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  • Oxford University Press (OUP)  (33)
  • 1
    Online Resource
    Online Resource
    Recursive Paleohexaploidization Shaped the Durian Genome
    Oxford University Press (OUP) ; 2019
    In:  Plant Physiology Vol. 179, No. 1 ( 2019-01), p. 209-219
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 179, No. 1 ( 2019-01), p. 209-219
    Type of Medium: Online Resource
    ISSN: 0032-0889 , 1532-2548
    URL: Article
    DOI: 10.1104/pp.18.00921
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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  • 2
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    Glycolytic Activation of CD14+ Intestinal Macrophages Contributes to the Inflammatory Responses via Exosomal Membrane Tumor Necrosis Factor in Crohn’s Disease
    Oxford University Press (OUP) ; 2023
    In:  Inflammatory Bowel Diseases ( 2023-07-05)
    Details
    In: Inflammatory Bowel Diseases, Oxford University Press (OUP), ( 2023-07-05)
    Abstract: Macrophage (Mφ) activation plays a critical role in the inflammatory response. Activated Mφ go through profound reprogramming of cellular metabolism. However, changes in their intracellular energy metabolism and its effect on inflammatory responses in Crohn’s disease (CD) remain currently unclear. The aim of this study is to explore metabolic signatures of CD14+ Mφ and their potential role in CD pathogenesis as well as the underlying mechanisms. Methods CD14+ Mφ were isolated from peripheral blood or intestinal tissues of CD patients and control subjects. Real-time flux measurements and enzyme-linked immunosorbent assay were used to determine the inflammatory states of Mφ and metabolic signatures. Multiple metabolic routes were suppressed to determine their relevance to cytokine production. Results Intestinal CD14+ Mφ in CD patients exhibited activated glycolysis compared with those in control patients. Specifically, macrophagic glycolysis in CD largely induced inflammatory cytokine release. The intestinal inflammatory microenvironment in CD elicited abnormal glycolysis in Mφ. Mechanistically, CD14+ Mφ derived exosomes expressed membrane tumor necrosis factor (TNF), which engaged TNFR2 and triggered glycolytic activation via TNF/nuclear factor κB autocrine and paracrine signaling. Importantly, clinically applicable anti-TNF antibodies effectively prevented exosomal membrane TNF–induced glycolytic activation in CD14+ Mφ. Conclusions CD14+ Mφ take part in CD pathogenesis by inducing glycolytic activation via membrane TNF–mediated exosomal autocrine and paracrine signaling. These results provide novel insights into pathogenesis of CD and enhance understanding of the mechanisms of anti-TNF agents.
    Type of Medium: Online Resource
    ISSN: 1078-0998 , 1536-4844
    URL: Article
    DOI: 10.1093/ibd/izad117
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
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  • 3
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    Alteration of CTCF-associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis
    Oxford University Press (OUP) ; 2020
    In:  Nucleic Acids Research Vol. 48, No. 6 ( 2020-04-06), p. 3119-3133
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. 6 ( 2020-04-06), p. 3119-3133
    Abstract: Aberrant activation of the TAL1 is associated with up to 60% of T-ALL cases and is involved in CTCF-mediated genome organization within the TAL1 locus, suggesting that CTCF boundary plays a pathogenic role in T-ALL. Here, we show that −31-Kb CTCF binding site (−31CBS) serves as chromatin boundary that defines topologically associating domain (TAD) and enhancer/promoter interaction required for TAL1 activation. Deleted or inverted −31CBS impairs TAL1 expression in a context-dependent manner. Deletion of −31CBS reduces chromatin accessibility and blocks long-range interaction between the +51 erythroid enhancer and TAL1 promoter-1 leading to inhibition of TAL1 expression in erythroid cells, but not T-ALL cells. However, in TAL1-expressing T-ALL cells, the leukemia-prone TAL1 promoter-IV specifically interacts with the +19 stem cell enhancer located 19 Kb downstream of TAL1 and this interaction is disrupted by the −31CBS inversion in T-ALL cells. Inversion of −31CBS in Jurkat cells alters chromatin accessibility, histone modifications and CTCF-mediated TAD leading to inhibition of TAL1 expression and TAL1-driven leukemogenesis. Thus, our data reveal that −31CBS acts as critical regulator to define +19-enhancer and the leukemic prone promoter IV interaction for TAL1 activation in T-ALL. Manipulation of CTCF boundary can alter TAL1 TAD and oncogenic transcription networks in leukemogenesis.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkaa098
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 4
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    An artificial intelligence model based on transrectal ultrasound images of biopsy needle tract tissues to differentiate prostate cancer
    Oxford University Press (OUP) ; 2023
    In:  Postgraduate Medical Journal ( 2023-12-23)
    Details
    In: Postgraduate Medical Journal, Oxford University Press (OUP), ( 2023-12-23)
    Abstract: We aimed to develop an artificial intelligence (AI) model based on transrectal ultrasonography (TRUS) images of biopsy needle tract (BNT) tissues for predicting prostate cancer (PCa) and to compare the PCa diagnostic performance of the radiologist model and clinical model. Methods A total of 1696 2D prostate TRUS images were involved from 142 patients between July 2021 and May 2022. The ResNet50 network model was utilized to train classification models with different input methods: original image (Whole model), BNT (Needle model), and combined image [Feature Pyramid Networks (FPN) model]. The training set, validation set, and test set were randomly assigned, then randomized 5-fold cross-validation between the training set and validation set was performed. The diagnostic effectiveness of AI models and image combination was accessed by an independent testing set. Then, the optimal AI model and image combination were selected to compare the diagnostic efficacy with that of senior radiologists and the clinical model. Results In the test set, the area under the curve, specificity, and sensitivity of the FPN model were 0.934, 0.966, and 0.829, respectively; the diagnostic efficacy was improved compared with the Whole and Needle models, with statistically significant differences (P & lt; 0.05), and was better than that of senior radiologists (area under the curve: 0.667). The FPN model detected more PCa compared with senior physicians (82.9% vs. 55.8%), with a 61.3% decrease in the false-positive rate and a 23.2% increase in overall accuracy (0.887 vs. 0.655). Conclusion The proposed FPN model can offer a new method for prostate tissue classification, improve the diagnostic performance, and may be a helpful tool to guide prostate biopsy.
    Type of Medium: Online Resource
    ISSN: 0032-5473 , 1469-0756
    URL: Article
    DOI: 10.1093/postmj/qgad127
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2009568-5
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  • 5
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    IL33-mediated NPM1 promotes fibroblast-to-myofibroblast transition via ERK/AP-1 signaling in silica-induced pulmonary fibrosis
    Oxford University Press (OUP) ; 2023
    In:  Toxicological Sciences Vol. 195, No. 1 ( 2023-08-29), p. 71-86
    Details
    In: Toxicological Sciences, Oxford University Press (OUP), Vol. 195, No. 1 ( 2023-08-29), p. 71-86
    Abstract: Silicosis is a global occupational pulmonary disease due to the accumulation of silica dust in the lung. Lacking effective clinical drugs makes the treatment of this disease quite challenging in clinics largely because the pathogenic mechanisms remain obscure. Interleukin 33 (IL33), a pleiotropic cytokine, could promote wound healing and tissue repair via the receptor ST2. However, the mechanisms governing the involvement of IL33 in silicosis progression remain to be further explored. Here, we demonstrated that the IL33 levels in the lung sections were significantly overexpressed after bleomycin and silica treatment. Chromatin immunoprecipitation assay, knockdown, and reverse experiments were performed in lung fibroblasts to prove gene interaction following exogenous IL33 treatment or cocultured with silica-treated lung epithelial cells. Mechanistically, we illustrated that silica-stimulated lung epithelial cells secreted IL33 and further promoted the activation, proliferation, and migration of pulmonary fibroblasts by activating the ERK/AP-1/NPM1 signaling pathway in vitro. And more, treatment with NPM1 siRNA-loaded liposomes markedly protected mice from silica-induced pulmonary fibrosis in vivo. In conclusion, the involvement of NPM1 in the progression of silicosis is regulated by the IL33/ERK/AP-1 signaling axis, which is the potential therapeutic target candidate in developing novel antifibrotic strategies for pulmonary fibrosis.
    Type of Medium: Online Resource
    ISSN: 1096-6080 , 1096-0929
    URL: Article
    DOI: 10.1093/toxsci/kfad061
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1471974-5
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  • 6
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    Magnesium absorption, translocation, subcellular distribution and chemical forms in citrus seedlings
    Oxford University Press (OUP) ; 2022
    In:  Tree Physiology Vol. 42, No. 4 ( 2022-04-07), p. 862-876
    Details
    In: Tree Physiology, Oxford University Press (OUP), Vol. 42, No. 4 ( 2022-04-07), p. 862-876
    Abstract: Magnesium (Mg) is an essential macronutrient for plant growth and development; however, the adaptive mechanisms of Mg deficiency to underlying changes in Mg translocation, subcellular distribution and chemical forms in citrus plants are unknown. In this study, we conducted a sand culture experiment with 0 (Mg-deficiency) or 2 (Mg-sufficiency) mmol l−1 Mg2+ treatments to investigate the responses underlying Mg adaptability, as well as the resulting growth and Mg transport features in citrus seedlings [Citrus sinensis (L.) Osbeck cv. ‘Xuegan’]. We found that Mg-deficiency significantly depressed biomass by 39% in the whole plant and by 66% in branch organs compared with Mg-sufficient conditions, which further resulted in a subsequent decrease in Mg concentration and accumulation with changes in its distribution in different organs and a reduction in root growth. Under Mg-sufficiency, & gt;50% of Mg was sequestered in the soluble fraction and this was reduced by 30% under Mg-deficiency. Furthermore, & gt;70% of Mg existed as inorganic (42%) and water-soluble (31%) forms with high mobility across treatments and organs. Under Mg-deficiency, the proportion of water-soluble Mg was reduced in leaf and increased in root, whereas the proportion of inorganic Mg increased in main stem leaves and decreased in branch leaves and root. However, under Mg-deficiency, the proportion of Mg forms with low mobility, including pectates and proteins, phosphates, oxalates and residues, was increased in leaf and root organs, with the exception of pectate and protein Mg, which was decreased in root. The Mg transfer factor showed that Mg-deficiency improved Mg transport from parent to branch organs, which was related to Mg subcellular distribution and chemical forms. Taken together, our study establishes a defined process to clarify the mechanisms of Mg absorption and translocation and reveals a possible strategy to effectively improve Mg mobility and availability in citrus plants.  
    Type of Medium: Online Resource
    ISSN: 1758-4469
    URL: Article
    DOI: 10.1093/treephys/tpab148
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1473475-8
    SSG: 12
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  • 7
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    Interpretable-ADMET: a web service for ADMET prediction and optimization based on deep neural representation
    Oxford University Press (OUP) ; 2022
    In:  Bioinformatics Vol. 38, No. 10 ( 2022-05-13), p. 2863-2871
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 38, No. 10 ( 2022-05-13), p. 2863-2871
    Abstract: In the process of discovery and optimization of lead compounds, it is difficult for non-expert pharmacologists to intuitively determine the contribution of substructure to a particular property of a molecule. Results In this work, we develop a user-friendly web service, named interpretable-absorption, distribution, metabolism, excretion and toxicity (ADMET), which predict 59 ADMET-associated properties using 90 qualitative classification models and 28 quantitative regression models based on graph convolutional neural network and graph attention network algorithms. In interpretable-ADMET, there are 250 729 entries associated with 59 kinds of ADMET-associated properties for 80 167 chemical compounds. In addition to making predictions, interpretable-ADMET provides interpretation models based on gradient-weighted class activation map for identifying the substructure, which is important to the particular property. Interpretable-ADMET also provides an optimize module to automatically generate a set of novel virtual candidates based on matched molecular pair rules. We believe that interpretable-ADMET could serve as a useful tool for lead optimization in drug discovery. Availability and implementation Interpretable-ADMET is available at http://cadd.pharmacy.nankai.edu.cn/interpretableadmet/. Supplementary information Supplementary data are available at Bioinformatics online.
    Type of Medium: Online Resource
    ISSN: 1367-4803 , 1367-4811
    URL: Article
    DOI: 10.1093/bioinformatics/btac192
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1468345-3
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  • 8
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    The transcription factor RhMYB17 regulates the homeotic transformation of floral organs in rose ( Rosa hybrida ) under cold stress
    Oxford University Press (OUP) ; 2024
    In:  Journal of Experimental Botany Vol. 75, No. 10 ( 2024-05-20), p. 2965-2981
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 75, No. 10 ( 2024-05-20), p. 2965-2981
    Abstract: Low temperatures affect flower development in rose (Rosa hybrida), increasing petaloid stamen number and reducing normal stamen number. We identified the low-temperature-responsive R2R3-MYB transcription factor RhMYB17, which is homologous to Arabidopsis MYB17 by similarity of protein sequences. RhMYB17 was up-regulated at low temperatures, and RhMYB17 transcripts accumulated in floral buds. Transient silencing of RhMYB17 by virus-induced gene silencing decreased petaloid stamen number and increased normal stamen number. According to the ABCDE model of floral organ identity, class A genes APETALA 1 (AP1) and AP2 contribute to sepal and petal formation. Transcription factor binding analysis identified RhMYB17 binding sites in the promoters of rose APETALA 2 (RhAP2) and APETALA 2-LIKE (RhAP2L). Yeast one-hybrid assays, dual-luciferase reporter assays, and electrophoretic mobility shift assays confirmed that RhMYB17 directly binds to the promoters of RhAP2 and RhAP2L, thereby activating their expression. RNA sequencing further demonstrated that RhMYB17 plays a pivotal role in regulating the expression of class A genes, and indirectly influences the expression of the class C gene. This study reveals a novel mechanism for the homeotic transformation of floral organs in response to low temperatures.
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/erae099
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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  • 9
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    Chinese Bayberry Extract Regulates the Permeability of Blood-cerebrospinal Fluid Barrier and Ameliorates Experimental Colitis-Related Brain Comorbidities in Mice
    Oxford University Press (OUP) ; 2024
    In:  Food Quality and Safety ( 2024-05-25)
    Details
    In: Food Quality and Safety, Oxford University Press (OUP), ( 2024-05-25)
    Abstract: The anxiety, depression symptoms, and cognitive decline related to inflammatory bowel disease (IBD) are recognized to have an impact on patients’ health. The blood-cerebrospinal fluid barrier (BCSFB) is important in somatic disease-related psychiatric and cognitive disorders, however, few treatments show efficacy. The objective of this research was to seek the protective effect of Chinese bayberry extract on inflammatory bowel disease-related brain comorbidities. Materials and Methods C57BL/6J mice were induced with dextran sulfate sodium (DSS) solution to establish the experimental model, followed by the administration of Chinese bayberry extract. Oxidative stress indexes, immunofluorescence of choroid plexus, and BCSFB permeability were further investigated. Results Chinese bayberry extract improved behavioral markers and reduced the level of oxidative stress in the brain. In addition, administration of the bayberry extract increased the tight junction proteins in the choroid plexus and a significant decrease in the permeability of the BCSFB. Conclusions Chinese bayberry extract has the potential therapeutic effect of relieving inflammatory bowel disease-related brain comorbidities. The underlying mechanism is associated with a decrease in oxidative stress in the brain and a decrease in the permeability of the BCSFB.
    Type of Medium: Online Resource
    ISSN: 2399-1399 , 2399-1402
    URL: Article
    DOI: 10.1093/fqsafe/fyae028
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 2899899-6
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  • 10
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    Enhancement of microbial hydroxylation of 13-ethyl-gon-4-ene-3,17-dione by Metarhizium anisopliae using nano-liposome technique
    Oxford University Press (OUP) ; 2014
    In:  Journal of Industrial Microbiology and Biotechnology Vol. 41, No. 4 ( 2014-04-01), p. 619-627
    Details
    In: Journal of Industrial Microbiology and Biotechnology, Oxford University Press (OUP), Vol. 41, No. 4 ( 2014-04-01), p. 619-627
    Abstract: The introduction of 11α-hydroxy to 13-ethyl-gon-4-ene-3,17-dione (GD) by microbial transformation is a key step in the synthesis of oral contraceptive desogestrel, while low substrate solubility and uptake into cells are tough problems influencing biotransformation efficiency greatly. Nano-liposome technique was used in the hydroxylation of GD by Metarhizium anisopliae. The substrate GD was processed to be GD-loaded nano-liposomes (GNLs) with high stability and encapsulation efficiency, and then applied in microbial hydroxylation by M. anisopliae. The results proved that the yield of the main product 11α-hydroxy-13-ethyl-gon-4-ene-3,17-dione (HGD) tripled compared to regular solvent dimethylformamide dispersion method at 2 g/l of substrate feeding concentration, and the HGD conversion rate showed no obvious reduction when the substrate feeding concentration increased from 2 to 6 g/l, which indicated the improvement of GNL addition method on biotransformation. Furthermore, the main byproduct changed from 6β-hydroxy derivative of GD (with similar polarity to HGD) to 6β,11α-dihydroxy derivative, which benefits the following purification of HGD from fermentation broth. These advantages suggest a great potential for the application of nano-liposome technique in microbial steroid transformation.
    Type of Medium: Online Resource
    ISSN: 1476-5535 , 1367-5435
    URL: Article
    DOI: 10.1007/s10295-014-1414-7
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2014
    detail.hit.zdb_id: 1482484-X
    SSG: 12
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