanye / Wang, Xiaojia / Kuang, Gaoxiang / Jin, Kun / Liu, Xuedong

    Mitochondrial DNA. Part B, Resources

    2024  Volume 9, Issue 3, Page(s) 408–410

    Abstract: Livingstone's turaco, ...

    Abstract Livingstone's turaco,
    Language English
    Publishing date 2024-03-28
    Publishing country England
    Document type Journal Article
    ISSN 2380-2359
    ISSN (online) 2380-2359
    DOI 10.1080/23802359.2024.2334024
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: EMR Combined with CRB-65 Superior to CURB-65 in Predicting Mortality in Patients with Community-Acquired Pneumonia [Response to Letter].

    Sun, Yi / Wang, Hong / Gu, Minghao / Zhang, Xingyu / Han, Xiudi / Liu, Xuedong

    Infection and drug resistance

    2024  Volume 17, Page(s) 1321–1322

    Language English
    Publishing date 2024-04-04
    Publishing country New Zealand
    Document type Journal Article ; Comment
    ZDB-ID 2494856-1
    ISSN 1178-6973
    ISSN 1178-6973
    DOI 10.2147/IDR.S470587
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: EMR Combined with CRB-65 Superior to CURB-65 in Predicting Mortality in Patients with Community-Acquired Pneumonia.

    Sun, Yi / Wang, Hong / Gu, Minghao / Zhang, Xingyu / Han, Xiudi / Liu, Xuedong

    Infection and drug resistance

    2024  Volume 17, Page(s) 463–473

    Abstract: Background: Data about eosinophil-to-lymphocyte ratio (ELR) and eosinophil-to-monocyte ratio (EMR) in patients with community-acquired pneumonia (CAP) are rare. We aimed to evaluate the role of EMR and ELR in predicting disease severity and mortality in ...

    Abstract Background: Data about eosinophil-to-lymphocyte ratio (ELR) and eosinophil-to-monocyte ratio (EMR) in patients with community-acquired pneumonia (CAP) are rare. We aimed to evaluate the role of EMR and ELR in predicting disease severity and mortality in patients with CAP.
    Methods: A total of 454 patients (76 with severe CAP (SCAP), 378 with non-SCAP) were enrolled from November 18, 2020, and November 21, 2021. Laboratory examination on day 1 after admission was measured. The ELR and EMR values were calculated for patients. Propensity score matching (PSM) was performed to balance potential confounding factors. Binary logistic regression model was fitted to identify the potential risk factors for disease severity and Cox proportional hazards regression model analysis for mortality in CAP. Receiver operating characteristic (ROC) analysis was performed to distinguish disease severity and mortality.
    Results: EMR and ELR at admission were significantly lower in SCAP patients than in non-SCAP patients (
    Conclusion: EMR combined with CRB-65 was superior to CURB-65 in predicting mortality in patients with CAP. This new combination was simpler and easier to obtain for physicians in clinics or admission, and it was more convenient for early recognition of patients with poor prognoses.
    Language English
    Publishing date 2024-02-08
    Publishing country New Zealand
    Document type Journal Article
    ZDB-ID 2494856-1
    ISSN 1178-6973
    ISSN 1178-6973
    DOI 10.2147/IDR.S443045
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Cloflucarban Illuminates Specificity and Context-Dependent Activation of the PINK1-Parkin Pathway by Mitochondrial Complex Inhibition.

    Ramirez, Adrian T / Liu, Zeyu / Xu, Quanbin / Nowosadtko, Sarah / Liu, Xuedong

    Biomolecules

    2024  Volume 14, Issue 3

    Abstract: The PTEN-induced kinase 1 (PINK1)-Parkin pathway plays a vital role in maintaining a healthy pool of mitochondria in higher eukaryotic cells. While the downstream components of this pathway are well understood, the upstream triggers remain less explored. ...

    Abstract The PTEN-induced kinase 1 (PINK1)-Parkin pathway plays a vital role in maintaining a healthy pool of mitochondria in higher eukaryotic cells. While the downstream components of this pathway are well understood, the upstream triggers remain less explored. In this study, we conducted an extensive analysis of inhibitors targeting various mitochondrial electron transport chain (ETC) complexes to investigate their potential as activators of the PINK1-Parkin pathway. We identified cloflucarban, an antibacterial compound, as a novel pathway activator that simultaneously inhibits mitochondrial complexes III and V, and V. RNA interference (RNAi) confirmed that the dual inhibition of these complexes activates the PINK1-Parkin pathway. Intriguingly, we discovered that albumin, specifically bovine serum albumin (BSA) and human serum albumin (HSA) commonly present in culture media, can hinder carbonyl cyanide m-chlorophenyl hydrazone (CCCP)-induced pathway activation. However, cloflucarban's efficacy remains unaffected by albumin, highlighting its reliability for studying the PINK1-Parkin pathway. This study provides insights into the activation of the upstream PINK1-Parkin pathway and underscores the influence of culture conditions on research outcomes. Cloflucarban emerges as a promising tool for investigating mitochondrial quality control and neurodegenerative diseases.
    MeSH term(s) Humans ; Protein Kinases/metabolism ; Reproducibility of Results ; Ubiquitin-Protein Ligases/metabolism ; Mitochondria/metabolism ; Albumins/metabolism ; Carbanilides
    Chemical Substances cloflucarban (I5ZZY3DC5G) ; Protein Kinases (EC 2.7.-) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Albumins ; Carbanilides
    Language English
    Publishing date 2024-02-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom14030248
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Analysis of Correlation Between Serum Oncostatin-M and Disease Severity and Mortality in Hospitalized Patients with Community-Acquired Pneumonia.

    Teng, Peikun / Zhang, Xingyu / Wang, Hong / Han, Xiudi / Liu, Xuedong

    Journal of inflammation research

    2023  Volume 16, Page(s) 6257–6269

    Abstract: Purpose: The aim of this study was to investigate the level of serum tumor suppressor factor (Oncostatin-M, OSM) in patients with community-acquired pneumonia (CAP) and evaluate its predictive value for the severity and prognosis of pneumonia, so as to ... ...

    Abstract Purpose: The aim of this study was to investigate the level of serum tumor suppressor factor (Oncostatin-M, OSM) in patients with community-acquired pneumonia (CAP) and evaluate its predictive value for the severity and prognosis of pneumonia, so as to improve the ability to identify the risk of death in CAP patients.
    Patients and methods: A total of 110 patients with CAP admitted to the hospital from November 2020 to November 2021 were enrolled in this prospective study. Clinical data of all patients were collected. According to the 2016 edition of "Guidelines for the Diagnosis and Treatment of Community-acquired Pneumonia in Chinese Adults", the patients were divided into non-severe CAP (NSCAP)(n=55) and severe CAP (SCAP)(n=55). At the same time, they were divided into a survival group (n=96) and a death group (n=14) by tracking the survival of patients in the hospital. The OSM concentration of CAP patients on the first day after admission was determined by enzyme-linked immunosorbent assay. All clinical data were statistically and graphed using SPSS V23.0 and Grahpad Prim 8.
    Results: Compared with NSCAP, patients with SCAP had higher serum OSM concentration on the day of admission, which was negatively correlated with LYM and positively correlated with WBC, NEU, CRP, IL-6, IL-8, IL-10, CURB-65 score, and PSI score. The level of OSM in the dead patient group was significantly higher than that in the surviving patient group. OSM and PSI scores were independent risk factors for in-hospital mortality in CAP patients. Kaplan-Meier survival curve showed that OSM≥76pg/mL was more advantageous in predicting mortality in patients with CAP.
    Conclusion: The level of the OSM is closely related to the severity and prognosis of CAP and may be a new biomarker for the prognosis of CAP patients.
    Language English
    Publishing date 2023-12-21
    Publishing country New Zealand
    Document type Journal Article
    ZDB-ID 2494878-0
    ISSN 1178-7031
    ISSN 1178-7031
    DOI 10.2147/JIR.S445484
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: In-Silico Multi-Omics Analysis of the Functional Significance of Calmodulin 1 in Multiple Cancers.

    Yao, Maolin / Fu, Lanyi / Liu, Xuedong / Zheng, Dong

    Frontiers in genetics

    2022  Volume 12, Page(s) 793508

    Abstract: Aberrant activation of calmodulin 1 ( ...

    Abstract Aberrant activation of calmodulin 1 (
    Language English
    Publishing date 2022-01-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.793508
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Live Cell Imaging of Spatiotemporal Ca

    Liu, Zeyu / Ramirez, Adrian / Liu, Xuedong

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2488, Page(s) 227–236

    Abstract: Synthetic triterpenoids, 2-cyano-3,12-dioxooleana-1,9-dien-28-oic acid (CDDO) and its derivatives are known to have potent anti-cancer and anti-inflammatory activities. The mechanisms of actions of CDDO and its derivatives as potential therapeutics ... ...

    Abstract Synthetic triterpenoids, 2-cyano-3,12-dioxooleana-1,9-dien-28-oic acid (CDDO) and its derivatives are known to have potent anti-cancer and anti-inflammatory activities. The mechanisms of actions of CDDO and its derivatives as potential therapeutics remain elusive. Previous studies found that CDDO-Me triggers apoptosis by inducing extracellular Ca
    MeSH term(s) Antineoplastic Agents/pharmacology ; Apoptosis ; Oleanolic Acid/analogs & derivatives ; Oleanolic Acid/pharmacology ; Triterpenes
    Chemical Substances Antineoplastic Agents ; Triterpenes ; Oleanolic Acid (6SMK8R7TGJ) ; bardoxolone (7HT68L8941)
    Language English
    Publishing date 2022-03-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2277-3_15
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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  9. Article: Using bioinformatics and systems biology to discover common pathogenetic processes between sarcoidosis and COVID-19.

    Fu, Lanyi / Yao, Maolin / Liu, Xuedong / Zheng, Dong

    Gene reports

    2022  Volume 27, Page(s) 101597

    Abstract: The coronavirus disease (COVID-19) pandemic caused by SARS-CoV-2 is ongoing. Individuals with sarcoidosis tend to develop severe COVID-19; however, the underlying pathological mechanisms remain elusive. To determine common transcriptional signatures and ... ...

    Abstract The coronavirus disease (COVID-19) pandemic caused by SARS-CoV-2 is ongoing. Individuals with sarcoidosis tend to develop severe COVID-19; however, the underlying pathological mechanisms remain elusive. To determine common transcriptional signatures and pathways between sarcoidosis and COVID-19, we investigated the whole-genome transcriptome of peripheral blood mononuclear cells (PBMCs) from patients with COVID-19 and sarcoidosis and conducted bioinformatic analysis, including gene ontology and pathway enrichment, protein-protein interaction (PPI) network, and gene regulatory network (GRN) construction. We identified 33 abnormally expressed genes that were common between COVID-19 and sarcoidosis. Functional enrichment analysis showed that these differentially expressed genes were associated with cytokine production involved in the immune response and T cell cytokine production. We identified several hub genes from the PPI network encoded by the common genes. These hub genes have high diagnostic potential for COVID-19 and sarcoidosis and can be potential biomarkers. Moreover, GRN analysis identified important microRNAs and transcription factors that regulate the common genes. This study provides a novel characterization of the transcriptional signatures and biological processes commonly dysregulated in sarcoidosis and COVID-19 and identified several critical regulators and biomarkers. This study highlights a potential pathological association between COVID-19 and sarcoidosis, establishing a theoretical basis for future clinical trials.
    Language English
    Publishing date 2022-03-18
    Publishing country United States
    Document type Journal Article
    ISSN 2452-0144
    ISSN 2452-0144
    DOI 10.1016/j.genrep.2022.101597
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Comparison of genome-wide DNA methylation patterns between antler precartilage and cartilage

    Wu, Jin / Yang, Fan / Wu, Xuanye / Liu, Xuedong / Zheng, Dong

    Mol Genet Genomics. 2023 Mar., v. 298, no. 2 p.343-352

    2023  

    Abstract: Deer antlers are the only mammalian organs that can fully regenerate after being lost and provide a valuable model for cartilage development. As one of the best-studied epigenetic mechanisms, DNA methylation is known to engage in organ and tissue ... ...

    Abstract Deer antlers are the only mammalian organs that can fully regenerate after being lost and provide a valuable model for cartilage development. As one of the best-studied epigenetic mechanisms, DNA methylation is known to engage in organ and tissue development. This study aimed to investigate the role of DNA methylation in antler chondrogenesis by comparing whole-genome DNA methylation between precartilage and cartilage. Quantitative reverse transcription PCR (RT-qPCR) showed significant differences in the expression levels of DNA methyltransferase genes (DNMT1, DNMT3A, and DNMT3B) between precartilage and cartilage. Subsequently, we obtained DNA methylation profiles of antler precartilage and cartilage tissues by whole-genome bisulfite sequencing. Although sequencing data indicated that overall methylation levels at CpG and non-CpG sites were similar between precartilage and cartilage, 140,784 differentially methylated regions (DMRs, P < 0.05) and 3,941 DMR-related genes were identified. Gene ontology (GO) analysis of DMR-related genes demonstrated some significantly enriched GO terms (P < 0.05) related to chondrogenesis, including insulin receptor binding, collage trimer, integrin binding, and extracellular matrix structural constituent. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DMR-related genes uncovered that the PI3K/AKT, cortisol synthesis and secretion, glycosaminoglycan biosynthesis-keratan sulfate, Hippo, and NF-κB signaling pathways might play a pivotal role in the transition of precartilage to cartilage. Moreover, we found that 25 DMR-related genes, including CD44, IGF1, ITGAV, ITGB1, RUNX1, COL2A1, COMP, and TAGLN, were most likely involved in antler chondrogenesis. In conclusion, this study revealed the genome-wide DNA methylation patterns of antler precartilage and cartilage, which may contribute to understanding the epigenetic regulation of antler chondrogenesis.
    Keywords DNA methylation ; DNA methyltransferase ; bisulfites ; cartilage ; chondrogenesis ; cortisol ; epigenetics ; extracellular matrix ; gene ontology ; genome ; genomics ; glycosaminoglycans ; insulin receptors ; integrins ; mammals ; models ; reverse transcriptase polymerase chain reaction ; secretion ; sulfates
    Language English
    Dates of publication 2023-03
    Size p. 343-352.
    Publishing place Springer Berlin Heidelberg
    Document type Article ; Online
    ZDB-ID 2044817-X
    ISSN 1617-4615
    ISSN 1617-4615
    DOI 10.1007/s00438-022-01983-2
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

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