Journal: Bioinformatics

Article Title: Knowledge-enhanced protein subcellular localization prediction from 3D fluorescence microscope images

doi: 10.1093/bioinformatics/btaf331

Figure Lengend Snippet: The effects of asymmetric loss (ASL) and class confidence weights (CCW) on the class imbalance and weak annotation issues. (A) Results on the 11 categories with small sample sizes before and after using ASL. (B) Results of the prediction with and without using ASL or CCW. The red protein labels in the examples are not reflected in the shown single cells. Incorporating ASL and CCW enables the model to identify the categories of the single cells more accurately, even under weak annotation influence.

Article Snippet: The results indicated that the most critical components in classification performance were the ASL and the 2D branch, and CCW has the most significant impact on the OpenCell dataset, which aligns closely with its weak annotation issue. shows that incorporating ASL has enhanced the accuracy for categories with small sample sizes, demonstrating that ASL could perform well in the class imbalance situation.

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Journal: Journal of Inflammation Research

Article Title: Si-Ni Decoction as a Potential Treatment for Ulcerative Colitis: Modulation of Gut Microbiota and AKT1 Inhibition Through Network Pharmacology and in vivo Validation

doi: 10.2147/JIR.S516556

Figure Lengend Snippet: Specific chemical formulae for the first 15 active compounds. From ( A – O ) are Sexangularetin, DFV, Jaranol.naringenin.6-prenylated eriodictyol, Quercetin der., Glabridin, Sigmoidin-B, licoisoflavanone, glyuranolide, 7,2’,4’-trihydroxy–5-methoxy-3–arylcoumarin, isorhamnetin, kanzonols W, Karanjin, Delphin_qt. Protein-protein interaction (PPI) network depicting the interactions of SND-related proteins involved in UC treatment.

Article Snippet: Figure 6 Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin).

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Journal: Journal of Inflammation Research

Article Title: Si-Ni Decoction as a Potential Treatment for Ulcerative Colitis: Modulation of Gut Microbiota and AKT1 Inhibition Through Network Pharmacology and in vivo Validation

doi: 10.2147/JIR.S516556

Figure Lengend Snippet: GO and KEGG enrichment analysis of the target of OA treated by CR. ( A ) GO analysis was performed to predict biological processes/cellular components/ molecular functions affected by SND. The horizontal axis as well as the large of the dots indicate the number of small, enriched genes, the closer the colour to red means the closer the P-value is to zero, and the vertical axis indicates the name of the term. ( B ) KEGG analysis was performed to predict pathways affected by snd. The horizontal axis is the number of genes, and the vertical axis is the term name.

Article Snippet: Figure 6 Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin).

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Journal: Journal of Inflammation Research

Article Title: Si-Ni Decoction as a Potential Treatment for Ulcerative Colitis: Modulation of Gut Microbiota and AKT1 Inhibition Through Network Pharmacology and in vivo Validation

doi: 10.2147/JIR.S516556

Figure Lengend Snippet: Molecular docking of key components of SND and AKT1. From ( A – J ) are Q Quercetin der., Delphin_qt, licoisoflavanone, Jaranol, 6-prenylated eriodictyol, 7,2’,4’-trihydroxy–5-methoxy-3–arylcoumarin, Glabridin, kanzonols W, Sexangularetin, DFV.

Article Snippet: Figure 6 Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin).

Techniques:

Journal: Journal of Inflammation Research

Article Title: Si-Ni Decoction as a Potential Treatment for Ulcerative Colitis: Modulation of Gut Microbiota and AKT1 Inhibition Through Network Pharmacology and in vivo Validation

doi: 10.2147/JIR.S516556

Figure Lengend Snippet: Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin). A The root mean square deviation (RMSD) of AKT1-Delphin complex system, AKT1-Quercetin complex system, and AKT1-Sexangularetin complex system, the smaller the deviation, the better the conformational stability. B-C Radius of Gyration (Rg) and solvent-accessible surface area (SASA) of AKT1-Delphin, AKT1-Quercetin and AKT1-Sexangularetin composite systems, the slight fluctuation of the complex during movement indicates that the complex system has undergone conformational changes during movement. D The number of hydrogen bonds between small molecules and target proteins in the kinetic process, and the number of hydrogen bonds between AKT1-Delphin complex systems ranged from 0 to 9. In most cases, the complex has about six hydrogen bonds. The number of hydrogen bonds between the AKT1-Quercetin der complex systems ranges from 0 to 4. In most cases, the complex has about three hydrogen bonds. The number of hydrogen bonds between the AKT1-Sexangularetin complex systems ranges from 0 to 6. In most cases, the complex has about four hydrogen bonds. E Root mean square fluctuation (RMSF) of AKT1-Delphin, AKT1-Quercetin der and AKT1-Sexangularetin complex Systems.

Article Snippet: Figure 6 Molecular dynamics modelling of three herbal components of SND (Quercetin der, Delphin_gt and Sexangularetin).

Techniques: Solvent