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Benchmarking automated feature engineering in oxidative coupling of methane and the impact of domain knowledge
No full textIn materials informatics, feature engineering is an essential process that improves model accuracy and model interpretability. In this study, efficient methods for feature engineering were investigated. Existing libraries (TPOT, autofeat, Feature-engine, and xfeat) that automatically or semi-automatically perform feature engineering were used, and feature creation and selection were performed by these libraries. The libraries are unique, with some focusing on automation and others on high-performance feature selection. The target data was an oxidative coupling of methane (OCM) reaction downloaded from the catalytic reaction database. In addition, feature engineering using domain knowledge was performed, and the results obtained using each library were compared. These libraries showed practical performance, especially in feature selection. However, the domain knowledge-based method was more effective in terms of feature creation. Therefore, in order to efficiently construct models with higher performance, it is effective to combine feature creation using domain knowledge and feature selection using libraries. Adsorption of methane or oxygen on the catalyst surface is an essential factor in the OCM reaction, and the metal elements selected as important features in this study could havecontributed to the reaction in the above sense.journal articl
Comparative effects of dietary stigmasterol and oxidised stigmasterol on cholesterol absorption and metabolism in mice
No full textDietary phytosterols exert hypocholesterolemic effects by inhibiting cholesterol absorption in the small intestine. However, oxidised phytosterols exert harmful effects. In this study, we compared the effects of dietary stigmasterol or oxidised stigmasterol (OS) on cholesterol absorption and metabolism in mice. Institute of Cancer Research (ICR) male mice were fed one of the following diets: a standard American Institute of Nutrition (AIN) diet; the standard diet plus 0·25 % cholesterol; the standard diet plus 0·25 % cholesterol and 0·25 % stigmasterol or the standard diet plus 0·25 % cholesterol and 0·25 % OS. Stigmasterol, but not OS, decreased plasma total cholesterol levels. Unlike stigmasterol, dietary OS increased the cholesterol levels in micellar solutions. Thus, OS could not exert hypocholesterolemic effects as it could not displace cholesterol in micellar solutions. In contrast, dietary OS downregulates the mRNA expression of genes involved in cholesterol synthesis and upregulates the mRNA expression of genes involved in cholesterol catabolism in mice fed cholesterol. In addition, dietary stigmasterol and OS increased the levels of faecal-neutral steroids by downregulating the mRNA expression of Niemann-Pick C1-like 1 protein (NPC1L1) in the small intestine. Dietary stigmasterol may directly regulate the mRNA expression of NPC1L1, whereas dietary OS may reduce the mRNA expression of sterol regulatory element-binding protein 2 and act as a Liver X receptor α agonist, reducing the mRNA expression of NPC1L1. Therefore, OS may affect cholesterol absorption and metabolism through a mechanism different from that of stigmasterol.This article is the accepted version of "British Journal of Nutrition".journal articl
Superior thermostability and divalent cation sensitivity of isoamylase CMI294C from Cyanidioschyzon merolae
No full textA storage polysaccharide in the red alga Cyanidioschyzon merolae is semi-amylopectin, a glucan with properties intermediate between noncrystalline glycogen and semicrystalline amylopectin. The debranching enzyme isoamylase plays a crucial role in determining the semicrystalline nature of glucans. In amylopectin-storing organisms, isoamylases consist of the isozymes ISA1, ISA2, and ISA3, with the former two primarily responsible for semicrystallinity. While the semicrystallinity of C. merolae semi-amylopectin is weaker than that of amylopectin, it retains a semicrystalline structure. Based on a previous analysis of isoamylase-deficient strains of C. merolae, the isoform CMI294C is the main contributor to glucan synthesis. Although the biochemical properties of isoamylases involved in amylopectin synthesis have been characterized, those of isoamylases involved in semi-amylopectin synthesis remain largely unknown. Here, we performed a detailed biochemical analysis of CMI294C to gain insights of isoamylases in semi-amylopectin synthesis. Similar to isoamylases in amylopectin-synthesizing organisms, CMI294C hydrolyzes amylopectin more efficiently than glycogen. However, unlike typical isoamylases, CMI294C is uniquely more active against pullulan than against glycogen; and it is strongly inhibited by Zn²⁺. Our results indicate that CMI294C can be potentially used for industrial maltose production due to its enzymatic properties. Overall, our findings provide molecular insights into the isoamylase in glucan structure modulation and enhance our understanding of glucan metabolism in C. merolae.journal articl
Loss of Calpain-2 attenuates TGF-β–driven Epithelial–Mesenchymal transition and invasive behavior in A549 lung cancer cells
No full textLung cancer accounts for the highest number of cancer-related deaths globally,largely due to its high propensity for early and widespread metastasis. Calpains,a family of calcium-dependent cysteine proteases,are involved in various physiological processes,including cytoskeletal remodeling,migration,and invasion. Among them,calpain-2 has been implicated in promoting cancer cell invasiveness and metastatic behavior,although its precise role in non-small cell lung cancer (NSCLC) remains poorly understood. In this study, calpain-2–deficient cells were generated from the A549 lung adenocarcinoma cell line using CRISPR/Cas9 technology, and the effects of calpain-2 loss on cell migration,invasion,and epithelial–mesenchymal transition（EMT）were evaluated in comparison with control cells. We also evaluated the effects of transforming growth factor-β（TGF-β）,a cytokine known to regulate diverse cellular processes,including proliferation,migration,and differentiation. Our results demonstrated that calpain-2 deficiency significantly reduced cell migratory capacity, EMT progression,and invasive potential following TGF-β stimulation. These effects were mediated by multiple molecular mechanisms,including impaired actin filament remodeling due to calpain-2 deficiency,reduced activation of Matrix Metalloproteinase（MMP）-2 and MMP-9,and decreased expression of EMT-related transcription factors such as Snail,Slug,and ZEB1. Collectively,these findings suggest that calpain-2 plays a central role in TGF-β–mediated cancer cell migration, invasion,and EMT progression,and that targeting calpain-2 function may represent a potential therapeutic strategy for inhibiting lung cancer metastasis.journal articl
