Efficient Sharpness-aware Minimization for Improved Training of Neural Networks

Overparametrized Deep Neural Networks (DNNs) often achieve astounding performances, but may potentially result in severe generalization error. Recently, the relation between the sharpness of the loss landscape and the generalization error has been established by Foret et al. (2020), in which the Sharpness Aware Minimizer (SAM) was proposed to mitigate the degradation of the generalization. Unfortunately, SAM s computational cost is roughly double that of base optimizers, such as Stochastic Gradient Descent (SGD). This paper thus proposes Efficient Sharpness Aware Minimizer (ESAM), which boosts SAM s efficiency at no cost to its generalization performance. ESAM includes two novel and efficient training strategies-StochasticWeight Perturbation and Sharpness-Sensitive Data Selection. In the former, the sharpness measure is approximated by perturbing a stochastically chosen set of weights in each iteration; in the latter, the SAM loss is optimized using only a judiciously selected subset of data that is sensitive to the sharpness. We provide theoretical explanations as to why these strategies perform well. We also show, via extensive experiments on the CIFAR and ImageNet datasets, that ESAM enhances the efficiency over SAM from requiring 100% extra computations to 40% vis-a-vis base optimizers, while test accuracies are preserved or even improved

Delineating effect of corn microRNAs and matrix, ingested as whole food, on gut microbiota in a rodent model

Dietary microRNAs (miRNAs) are thought to regulate a wide range of biological processes, including the gut microbiota. However, it is difficult to separate specific effect(s) of miRNA from that of the food matrix. This study aims to elucidate the specific effect(s) of dietary corn miRNAs, ingested as a whole food, on the gut microbiota. We developed an autoclave procedure to remove 98% of miRNA from corn. A mouse feeding study was conducted comparing autoclaved corn to nonautoclaved corn and purified corn miRNA. Compared to nonspecific nucleotides and corn devoid of miRNAs, feeding purified corn miRNAs or corn to C57BL/6 mice via gavage or diet supplementation for two weeks lead to a decrease in total bacteria in the cecum. The effect appeared to be due to changes in Firmicutes. Additionally, corn matrix minus miRNA and processing also affected gut bacteria. In silico analysis identified corn miRNAs that aligned to Firmicutes genome sequences lending further support to the interaction between corn miRNAs and this bacterium. These data support interactions between plant food miRNA, as well as matrix, and the gut microbiota exist but complex. However, it provides additional support for mechanism by which bioactive dietary components interact with the gut microbiota

Delineating effect of corn microRNAs and matrix, ingested as whole food, on gut microbiota in a rodent model

Dietary microRNAs (miRNAs) are thought to regulate a wide range of biological processes, including the gut microbiota. However, it is difficult to separate specific effect(s) of miRNA from that of the food matrix. This study aims to elucidate the specific effect(s) of dietary corn miRNAs, ingested as a whole food, on the gut microbiota. We developed an autoclave procedure to remove 98% of miRNA from corn. A mouse feeding study was conducted comparing autoclaved corn to nonautoclaved corn and purified corn miRNA. Compared to nonspecific nucleotides and corn devoid of miRNAs, feeding purified corn miRNAs or corn to C57BL/6 mice via gavage or diet supplementation for two weeks lead to a decrease in total bacteria in the cecum. The effect appeared to be due to changes in Firmicutes. Additionally, corn matrix minus miRNA and processing also affected gut bacteria. In silico analysis identified corn miRNAs that aligned to Firmicutes genome sequences lending further support to the interaction between corn miRNAs and this bacterium. These data support interactions between plant food miRNA, as well as matrix, and the gut microbiota exist but complex. However, it provides additional support for mechanism by which bioactive dietary components interact with the gut microbiota

Gypenosides Reduced the Risk of Overweight and Insulin Resistance in C57BL/6J Mice through Modulating Adipose Thermogenesis and Gut Microbiota

This study investigated whether and how gypenosides from jiaogulan tea at 100 and 300 mg/kg/day levels could reduce the development of overweight and insulin resistance in C57 BL/6J mice fed a high-fat diet in 12 weeks. The 300 mg/kg/ day gypenosides supplement significantly reduced final body weight, plasma total cholesterol, and homeostasis model assessment-estimated insulin resistance (HOMA-IR) index by 19.9%, 40%, and 36%, respectively, compared with the high-fat diet control group. Gypenosides also increased brown adipocyte tissue activity and white adipose tissue browning. The expression of genes involved in mitochondrial activity and fatty acid β-oxidation were also increased in both brown and white adipocyte tissues. In addition, gypenosides at 100 and 300 mg/kg/day levels decreased the ratio of Firmicutes to Bacteroidetes by 20% and 58.6%, respectively, and increased Akkermansia muciniphila abundance in the gut microbiota

Identification and elucidation of cross talk between SLAM Family Member 7 (SLAMF7) and Toll-like receptor (TLR) pathways in monocytes and macrophages

Abstract To further elucidate the expression, regulation and function of Signaling Lymphocytic Activation Molecule Family (SLAMF) protein members in human monocytes and macrophages. Un-differentiated monocytic THP-1 cell (u-THP-1) and differentiated THP-1 macrophage (d-THP-1) were used as culture models in the study. Responses of cells to the differentiation agents phorbol ester (25 ng/ml) and TLR (Toll-like receptor) ligands were assessed. RT-PCR and Western blot analysis were used to determine mRNA and protein level. Pro-inflammatory cytokine mRNA expression levels and phagocytosis were used as functional markers. Data analyzed using t-test, one-way or two-way ANOVA followed by post hoc test. SLAMFs were differentially expressed in THP-1 cells. Differentiation of u-THP-1 to d-THP-1 led to significantly higher SLAMF7 mRNA and protein levels than other SLAMF. In addition, TLR stimuli increased SLAMF7 mRNA expression but not protein expression. Importantly, SLAMF7 agonist antibody and TLR ligands synergistically increased the mRNA expression levels of IL-1β, IL-6 and TNF-α, but had no effect on phagocytosis. SLAMF7 knocked-down in d-THP-1 significantly lowered TLR-induced mRNA expressions of pro-inflammatory markers. SLAM family proteins are differentially regulated by differentiation and TLRs. SLAMF7 enhanced TLR-mediated induction of pro-inflammatory cytokines in monocytes and macrophages but not phagocytosis

Transcriptomic Analysis of LNCaP Tumor Xenograft to Elucidate the Components and Mechanisms Contributed by Tumor Environment as Targets for Dietary Prostate Cancer Prevention Studies

LNCaP athymic xenograft model has been widely used to allow researchers to examine the effects and mechanisms of experimental treatments such as diet and diet-derived cancer preventive and therapeutic compounds on prostate cancer. However, the biological characteristics of human LNCaP cells before/after implanting in athymic mouse and its relevance to clinical human prostate outcomes remain unclear and may dictate interpretation of biological efficacies/mechanisms of diet/diet-derived experimental treatments. In this study, transcriptome profiles and pathways of human prostate LNCaP cells before (in vitro) and after (in vivo) implanting into xenograft mouse were compared using RNA-sequencing technology (RNA-seq) followed by bioinformatic analysis. A shift from androgen-responsive to androgen nonresponsive status was observed when comparing LNCaP xenograft tumor to culture cells. Androgen receptor and aryl-hydrocarbon pathway were found to be inhibited and interleukin-1 (IL-1) mediated pathways contributed to these changes. Coupled with in vitro experiments modeling for androgen exposure, cell-matrix interaction, inflammation, and hypoxia, we identified specific mechanisms that may contribute to the observed changes in genes and pathways. Our results provide critical baseline transcriptomic information for a tumor xenograft model and the tumor environments that might be associated with regulating the progression of the xenograft tumor, which may influence interpretation of diet/diet-derived experimental treatments

Chemical composition of cold‐pressed blackberry seed flour extract and its potential health‐beneficial properties

The blackberry seed flour was cold-extracted using 50% acetone and examined for its phytochemical composition and health-beneficial properties including in vitro gut microbiota modulatory, free radical scavenging, anti-inflammatory, and antiproliferative capacities. Among identified thirteen components of blackberry seed flour extract through UHPLC-MS analysis, sanguiin H6 was the primary component and followed by ellagic acid and pedunculagin. For health-beneficial properties, the blackberry seed flour extract increased the total number of gut bacteria and shifted the abundance of specific bacterial phylum, family, or genus. The extract had RDSC, ORAC, HOSC, and ABTS•+ scavenging capacities of 362, 304, 2,531, and 267 μmol Trolox equivalents (TE)/g, respectively. In addition, the blackberry seed flour extract showed capacities for anti-inflammation and antiproliferation by suppressing LPS induced IL-1β mRNA expressions in the cultured J774A.1 mouse macrophages and the proliferation of LNCaP prostate cancer cells. The results suggest potential health benefits and further utilization of blackberry seed flour as functional foods

Chemical composition of cold-pressed blackberry seed flour extract and its potential health-beneficial properties

The blackberry seed flour was cold-extracted using 50% acetone and examined for its phytochemical composition and health-beneficial properties including in vitro gut microbiota modulatory, free radical scavenging, anti-inflammatory, and antiproliferative capacities. Among identified thirteen components of blackberry seed flour extract through UHPLC-MS analysis, sanguiin H6 was the primary component and followed by ellagic acid and pedunculagin. For health-beneficial properties, the blackberry seed flour extract increased the total number of gut bacteria and shifted the abundance of specific bacterial phylum, family, or genus. The extract had RDSC, ORAC, HOSC, and ABTS•+ scavenging capacities of 362, 304, 2,531, and 267 μmol Trolox equivalents (TE)/g, respectively. In addition, the blackberry seed flour extract showed capacities for anti-inflammation and antiproliferation by suppressing LPS induced IL-1β mRNA expressions in the cultured J774A.1 mouse macrophages and the proliferation of LNCaP prostate cancer cells. The results suggest potential health benefits and further utilization of blackberry seed flour as functional foods

Indole-3-Carbinol Inhibits Citrobacter rodentium Infection through Multiple Pathways Including Reduction of Bacterial Adhesion and Enhancement of Cytotoxic T Cell Activity

Intestinal inflammation is associated with an increased risk of developing colorectal cancer and may result from dysregulated responses to commensal bacteria or exposure to bacterial pathogens. Dietary modulation of intestinal inflammation may protect against development of colon cancer. However, the precise diet-derived components and underlying mechanisms remain elusive. Citrobacter rodentium (Cr) induces acute intestinal inflammation and has been used to study the role of inflammation in the susceptibility to colon cancer. Here we examine the effects of indole-3-carbinol (I3C), a dietary compound with anticarcinogenic properties, on intestinal immune and inflammatory responses to Cr infection and adhesion to colonic cells in vitro. C57BL/6J mice were fed a diet with/without 1 μmol/g I3C and infected with Cr. Compared to infected mice fed with a control diet, consumption of a 1 μmol I3C/g diet significantly reduced fecal excretion of Cr, Cr colonization of the colon, and reduced colon crypt hyperplasia. Furthermore, expression of Cr-induced inflammatory markers such as IL-17A, IL-6, and IL1β were attenuated in infected mice fed with the I3C diet, compared to mice fed a control diet. The expression of cytotoxic T cell markers CD8 and FasL mRNA were increased in I3C-fed infected mice. In-vitro, I3C inhibited Cr growth and adhesion to Caco-2 cells. I3C alleviates Cr-induced murine colitis through multiple mechanisms including inhibition of Cr growth and adhesion to colonic cells in vitro and enhancement of cytotoxic T cell activity