250 research outputs found

    sj-docx-1-ajr-10.1177_19458924221124363 - Supplemental material for Daphnetin Mitigates Ovalbumin-Induced Allergic Rhinitis in Mice by Regulating Nrf2/HO-1 and TLR4/NF-kB Signaling

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    Supplemental material, sj-docx-1-ajr-10.1177_19458924221124363 for Daphnetin Mitigates Ovalbumin-Induced Allergic Rhinitis in Mice by Regulating Nrf2/HO-1 and TLR4/NF-kB Signaling by Bo Tian, Xin Ma and Rui Jiang in American Journal of Rhinology & Allergy</p

    DNABP: Identification of DNA-Binding Proteins Based on Feature Selection Using a Random Forest and Predicting Binding Residues

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    <div><p>DNA-binding proteins are fundamentally important in cellular processes. Several computational-based methods have been developed to improve the prediction of DNA-binding proteins in previous years. However, insufficient work has been done on the prediction of DNA-binding proteins from protein sequence information. In this paper, a novel predictor, DNABP (DNA-binding proteins), was designed to predict DNA-binding proteins using the random forest (RF) classifier with a hybrid feature. The hybrid feature contains two types of novel sequence features, which reflect information about the conservation of physicochemical properties of the amino acids, and the binding propensity of DNA-binding residues and non-binding propensities of non-binding residues. The comparisons with each feature demonstrated that these two novel features contributed most to the improvement in predictive ability. Furthermore, to improve the prediction performance of the DNABP model, feature selection using the minimum redundancy maximum relevance (mRMR) method combined with incremental feature selection (IFS) was carried out during the model construction. The results showed that the DNABP model could achieve 86.90% accuracy, 83.76% sensitivity, 90.03% specificity and a Matthews correlation coefficient of 0.727. High prediction accuracy and performance comparisons with previous research suggested that DNABP could be a useful approach to identify DNA-binding proteins from sequence information. The DNABP web server system is freely available at <a href="http://www.cbi.seu.edu.cn/DNABP/" target="_blank">http://www.cbi.seu.edu.cn/DNABP/</a>.</p></div

    sj-tif-2-ajr-10.1177_19458924221124363 - Supplemental material for Daphnetin Mitigates Ovalbumin-Induced Allergic Rhinitis in Mice by Regulating Nrf2/HO-1 and TLR4/NF-kB Signaling

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    Supplemental material, sj-tif-2-ajr-10.1177_19458924221124363 for Daphnetin Mitigates Ovalbumin-Induced Allergic Rhinitis in Mice by Regulating Nrf2/HO-1 and TLR4/NF-kB Signaling by Bo Tian, Xin Ma and Rui Jiang in American Journal of Rhinology & Allergy</p

    Comparison of the performances of various features using the RF algorithm based on Mainset with five-fold cross-validation

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    <p>Comparison of the performances of various features using the RF algorithm based on Mainset with five-fold cross-validation</p

    Comparison of the performances of DNABP and enDNA-Prot based on various test dataset

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    <p>Comparison of the performances of DNABP and enDNA-Prot based on various test dataset</p

    The performance of DNABP, enDNA-Port, iDNA-Prot|dis and nDNA-Prot based on the Testset

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    <p>The performance of DNABP, enDNA-Port, iDNA-Prot|dis and nDNA-Prot based on the Testset</p

    The IFS curve showing MCC values plotted against feature numbers.

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    <p>The maximum MCC value was 0.727 when the top 64 features were selected.</p

    Comparison of the performances of various dataset using the RF algorithm based on 292 features with five-fold cross-validation

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    <p>Comparison of the performances of various dataset using the RF algorithm based on 292 features with five-fold cross-validation</p

    Additional file 1: of Widespread signatures of selection for secreted peptidases in a fungal plant pathogen

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    Widespread signatures of selection for secreted peptidases in a fungal plant pathogen. (DOCX 23507 kb

    Cow’s Milk Allergy May Induce Lipid Metabolism Disorder in BALB/c Mice via Exosomes

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    Allergic diseases and lipid-metabolism-disorder-derived diseases are both significant public health issues. Recent studies have shown that exosomes are associated with the course of allergic diseases and are involved in lipid metabolism. In this study, exosomes derived from cow’s milk allergic (CMA) mice medially loaded lesser proteins favoring cholesterol metabolism. The levels of total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-c) in the serum were increased in the CMA mice, and hepatic lipid deposition was observed in the liver, but these phenomena were improved by inhibiting the exosome release. Specifically, the higher expression of the sterol regulatory element binding factor 2 (SREBP2) protein and HMGCR gene in the liver of CMA mice indicated an increase in cholesterol synthesis. NPC1L1 was also highly expressed in the small intestine of CMA mice, and fecal TC level was decreased, suggesting that the reabsorption of cholesterol was elevated. The biosynthesis of cholesterol, the reverse cholesterol transport (RCT) process, and the synthesis of bile acid in the liver were improved by inhibiting exosome release, as well as the reabsorption of cholesterol in the small intestine. This study has for the first time demonstrated the lipid metabolism disorder caused by CMA, especially the important role of exosomes in food allergies and lipid metabolism
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