Random projection forest initialization for graph convolutional networks.

Graph convolutional networks (GCNs) were a great step towards extending deep learning to graphs. GCN uses the graph G and the feature matrix X as inputs. However, in most cases the graph G is missing and we are only provided with the feature matrix X. To solve this problem, classical graphs such as k-nearest neighbor (k-nn) are usually used to construct the graph G and initialize the GCN. Although it is computationally efficient to construct k-nn graphs, the constructed graph might not be very useful for learning. In a k-nn graph, points are restricted to have a fixed number of edges, and all edges in the graph have equal weights. Our contribution is Initializing GCN using a graph with varying weights on edges, which provides better performance compared to k-nn initialization. Our proposed method is based on random projection forest (rpForest). rpForest enables us to assign varying weights on edges indicating varying importance, which enhanced the learning. The number of trees is a hyperparameter in rpForest. We performed spectral analysis to help us setting this parameter in the right range. In the experiments, initializing the GCN using rpForest provides better results compared to k-nn initialization.•Constructing the graph G using rpForest sets varying weights on edges, which represents the similarity between a pair of samples.Unlike k-nearest neighbor graph where all weights are equal.•Using rpForest graph to initialize GCN provides better results compared to k-nn initialization. The varying weights in rpForest graph quantify the similarity between samples, which guided the GCN training to deliver better results.•The rpForest graph involves the tuning of the hyperparameter (number of trees T). We provided an informative way to set this hyperparameter through spectral analysis.

Effects of two triterpenoids from Nigella sativa seeds on insulin resistance of 3T3-L1 adipocytes.

Insulin resistance (IR) is a physiological abnormality that occurs when insulin fails to activate the signal transduction pathway in target organs. It was found that supplementation of Nigella sativa seeds with oral antidiabetic medicines helps improve blood glucose control by enhanced ß cells activity and alleviation of IR. However, the activities and related mechanisms of phytochemicals from N. sativa seeds have not been thoroughly explored. In this study, the effects of two triterpenoids, 3-O-[ß-D-xylopyranose-(1→3)-α-L-rhamnose-(1→2)-α-L-arabinose]-28-O-[α-L-rhamnose-(1→4)-ß-D-glucopyranose-L-(1→6)-ß-D-glucopyranose]-hederagenin (Hxrarg) and 3-O-[ß-D-xylopyranose-(1→3)-α-L-rhamnose-(1→2)-α-L-arabinose]-hederagenin (Hxra), on IR were studied by 3T3-L1 adipocytes model. The results demonstrated that Hxrarg and Hxra inhibited maturation of 3T3-L1 preadipocytes, dramatically stimulated glucose uptake of IR-3T3-L1 adipocytes, promoted transcription of IRS, AKT, PI-3K, and GLUT4 mRNA. Western Blot results suggested that Hxrarg and Hxra were able to markedly up-regulate expression of p-IRS, p-AKT, PI-3K, and GLUT4 proteins. These findings could provide a basic foundation for the continued development and application of N. sativa in medicine and functional foods.

The Immunomodulatory Effects of Active Ingredients From Nigella sativa in RAW264.7 Cells Through NF-κB/MAPK Signaling Pathways.

Nigella sativa is a valuable herb for its functional compositions in both food and medication. N. sativa seeds can enhance immunity, anti-inflammation and analgesia and hypoglycemia, but most of the related researches are related to volatile oil and extracts, and the activity and mechanism of compounds is not clear. In this study, Ethyl-α-D-galactopyranoside (EG), Methyl-α-D-glucoside (MG), 3-O-[ß-D-xylopyranose-(1 → 3)-α-L-rhamnose-(1 → 2)-α-L-arabinose]-28-O-[α-L-rhamnose-(1 → 4)-ß-D-glucopyranose-L-(1 → 6)-ß-D-glucopyranose]-hederagenin (HXRARG) and 3-O-[ß-D-xylopyranose-(1 → 3)-α-L-rhamnose-(1 → 2)-α-L-arabinose]-hederagenin (HXRA) were isolated and identified from N. sativa seeds. In addition, four compounds could activate NF-κB pathway by promoting the expression of phosphorylation of P65 and IκBα, promoting the phosphorylation of JNK, Erk and P38 to activate MAPK signaling pathway, enhancing the proliferation and phagocytic activity of RAW264.7 cells, and promoting the release of NO, TNF-α and IL-6 on RAW264.7 cell in vitro. The results showed that N. sativa can be used as dietary supplement to enhance immune.

Nigella sativa: A Dietary Supplement as an Immune-Modulator on the Basis of Bioactive Components.

Nutrients can be considered as functional foods, which exert physiological benefits on immune system. The seeds of Nigella sativa, which have many active constituents, are mainly used for medicine, food spice, and nutritional supplements in Egypt. Much attention has been paid to N. sativa seeds for their anticancer, antibacterial, anti-inflammatory, and immune properties. However, their active constituents and mechanisms underlying functions from N. sativa seeds is unclear. Thus, the bioactive constituents with immune regulation in N. sativa seeds were systematically studied. A new compound (3-methoxythymol-6-O-ß-D-apiofuranosyl-(1→6)-ß-D-glucopyranoside 1) and 11 known compounds (2-12) were separated from the N. sativa seeds by chromatographic methods. Their structures were then elucidated by spectroscopic analysis of MS, UV, IR, 1H-, and 13C-NMR. Furthermore, immunomodulatory effects of those compounds in RAW 264.7 cells were evaluated by phagocytosis, nitric oxide (NO) and cytokine release, related mRNA transcription, and key proteins expression in vitro. Monosaccharide derivatives, Ethyl-α-D-furaarabinose (5), and Ethyl-ß-D-fructofuranoside (8) were shown to played bidirectional regulatory roles in immunity and anti-inflammation through the regulation of nuclear factor-κB (NF-κB) signaling pathways. The results showed the active compounds and mechanisms of immune regulation in N. sativa, thus indicating that N. sativa seeds could be used as dietary supplements in immunomodulation.

Immunomodulatory effects of Nigella sativa seed polysaccharides by gut microbial and proteomic technologies.

Cyclophosphamide (CTX) was used to establish the immunosuppressive mice model. The immune organ viscera index, phagocytes vitality, the levels of cytokines in serum, the oxidative stress resistance, proteomics and intestinal flora in mice were investigated to evaluate the effect of immune regulation of Nigella sativa seed polysaccharide (NSSP). The results showed that the high-dose NSSP group could significantly increase the thymus and spleen index. The levels of ACP, LDH, T-AOC, SOD, IL-2, IL-4 and IL-6 were significantly increased and the levels of TNF-α and MDA were reduced. All evidences indicated that NSSP could improve the immune effects of the immunosuppressed mice. Proteomics investigation showed that NSSP could improve the immune by regulating the differential proteins of PI3K and PTEN, and regulating the metabolism-related pathways such as autoimmune diseases and PI3K-Akt signaling pathway. of Gut microbes analysis showed that NSSP could exert immunomodulatory effects by improving the structure of the intestinal flora, increasing the diversity of the flora, and regulating metabolic pathways such as lipid metabolism, polysaccharide synthesis and signal transduction by the prediction of flora metabolic functions. In addition, NSSP could regulate intestinal environment by regulating the content of short chain fatty acids.

The effect of microbial composition and proteomic on improvement of functional constipation by Chrysanthemum morifolium polysaccharide.

In this paper, SD rat constipation model was established with loperamide hydrochloride to study the effect of Chrysanthemum morifolium polysaccharide on the improvement of functional constipation, and the mechanism of improving constipation was investigated with the proteomics and intestinal flora. The results showed that the HD group of C. morifolium polysaccharide could significantly increase the levels of water content of stool pellets, small intestine propulsion rate, gastrin (MTL), gastrin (GAS) and substance P (SP), decrease the level of growth inhibitor (SS) and improved gastrointestinal motility in rats. Gut microbial studies showed that C. morifolium polysaccharide could significantly increase species abundance and flora diversity and improve flora structure. The relative abundance of Lactobacillus and Romboutsia increased, while the relative abundance of Lachnospiraceae_NK4A136_group and Roseburia decreased compared with the MC group. Proteomics studies suggested that C. morifolium polysaccharides could reduce intestinal lesions, enhance intestinal homeostasis, increase amino acid uptake, promote intestinal motility and relieve constipation by regulating the expression of RAS, FABP1 and SLC1A5 proteins.