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  • Online Resource  (9)
  • Oxford University Press (OUP)  (9)
  • 1
    Online Resource
    Online Resource
    Genome-Wide 5-Hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer
    Oxford University Press (OUP) ; 2021
    In:  Genomics, Proteomics & Bioinformatics Vol. 19, No. 1 ( 2021-02-01), p. 64-79
    Details
    In: Genomics, Proteomics & Bioinformatics, Oxford University Press (OUP), Vol. 19, No. 1 ( 2021-02-01), p. 64-79
    Abstract: Although DNA 5-hydroxymethylcytosine (5hmC) is recognized as an important epigenetic mark in cancer, its precise role in lymph node metastasis remains elusive. In this study, we investigated how 5hmC associates with lymph node metastasis in breast cancer. Accompanying with high expression of TET1 and TET2 proteins, large numbers of genes in the metastasis-positive primary tumors exhibit higher 5hmC levels than those in the metastasis-negative primary tumors. In contrast, the TET protein expression and DNA 5hmC decrease significantly within the metastatic lesions in the lymph nodes compared to those in their matched primary tumors. Through genome-wide analysis of 8 sets of primary tumors, we identified 100 high-confidence metastasis-associated 5hmC signatures, and it is found that increased levels of DNA 5hmC and gene expression of MAP7D1 associate with high risk of lymph node metastasis. Furthermore, we demonstrate that MAP7D1, regulated by TET1, promotes tumor growth and metastasis. In conclusion, the dynamic 5hmC profiles during lymph node metastasis suggest a link between DNA 5hmC and lymph node metastasis. Meanwhile, the role of MAP7D1 in breast cancer progression suggests that the metastasis-associated 5hmC signatures are potential biomarkers to predict the risk for lymph node metastasis, which may serve as diagnostic and therapeutic targets for metastatic breast cancer.
    Type of Medium: Online Resource
    ISSN: 1672-0229 , 2210-3244
    URL: Article
    DOI: 10.1016/j.gpb.2019.05.005
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 2233708-8
    detail.hit.zdb_id: 2240213-5
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  • 2
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    Online Resource
    Large expert-curated database for benchmarking document similarity detection in biomedical literature search
    Oxford University Press (OUP) ; 2019
    In:  Database Vol. 2019 ( 2019-01-01)
    Details
    In: Database, Oxford University Press (OUP), Vol. 2019 ( 2019-01-01)
    Abstract: Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
    Type of Medium: Online Resource
    ISSN: 1758-0463
    URL: Article
    DOI: 10.1093/database/baz085
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2496706-3
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  • 3
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    Online Resource
    Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota are Attributable to Its Key Ingredient Berberine
    Oxford University Press (OUP) ; 2020
    In:  Genomics, Proteomics & Bioinformatics Vol. 18, No. 6 ( 2020-12-01), p. 721-736
    Details
    In: Genomics, Proteomics & Bioinformatics, Oxford University Press (OUP), Vol. 18, No. 6 ( 2020-12-01), p. 721-736
    Abstract: Gegen Qinlian Decoction (GQD), a traditional Chinese medicine (TCM) formula, has long been used for the treatment of common metabolic diseases, including type 2 diabetes mellitus. However, the main limitation of its wider application is ingredient complexity of this formula. Thus, it is critically important to identify the major active ingredients of GQD and to illustrate mechanisms underlying its action. Here, we compared the effects of GQD and berberine, a hypothetical key active pharmaceutical ingredient of GQD, on a diabetic rat model by comprehensive analyses of gut microbiota, short-chain fatty acids, proinflammatory cytokines, and ileum transcriptomics. Our results show that berberine and GQD had similar effects on lowering blood glucose levels, modulating gut microbiota, inducing ileal gene expression, as well as relieving systemic and local inflammation. As expected, both berberine and GQD treatment significantly altered the overall gut microbiota structure and enriched many butyrate-producing bacteria, including Faecalibacterium and Roseburia, thereby attenuating intestinal inflammation and lowering glucose. Levels of short-chain fatty acids in rat feces were also significantly elevated after treatment with berberine or GQD. Moreover, concentration of serum proinflammatory cytokines and expression of immune-related genes, including Nfkb1, Stat1, and Ifnrg1, in pancreatic islets were significantly reduced after treatment. Our study demonstrates that the main effects of GQD can be attributed to berberine via modulating gut microbiota. The strategy employed would facilitate further standardization and widespread application of TCM in many diseases.
    Type of Medium: Online Resource
    ISSN: 1672-0229 , 2210-3244
    URL: Article
    DOI: 10.1016/j.gpb.2019.09.007
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2233708-8
    detail.hit.zdb_id: 2240213-5
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  • 4
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    Chemical genomic analysis of GPR35 signaling
    Oxford University Press (OUP) ; 2017
    In:  Integrative Biology Vol. 9, No. 5 ( 2017-05-01), p. 451-463
    Details
    In: Integrative Biology, Oxford University Press (OUP), Vol. 9, No. 5 ( 2017-05-01), p. 451-463
    Type of Medium: Online Resource
    ISSN: 1757-9708
    URL: Article
    DOI: 10.1039/c7ib00005g
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2017
    detail.hit.zdb_id: 2480063-6
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  • 5
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    Asymmetric Vinylogous Michael Reaction of α,β-Unsaturated Aldehyde with Buteno-4-lactone
    Oxford University Press (OUP) ; 2011
    In:  Chemistry Letters Vol. 40, No. 5 ( 2011-05-05), p. 518-520
    Details
    In: Chemistry Letters, Oxford University Press (OUP), Vol. 40, No. 5 ( 2011-05-05), p. 518-520
    Abstract: The asymmetric vinylogous Michael reactions of α,β-unsaturated aldehydes with γ-butenolide(buteno-4-lactone) were efficiently catalyzed by the Jørgensen–Hayashi catalyst and LiOAc. The desired products were obtained in satisfactory yields with excellent enantioselectivities and moderate diastereoselectivities.
    Type of Medium: Online Resource
    ISSN: 0366-7022 , 1348-0715
    URL: Article
    DOI: 10.1246/cl.2011.518
    RVK:
    VA 3560
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2011
    detail.hit.zdb_id: 2063626-X
    detail.hit.zdb_id: 184719-3
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  • 6
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    N -Hydroxysuccinimide-promoted Oxidation of Primary Alcohols and Aldehydes to Form Active Esters with Hypervalent(III) Iodine
    Oxford University Press (OUP) ; 2006
    In:  Chemistry Letters Vol. 35, No. 6 ( 2006-06-01), p. 566-567
    Details
    In: Chemistry Letters, Oxford University Press (OUP), Vol. 35, No. 6 ( 2006-06-01), p. 566-567
    Abstract: A simple, mild, and efficient method for the conversion of primary alcohols and aldehydes to N-hydroxysuccinimide esters with (diacetoxyiodo)benzene in high yield is developed. N-Hydroxysuccinimide acts not only as an esterification partner but also as an activator of PhI(OAc)2 in this reaction.
    Type of Medium: Online Resource
    ISSN: 0366-7022 , 1348-0715
    URL: Article
    DOI: 10.1246/cl.2006.566
    RVK:
    VA 3560
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2006
    detail.hit.zdb_id: 2063626-X
    detail.hit.zdb_id: 184719-3
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  • 7
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    Complete-genome sequence and in vitro probiotic characteristics analysis of Bifidobacterium pseudolongum YY-26
    Oxford University Press (OUP) ; 2022
    In:  Journal of Applied Microbiology Vol. 133, No. 4 ( 2022-10-01), p. 2599-2617
    Details
    In: Journal of Applied Microbiology, Oxford University Press (OUP), Vol. 133, No. 4 ( 2022-10-01), p. 2599-2617
    Abstract: The aim was to isolate a neotype bifidobacteria strain and evaluate its in vitro probiotic potential. Methods and Results Bifidobacterium pseudolongum YY-26 (CGMCC 24310) was isolated from faeces of mice treated with low-molecular-weight hydrolyzed guar gum (GMPS) and identified based on 16S rRNA sequence and genome sequence. Whole-genome sequencing obtained using PacBio's single-molecular and Illumina's paired-end sequencing technology. A genome of 2.1 Mb in length, with 1877 predicted protein-coding sequences was obtained. Carbohydrate-Activity enZyme analysis revealed that YY-26 encodes 66 enzymes related to carbohydrate metabolism. Whole genome sequence analysis revealed the typical probiotic characteristics of YY-26, including safety in genetic level and ability to produce beneficial metabolites and extracellular polysaccharides. Ability of extensive carbon source utilization and short-chain fatty acid production was observed with single YY-26 cultivation. Considerable acetic acids and lactic acids were determined in GMPS utilization. YY-26 showed tolerance to simulated gastrointestinal tract and displayed appreciable antioxidant activity of free radical scavenging. Conclusions B. pseudolongum YY-26 was identified with numerous probiotic-associated genes and its probiotic characteristics were verified in vitro. Significance and Impact of Study This study supplemented with limited publicly information regarding the genomes of B. pseudolongum strains and revealed the probiotic potential of YY-26.
    Type of Medium: Online Resource
    ISSN: 1365-2672 , 1364-5072
    URL: Article
    DOI: 10.1111/jam.15730
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2020421-8
    detail.hit.zdb_id: 1358023-1
    SSG: 12
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  • 8
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    Revolutionizing GPCR–ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery
    Oxford University Press (OUP) ; 2024
    In:  Briefings in Bioinformatics Vol. 25, No. 4 ( 2024-05-23)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 25, No. 4 ( 2024-05-23)
    Abstract: G-protein coupled receptors (GPCRs), crucial in various diseases, are targeted of over 40% of approved drugs. However, the reliable acquisition of experimental GPCRs structures is hindered by their lipid-embedded conformations. Traditional protein–ligand interaction models falter in GPCR–drug interactions, caused by limited and low-quality structures. Generalized models, trained on soluble protein–ligand pairs, are also inadequate. To address these issues, we developed two models, DeepGPCR_BC for binary classification and DeepGPCR_RG for affinity prediction. These models use non-structural GPCR–ligand interaction data, leveraging graph convolutional networks and mol2vec techniques to represent binding pockets and ligands as graphs. This approach significantly speeds up predictions while preserving critical physical–chemical and spatial information. In independent tests, DeepGPCR_BC surpassed Autodock Vina and Schrödinger Dock with an area under the curve of 0.72, accuracy of 0.68 and true positive rate of 0.73, whereas DeepGPCR_RG demonstrated a Pearson correlation of 0.39 and root mean squared error of 1.34. We applied these models to screen drug candidates for GPR35 (Q9HC97), yielding promising results with three (F545-1970, K297-0698, S948-0241) out of eight candidates. Furthermore, we also successfully obtained six active inhibitors for GLP-1R. Our GPCR-specific models pave the way for efficient and accurate large-scale virtual screening, potentially revolutionizing drug discovery in the GPCR field.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbae281
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 2068142-2
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 9
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    Spatial multi-omics characterizes GPR35-relevant lipid metabolism signatures across liver zonation in MASLD
    Oxford University Press (OUP) ; 2024
    In:  Life Metabolism
    Details
    In: Life Metabolism, Oxford University Press (OUP)
    Abstract: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a metabolic disease that can progress to metabolic dysfunction-associated steatohepatitis (MASH), cirrhosis, and cancer. The zonal distribution of biomolecules in the liver is implicated in mediating the disease progression. Recently, G-protein-coupled receptor 35 (GPR35) has been highlighted to play a role in MASLD, but the precise mechanism is not fully understood, particularly, in a liver-zonal manner. Here, we aimed to identify spatially distributed specific genes and metabolites in different liver zonation that are regulated by GPR35 in MASLD, by combining lipid metabolomics, spatial transcriptomics (ST), and spatial metabolomics (SM). We found that GPR35 influenced lipid accumulation, inflammatory and metabolism-related factors in specific regions, notably affecting the anti-inflammation factor ELF4 (E74 like E-twenty six (ETS) transcription factor 4), lipid homeostasis key factor CIDEA (cell death-inducing DNA fragmentation factor alpha (DFFA)-like effector A), and the injury response-related genes serum amyloid A1/2/3 (SAA1/2/3), thereby impacting MASLD progression. Furthermore, SM elucidated specific metabolite distributions across different liver regions, such as C10H11N4O7P (3',5'-cyclic inosine monophosphate (3',5'-IMP)) for the central vein, and this metabolite significantly decreased in the liver zones of GPR35-deficient mice during MASLD progression. Taken together, GPR35 regulates hepatocyte damage repair, controls inflammation, and prevents MASLD progression by influencing phospholipid homeostasis and gene expression in a zonal manner
    Type of Medium: Online Resource
    ISSN: 2755-0230
    URL: Article
    DOI: 10.1093/lifemeta/loae021
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 3148293-4
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