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  • Oxford University Press (OUP)  (10)
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  • Oxford University Press (OUP)  (10)
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  • 1
    Online Resource
    Online Resource
    COIMMR: a computational framework to reveal the contribution of herbal ingredients against human cancer via immune microenvironment and metabolic reprogramming
    Oxford University Press (OUP) ; 2023
    In:  Briefings in Bioinformatics Vol. 24, No. 6 ( 2023-09-22)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 24, No. 6 ( 2023-09-22)
    Abstract: Immune evasion and metabolism reprogramming have been regarded as two vital hallmarks of the mechanism of carcinogenesis. Thus, targeting the immune microenvironment and the reprogrammed metabolic processes will aid in developing novel anti-cancer drugs. In recent decades, herbal medicine has been widely utilized to treat cancer through the modulation of the immune microenvironment and reprogrammed metabolic processes. However, labor-based herbal ingredient screening is time consuming, laborious and costly. Luckily, some computational approaches have been proposed to screen candidates for drug discovery rapidly. Yet, it has been challenging to develop methods to screen drug candidates exclusively targeting specific pathways, especially for herbal ingredients which exert anti-cancer effects by multiple targets, multiple pathways and synergistic ways. Meanwhile, currently employed approaches cannot quantify the contribution of the specific pathway to the overall curative effect of herbal ingredients. Hence, to address this problem, this study proposes a new computational framework to infer the contribution of the immune microenvironment and metabolic reprogramming (COIMMR) in herbal ingredients against human cancer and specifically screen herbal ingredients targeting the immune microenvironment and metabolic reprogramming. Finally, COIMMR was applied to identify isoliquiritigenin that specifically regulates the T cells in stomach adenocarcinoma and cephaelin hydrochloride that specifically targets metabolic reprogramming in low-grade glioma. The in silico results were further verified using in vitro experiments. Taken together, our approach opens new possibilities for repositioning drugs targeting immune and metabolic dysfunction in human cancer and provides new insights for drug development in other diseases. COIMMR is available at https://github.com/LYN2323/COIMMR.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbad346
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    MORE FLORET1 Encodes a MYB Transcription Factor That Regulates Spikelet Development in Rice
    Oxford University Press (OUP) ; 2020
    In:  Plant Physiology Vol. 184, No. 1 ( 2020-09), p. 251-265
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 184, No. 1 ( 2020-09), p. 251-265
    Type of Medium: Online Resource
    ISSN: 0032-0889 , 1532-2548
    URL: Article
    DOI: 10.1104/pp.20.00658
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    A case–control study of rheumatoid arthritis revealed abdominal obesity and environmental risk factor interactions in northern China
    Oxford University Press (OUP) ; 2018
    In:  Modern Rheumatology Vol. 28, No. 2 ( 2018-03-04), p. 249-257
    Details
    In: Modern Rheumatology, Oxford University Press (OUP), Vol. 28, No. 2 ( 2018-03-04), p. 249-257
    Type of Medium: Online Resource
    ISSN: 1439-7595 , 1439-7609
    URL: Article
    DOI: 10.1080/14397595.2017.1307711
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2018
    detail.hit.zdb_id: 2023498-3
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  • 4
    Online Resource
    Online Resource
    SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning
    Oxford University Press (OUP) ; 2023
    In:  Briefings in Bioinformatics Vol. 24, No. 1 ( 2023-01-19)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 24, No. 1 ( 2023-01-19)
    Abstract: Cell-penetrating peptides (CPPs) have received considerable attention as a means of transporting pharmacologically active molecules into living cells without damaging the cell membrane, and thus hold great promise as future therapeutics. Recently, several machine learning-based algorithms have been proposed for predicting CPPs. However, most existing predictive methods do not consider the agreement (disagreement) between similar (dissimilar) CPPs and depend heavily on expert knowledge-based handcrafted features. Results In this study, we present SiameseCPP, a novel deep learning framework for automated CPPs prediction. SiameseCPP learns discriminative representations of CPPs based on a well-pretrained model and a Siamese neural network consisting of a transformer and gated recurrent units. Contrastive learning is used for the first time to build a CPP predictive model. Comprehensive experiments demonstrate that our proposed SiameseCPP is superior to existing baseline models for predicting CPPs. Moreover, SiameseCPP also achieves good performance on other functional peptide datasets, exhibiting satisfactory generalization ability.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbac545
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2036055-1
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  • 5
    Online Resource
    Online Resource
    Exploring pharmacological active ingredients of traditional Chinese medicine by pharmacotranscriptomic map in ITCM
    Oxford University Press (OUP) ; 2023
    In:  Briefings in Bioinformatics Vol. 24, No. 2 ( 2023-03-19)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 24, No. 2 ( 2023-03-19)
    Abstract: With the emergence of high-throughput technologies, computational screening based on gene expression profiles has become one of the most effective methods for drug discovery. More importantly, profile-based approaches remarkably enhance novel drug–disease pair discovery without relying on drug- or disease-specific prior knowledge, which has been widely used in modern medicine. However, profile-based systematic screening of active ingredients of traditional Chinese medicine (TCM) has been scarcely performed due to inadequate pharmacotranscriptomic data. Here, we develop the largest-to-date online TCM active ingredients-based pharmacotranscriptomic platform integrated traditional Chinese medicine (ITCM) for the effective screening of active ingredients. First, we performed unified high-throughput experiments and constructed the largest data repository of 496 representative active ingredients, which was five times larger than the previous one built by our team. The transcriptome-based multi-scale analysis was also performed to elucidate their mechanism. Then, we developed six state-of-art signature search methods to screen active ingredients and determine the optimal signature size for all methods. Moreover, we integrated them into a screening strategy, TCM-Query, to identify the potential active ingredients for the special disease. In addition, we also comprehensively collected the TCM-related resource by literature mining. Finally, we applied ITCM to an active ingredient bavachinin, and two diseases, including prostate cancer and COVID-19, to demonstrate the power of drug discovery. ITCM was aimed to comprehensively explore the active ingredients of TCM and boost studies of pharmacological action and drug discovery. ITCM is available at http://itcm.biotcm.net.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbad027
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Plasma Fibronectin Levels Identified via Quantitative Proteomics Profiling Predicts Hepatitis B Surface Antigen Seroclearance in Chronic Hepatitis B
    Oxford University Press (OUP) ; 2019
    In:  The Journal of Infectious Diseases Vol. 220, No. 6 ( 2019-08-09), p. 940-950
    Details
    In: The Journal of Infectious Diseases, Oxford University Press (OUP), Vol. 220, No. 6 ( 2019-08-09), p. 940-950
    Abstract: Seroclearance of hepatitis B surface antigen (HBsAg) is a potentially achievable target of chronic hepatitis B (CHB). Plasma proteins relevant to HBsAg seroclearance remain undetermined. Methods We prospectively recruited treatment-naive CHB patients with spontaneous HBsAg seroclearance and matched HBsAg-positive controls. Plasma protein profiling was performed using isobaric tags for relative and absolute quantitation-based proteomics, with the expression of candidate proteins validated in a separate cohort. The predictive value of fibronectin was assessed at 3 years, 1 year (Year -1) before, and at the time (Year 0) of HBsAg seroclearance. Results Four hundred eighty-seven plasma proteins were identified via proteomics, with 97 proteins showing altered expression. In the verification cohort (n = 90), median plasma fibronectin levels in patients with HBsAg seroclearance was higher than in controls (P = .009). In the longitudinal cohort (n = 164), patients with HBsAg seroclearance, compared with controls, had a higher median fibronectin levels at Year -1 (413.26 vs 227.95 µg/mL) and Year 0 (349.45 vs 208.72 µg/mL) (both P 〈 .001). In patients with an annual HBsAg log reduction 〉 0.5, Year -1 fibronectin level achieved an area under the receiving operator characteristic of 0.884 in predicting HBsAg seroclearance. Conclusions Using proteomics-based technology, plasma fibronectin may be associated with HBsAg seroclearance and a potential predictor of “functional cure”.
    Type of Medium: Online Resource
    ISSN: 0022-1899 , 1537-6613
    URL: Article
    DOI: 10.1093/infdis/jiz223
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 1473843-0
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  • 7
    Online Resource
    Online Resource
    Influence of oral administration of Akkermansia muciniphila on the tissue distribution and gut microbiota composition of acute and chronic cadmium exposure mice
    Oxford University Press (OUP) ; 2019
    In:  FEMS Microbiology Letters Vol. 366, No. 13 ( 2019-07-01)
    Details
    In: FEMS Microbiology Letters, Oxford University Press (OUP), Vol. 366, No. 13 ( 2019-07-01)
    Abstract: Cadmium (Cd) contamination is a serious food safety problem. Acute and chronic Cd exposure changes the gut microbiota composition and damages the gut barrier function. Akkermansia muciniphila (AKK), a promising candidate for the next-generation probiotics, has been reported to protect the mucus layer in the colon and significantly decrease the effects of Cd exposure in mice. Thus, the mice model was adopted to investigate the influence of oral administration of AKK on the toxic distribution and changes of gut microbiota composition caused by acute and chronic Cd exposure. In both acute and chronic Cd exposure experiments, 40 mice were divided into four groups (normal group, AKK group, Cd group and Cd plus AKK group). The Cd contents in feces and tissues were measured by a flame or graphite furnace atomic absorption spectrophotometer and gut microbiota composition was determined through 16S rRNA gene sequencing. The results showed that the gavage of AKK could not reduce the accumulation of Cd in the liver and kidney. The oral administration of AKK showed a certain influence on the gut microbiota composition of acute Cd exposure mice and limited influence on that of chronic Cd exposure mice. These results indicate the failure of AKK, as a potential protective probiotic, to reduce Cd toxicity. However, the gavage of AKK did have an influence on the gut microbiota composition of normal mice, especially on some genera in the Clostridiales order. Besides, when considering AKK’s probiotic potential and its effects on host health and disease, we should take into consideration its influence on the gut microbiota composition and micro-environment.
    Type of Medium: Online Resource
    ISSN: 1574-6968
    URL: Article
    DOI: 10.1093/femsle/fnz160
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 1501716-3
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  • 8
    Online Resource
    Online Resource
    Serum IFN-γ Predicts the Therapeutic Effect of Mesenchymal Stem Cells Transplantation in Systemic Lupus Erythematosus Patients
    Oxford University Press (OUP) ; 2017
    In:  Stem Cells Translational Medicine Vol. 6, No. 9 ( 2017-09-01), p. 1777-1785
    Details
    In: Stem Cells Translational Medicine, Oxford University Press (OUP), Vol. 6, No. 9 ( 2017-09-01), p. 1777-1785
    Abstract: Umbilical cord (UC)-derived mesenchymal stem cells (MSCs) show immunoregulatory properties on various immune cells and display therapeutic effects on various autoimmune diseases such as systemic lupus erythematosus (SLE). The aim of this study was to investigate the effect of the SLE environment on UC MSCs and to identify a potential serum biomarker to predict the therapeutic effect. UC MSCs were cocultured with peripheral blood mononuclear cells (PBMCs) from active lupus patients, and the proliferation, apoptosis and surface markers of UC MSCs were observed. UC MSC functional molecules were assessed by real-time polymerase chain reaction, and the signaling pathways were analyzed by Western blot. The clinical effect of MSC transplantation (MSCT) for lupus patients was followed-up, whereas baseline serum cytokines were analyzed by enzyme-linked immunosorbent assay. The coculture of PBMC from lupus patients promoted MSC proliferation. Lupus PBMCs were more potent in stimulating UC MSCs to secrete vascular endothelial growth factor (VEGF) and CXCL-12. Furthermore, lupus PBMCs activated Akt, IκB, and Stat5 signaling pathways in UC MSCs but did not affect Erk1/2 and Smad1/5/8 pathways. Moreover, our clinical study showed that higher baseline levels of IFN-γ might predict a good response to MSCT in active lupus patients. Baseline IFN-γ levels may predict clinical response to MSC therapy for active lupus patients, which will help to choose suitable patients for clinical transplantation.
    Type of Medium: Online Resource
    ISSN: 2157-6564 , 2157-6580
    URL: Article
    DOI: 10.1002/sctm.17-0002
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2017
    detail.hit.zdb_id: 2642270-0
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  • 9
    Online Resource
    Online Resource
    Transcription factor CsMYB77 negatively regulates fruit ripening and fruit size in citrus
    Oxford University Press (OUP) ; 2024
    In:  Plant Physiology Vol. 194, No. 2 ( 2024-01-31), p. 867-883
    Details
    In: Plant Physiology, Oxford University Press (OUP), Vol. 194, No. 2 ( 2024-01-31), p. 867-883
    Abstract: MYB family transcription factors (TFs) play essential roles in various biological processes, yet their involvement in regulating fruit ripening and fruit size in citrus remains poorly understood. In this study, we have established that the R2R3-MYB TF, CsMYB77, exerts a negative regulatory influence on fruit ripening in both citrus and tomato (Solanum lycopersicum), while also playing a role in modulating fruit size in citrus. The overexpression of CsMYB77 in tomato and Hongkong kumquat (Fortunella hindsii) led to notably delayed fruit ripening phenotypes. Moreover, the fruit size of Hongkong kumquat transgenic lines was largely reduced. Based on DNA affinity purification sequencing and verified interaction assays, SEVEN IN ABSENTIA OF ARABIDOPSIS THALIANA4 (SINAT4) and PIN-FORMED PROTEIN5 (PIN5) were identified as downstream target genes of CsMYB77. CsMYB77 inhibited the expression of SINAT4 to modulate abscisic acid (ABA) signaling, which delayed fruit ripening in transgenic tomato and Hongkong kumquat lines. The expression of PIN5 was activated by CsMYB77, which promoted free indole-3-acetic acid decline and modulated auxin signaling in the fruits of transgenic Hongkong kumquat lines. Taken together, our findings revealed a fruit development and ripening regulation module (MYB77-SINAT4/PIN5-ABA/auxin) in citrus, which enriches the understanding of the molecular regulatory network underlying fruit ripening and size.
    Type of Medium: Online Resource
    ISSN: 0032-0889 , 1532-2548
    URL: Article
    DOI: 10.1093/plphys/kiad592
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 2004346-6
    detail.hit.zdb_id: 208914-2
    SSG: 12
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  • 10
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    Online Resource
    Metagenomic Analysis Reveals a Possible Association Between Respiratory Infection and Periodontitis
    Oxford University Press (OUP) ; 2022
    In:  Genomics, Proteomics & Bioinformatics Vol. 20, No. 2 ( 2022-04-01), p. 260-273
    Details
    In: Genomics, Proteomics & Bioinformatics, Oxford University Press (OUP), Vol. 20, No. 2 ( 2022-04-01), p. 260-273
    Abstract: Periodontitis is an inflammatory disease that is characterized by progressive destruction of the periodontium and causes tooth loss in adults. Periodontitis is known to be associated with dysbiosis of the oral microflora, which is often linked to various diseases. However, the complexity of plaque microbial communities of periodontitis, antibiotic resistance, and enhanced virulence make this disease difficult to treat. In this study, using metagenomic shotgun sequencing, we investigated the etiology, antibiotic resistance genes (ARGs), and virulence genes (VirGs) of periodontitis. We revealed a significant shift in the composition of oral microbiota as well as several functional pathways that were represented significantly more abundantly in periodontitis patients than in controls. In addition, we observed several positively selected ARGs and VirGs with the Ka/Ks ratio  & gt; 1 by analyzing our data and a previous periodontitis dataset, indicating that ARGs and VirGs in oral microbiota may be subjected to positive selection. Moreover, 5 of 12 positively selected ARGs and VirGs in periodontitis patients were found in the genomes of respiratory tract pathogens. Of note, 91.8% of the background VirGs with at least one non-synonymous single-nucleotide polymorphism for natural selection were also from respiratory tract pathogens. These observations suggest a potential association between periodontitis and respiratory infection at the gene level. Our study enriches the knowledge of pathogens and functional pathways as well as the positive selection of antibiotic resistance and pathogen virulence in periodontitis patients, and provides evidence at the gene level for an association between periodontitis and respiratory infection.
    Type of Medium: Online Resource
    ISSN: 1672-0229 , 2210-3244
    URL: Article
    DOI: 10.1016/j.gpb.2021.07.001
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2233708-8
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