DataSheet_1_Estimation of the Manning’s n coefficient in multi-constituent tidal models by assimilating satellite observations with the adjoint data assimilation.docx

The bottom friction is critical for the dissipation of the global tidal energy. The bottom friction coefficient is traditionally determined using the Manning’s n formulation in tidal models. The Manning’s n coefficient in the Manning’s n formulation is vital for the accurate simulation and prediction of the tide in coastal shallow waters, but it cannot be directly measured and contains large amounts of uncertainties. Based on a two-dimensional multi-constituent tidal model with the adjoint data assimilation, the estimation of the Manning’s n coefficient is investigated by assimilating satellite observations in the Bohai, Yellow and East China Seas with the simulation of four principal tidal constituents M2, S2, K1 and O1. In the twin experiments, the Manning’s n coefficient is assumed to be constant, and it is estimated by assimilating the synthetic observations at the spatial locations of the satellite tracks. Regardless the inclusion of artificial random observational errors associated with synthetic observations, the model performance is improved as evaluated by the independent synthetic observations. The prescribed ‘real’ Manning’s n coefficient is reasonably estimated, indicating that the adjoint data assimilation is an effective method to estimate the Manning’s n coefficient in multi-constituent tidal models. In the practical experiments, the errors between the independent observations at the tidal gauge stations and the corresponding simulated results of the four principal tidal constituents are substantially decreased under both scenarios of the constant and spatially-temporally varying Manning’s n coefficient estimated by assimilating the satellite observations with the adjoint data assimilation. In addition, the estimated spatial and temporal variation trend is robust and not affected by the model settings. The spatially-temporally varying Manning’s n coefficient is negatively correlated with the current speed and shows significant spatial variation in the shallow water areas. This study demonstrates that the Manning’s n coefficient can be reasonably estimated by the adjoint data assimilation, which allows significant improvement in accurate simulation of the ocean tide.</p

Data_Sheet_2_Complete Genome Sequencing and Comparative Phenotypic Analysis Reveal the Discrepancy Between Clostridioides difficile ST81 and ST37 Isolates.PDF

Toxin A-negative, toxin B-positive Clostridioides difficile strains, which primarily include the ST81 and ST37 genotypes, are predominant in C. difficile infections leading to antibiotic-associated diarrhea in China. Recently, ST81 has been reported as the most prevalent genotype rather than ST37, although the genetic and functional characteristics of the two genotypes remain ambiguous. In this study, we conducted comprehensive comparative analysis of these two genotypes through complete genome sequencing and phenotypic profiling. The whole genome sequencing revealed that the ST81 and ST37 isolates were closely related genetically with similar gene compositions, and high rate of the core genome shared. The integrative and conjugative elements identified in ST81 were similar to those in ST37, albeit with more diverse and insertion regions. By characterizing the phenotypes related to colonization or survival in the host, we found that the ST81 isolates exhibited robust colonization ability and survival both in vitro and in vivo, enhanced spore production, and slightly increased motility, which may be attributable to the discrepancy in non-synonymous single-nucleotide polymorphisms in the relevant functional genes. Furthermore, the ST81 isolates displayed a significantly higher rate of resistance to fluoroquinolones compared with the ST37 isolates (94.12% vs. 62.5%) and mostly carried the amino acid substitution Asp426Val in GyrB. In summary, the results of our study indicate that ST81 isolates exhibit enhanced ability to transmit between hosts and survive in harsh environments, providing key genetic insights for further epidemiological investigations and surveillance of C. difficile infection.</p

Data_Sheet_1_Complete Genome Sequencing and Comparative Phenotypic Analysis Reveal the Discrepancy Between Clostridioides difficile ST81 and ST37 Isolates.PDF

Toxin A-negative, toxin B-positive Clostridioides difficile strains, which primarily include the ST81 and ST37 genotypes, are predominant in C. difficile infections leading to antibiotic-associated diarrhea in China. Recently, ST81 has been reported as the most prevalent genotype rather than ST37, although the genetic and functional characteristics of the two genotypes remain ambiguous. In this study, we conducted comprehensive comparative analysis of these two genotypes through complete genome sequencing and phenotypic profiling. The whole genome sequencing revealed that the ST81 and ST37 isolates were closely related genetically with similar gene compositions, and high rate of the core genome shared. The integrative and conjugative elements identified in ST81 were similar to those in ST37, albeit with more diverse and insertion regions. By characterizing the phenotypes related to colonization or survival in the host, we found that the ST81 isolates exhibited robust colonization ability and survival both in vitro and in vivo, enhanced spore production, and slightly increased motility, which may be attributable to the discrepancy in non-synonymous single-nucleotide polymorphisms in the relevant functional genes. Furthermore, the ST81 isolates displayed a significantly higher rate of resistance to fluoroquinolones compared with the ST37 isolates (94.12% vs. 62.5%) and mostly carried the amino acid substitution Asp426Val in GyrB. In summary, the results of our study indicate that ST81 isolates exhibit enhanced ability to transmit between hosts and survive in harsh environments, providing key genetic insights for further epidemiological investigations and surveillance of C. difficile infection.</p

Additional file 1 of The regulatory subunits of CK2 complex mediate DNA damage response and virulence in Candida Glabrata

Supplementary Material

Additional file 5 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis

Additional file 5: Figure S3. Possible relationships between enterotype and clinical severity of sepsis. A Average relative proportions of genera in each enterotype. B Column diagrams showing the proportions of sepsis patients with a SOFA score ≥ 10, an ICU stay ≥ 30 days, and death. C Student’s t-test showing differences in the Shannon diversity index and Chao abundance index between the three enterotype subgroups; **p  3 are shown

Additional file 7 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis

Additional file 7: Figure S5. Sepsis-induced alteration of tryptophan metabolism. Sepsis-related metabolites are shown in color

Additional file 2 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis

Additional file 2: Clinical data of patients in the sepsis cohor

Additional file 10 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis

Additional file 10: Table S3. Clinical characteristics of sepsis patients categorized by enterotype

Additional file 3 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis

Additional file 3: Figure S1. Comparison of microbial alterations in the sepsis patients and the HCs after age matching (n = 17 per group). A PCoA for the sepsis and HC group samples, with plots based on the Bray–Curtis distance. Each point represents one sample and the colors represent different groups. The results of the ANOSIM test to compare dissimilarity indexes among samples are shown above the plots. B Wilcoxon rank sum tests performed to analyze between-group differences in the main bacterial load at the genus level. C Average relative proportions of genera in patients according to origin of infection

Additional file 6 of Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis

Additional file 6: Figure S4. Alterations of the gut microbiome and intestinal transcriptome in septic rats. A Student’s t-test showing no significant difference in the Shannon diversity index between septic and healthy rats (n = 6 per group). B KEGG pathway enrichment analysis of DEGs upregulated (left) and downregulated (right) in the septic ileum (n = 6) relative to their expression in the ileum of HCs. The top 15 pathways are shown. C Spearman’s correlation was conducted to evaluate associations between the top 50 central DEGs (identified by BC value) and differentially expressed OTUs (LDA > 2) in the ileum of septic rats (n = 6). The color gradient corresponds to the R value, where red represents the highest positive correlation and blue represents the lowest