Non-Oscillatory Hierarchical Reconstruction for Central and Finite Volume Schemes

This is the continuation of the paper "central discontinuous Galerkin methods on overlapping cells with a non-oscillatory hierarchical reconstruction" by the same authors. The hierarchical reconstruction introduced therein is applied to central schemes on overlapping cells and to nite volume schemes on non-staggered grids. This takes a new nite volume approach for approximating non-smooth solutions. A critical step for high order nite volume schemes is to reconstruct a nonoscillatory high degree polynomial approximation in each cell out of nearby cell averages. In the paper this procedure is accomplished in two steps: first to reconstruct a high degree polynomial in each cell by using e.g., a central reconstruction, which is easy to do despite the fact that the reconstructed polynomial could be oscillatory; then to apply the hierarchical reconstruction to remove the spurious oscillations while maintaining the high resolution. All numerical computations for systems of conservation laws are performed without characteristic decomposition. In particular, we demonstrate that this new approach can generate essentially non-oscillatory solutions even for 5th order schemes without characteristic decomposition.The research of Y. Liu was supported in part by NSF grant DMS-0511815. The research of C.-W. Shu was supported in part by the Chinese Academy of Sciences while this author was visiting the University of Science and Technology of China (grant 2004-1-8) and the Institute of Computational Mathematics and Scienti c/Engineering Computing. Additional support was provided by ARO grant W911NF-04-1-0291 and NSF grant DMS-0510345. The research of E. Tadmor was supported in part by NSF grant 04-07704 and ONR grant N00014-91-J-1076. The research of M. Zhang was supported in part by the Chinese Academy of Sciences grant 2004-1-8

Revisiting the Evaluation of Image Synthesis with GANs

A good metric, which promises a reliable comparison between solutions, is essential for any well-defined task. Unlike most vision tasks that have per-sample ground-truth, image synthesis tasks target generating unseen data and hence are usually evaluated through a distributional distance between one set of real samples and another set of generated samples. This study presents an empirical investigation into the evaluation of synthesis performance, with generative adversarial networks (GANs) as a representative of generative models. In particular, we make in-depth analyses of various factors, including how to represent a data point in the representation space, how to calculate a fair distance using selected samples, and how many instances to use from each set. Extensive experiments conducted on multiple datasets and settings reveal several important findings. Firstly, a group of models that include both CNN-based and ViT-based architectures serve as reliable and robust feature extractors for measurement evaluation. Secondly, Centered Kernel Alignment (CKA) provides a better comparison across various extractors and hierarchical layers in one model. Finally, CKA is more sample-efficient and enjoys better agreement with human judgment in characterizing the similarity between two internal data correlations. These findings contribute to the development of a new measurement system, which enables a consistent and reliable re-evaluation of current state-of-the-art generative models.Comment: NeurIPS 2023 datasets and benchmarks trac

Efficient detoxication of hydroxylamine and nitrite through heterotrophic nitrification and aerobic denitrification by Acinetobacter johnsonii EN-J1

The co-existence of hydroxylamine (NH2OH) and nitrite (NO2–-N) can aggravate the difficulty of wastewater treatment. The roles of hydroxylamine (NH2OH) and nitrite (NO2–-N) in accelerating the elimination of multiple nitrogen sources by a novel isolated strain of Acinetobacter johnsonii EN-J1 were investigated in this study. The results demonstrated that strain EN-J1 could eliminate 100.00% of NH2OH (22.73 mg/L) and 90.09% of NO2–-N (55.32 mg/L), with maximum consumption rates of 1.22 and 6.75 mg/L/h, respectively. Prominently, the toxic substances NH2OH and NO2–-N could both facilitate nitrogen removal rates. Compared with the control treatment, the elimination rates of nitrate (NO3–-N) and NO2–-N were enhanced by 3.44 and 2.36 mg/L/h after supplementation with 10.00 mg/L NH2OH, and those of ammonium (NH4+-N) and NO3–-N were improved by 0.65 and 1.00 mg/L/h after the addition of 50.00 mg/L NO2–-N. Furthermore, the nitrogen balance results indicated that over 55.00% of the initial total nitrogen was transformed into gaseous nitrogen by heterotrophic nitrification and aerobic denitrification (HN-AD). Ammonia monooxygenase (AMO), hydroxylamine oxidoreductase (HAO), nitrate reductase (NR), and nitrite reductase (NIR), which are essential for HN-AD, were detected at levels of 0.54, 0.15, 0.14, and 0.01 U/mg protein, respectively. All findings confirmed that strain EN-J1 could efficiently execute HN-AD, detoxify NH2OH and NO2–-N, and ultimately promote nitrogen removal rates

Integrative transcriptome and proteome revealed high-yielding mechanisms of epsilon-poly-L-lysine by Streptomyces albulus

Introductionε-poly-L-lysine (ε-PL) is a high value, widely used natural antimicrobial peptide additive for foods and cosmetic products that is mainly produced by Streptomyces albulus. In previous work, we developed the high-yield industrial strain S. albulus WG-608 through successive rounds of engineering.MethodsHere, we use integrated physiological, transcriptomic, and proteomics association analysis to resolve the complex mechanisms underlying high ε-PL production by comparing WG-608 with the progenitor strain M-Z18.ResultsOur results show that key genes in the glycolysis, pentose phosphate pathway, glyoxylate pathway, oxidative phosphorylation, and L-lysine biosynthesis pathways are differentially upregulated in WG-608, while genes in the biosynthetic pathways for fatty acids, various branched amino acids, and secondary metabolite by-products are downregulated. This regulatory pattern results in the introduction of more carbon atoms into L-lysine biosynthesis and ε-PL production. In addition, significant changes in the regulation of DNA replication, transcription, and translation, two component systems, and quorum sensing may facilitate the adaptability to environmental pressure and the biosynthesis of ε-PL. Overexpression of ppk gene and addition of polyP6 further enhanced the ε-PL production.DiscussionThis study enables comprehensive understanding of the biosynthetic mechanisms of ε-PL in S. albulus WG-608, while providing some genetic modification and fermentation strategies to further improve the ε-PL production

Exploring the pathogenesis of colorectal carcinoma complicated with hepatocellular carcinoma via microarray data analysis

Background: Despite the increasing number of research endeavors dedicated to investigating the relationship between colorectal carcinoma (CRC) and hepatocellular carcinoma (HCC), the underlying pathogenic mechanism remains largely elusive. The aim of this study is to shed light on the molecular mechanism involved in the development of this comorbidity.Methods: The gene expression profiles of CRC (GSE90627) and HCC (GSE45267) were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the common differentially expressed genes (DEGs) of psoriasis and atherosclerosis, three kinds of analyses were performed, namely, functional annotation, protein‐protein interaction (PPI) network and module construction, and hub gene identification, survival analysis and co-expression analysis.Results: A total of 150 common downregulated differentially expressed genes and 148 upregulated differentially expressed genes were selected for subsequent analyses. The significance of chemokines and cytokines in the pathogenesis of these two ailments is underscored by functional analysis. Seven gene modules that were closely connected were identified. Moreover, the lipopolysaccharide-mediated signaling pathway is intricately linked to the development of both diseases. Finally, 10 important hub genes were identified using cytoHubba, including CDK1, KIF11, CDC20, CCNA2, TOP2A, CCNB1, NUSAP1, BUB1B, ASPM, and MAD2L1.Conclusion: Our study reveals the common pathogenesis of colorectal carcinoma and hepatocellular carcinoma. These common pathways and hub genes may provide new ideas for further mechanism research