SmartSet Virtual Studio Solution: Validation Phase Test Results

The vision in the SmartSet project is to develop a low cost virtual studio solution that, despite being ten times less than the cost of comparable solutions on the market, will have the same quality of high cost solutions currently used by larger broadcast media companies, but with a simple and limited functionality. The project will increase the competitiveness of the European creative industries, particularly in the broadcast media sector. The SmartSet project objectives include mapping and prioritising the user requirements for the virtual studio solution to be developed. This report is based on the user consultation process with the end users and stakeholders of the SmartSet project to determine the functionality requirements for product development and integration. The research set out to detail a range of user requirements which will feed into the virtual studio specification

Additional file 4: Figure S3. of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

Use of an alternative classifier confirms the ability to predict urban/rural status from the microbiome, the metabolome, or metadata. ROC curve generated from predictions from the rpart R function, using leave-one-out predictions of urban or rural status. The area under the curve (AUC) is indicated in the legend. (TIFF 46875 kb

Additional file 9: Table S3. of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

Significant associations between microbial taxa identified through 16S rRNA sequencing, metabolites, and metadata. Significant associations (Benjamini and Hochberg-adjusted linear model P value < 0.05) between (A) the microbiome as assessed by 16S rRNA sequencing and metabolite data, (B) the microbiome as assessed by 16S rRNA sequencing, and metadata or (C) the metadata and metabolite data. (A–B) p indicates the phylum, c the class, o the order, f the family, and g the genus. Each section is ordered by taxonomic level and then by P value. (XLSX 40 kb

Additional file 17: Figure S11. of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

Taxa more abundant in urban samples have more genes than taxa that are more abundant in rural samples. For each OTU, the number of annotated genes in the closest finished genome in NCBI (Fig. 2c) was counted. The P value is from a t test comparing the 80 OTU consensus sequences with higher relative abundance in rural samples to the 91 OTUs with higher relative abundance in urban samples. (TIFF 5273 kb

Additional file 24: of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

Supplementary zip file. Code and input tables used to generate the figures and tables in this paper. (ZIP 16846 kb

Additional file 18: Figure S12. of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

KEGG pathways significantly different in relative abundance between urban and rural subjects tend to have a higher relative abundance in rural subjects. Volcano plots of the adjusted P values vs. fold change from whole genome sequencing for KEGG modules (left) and KEGG pathways (right). The P values given at the top of each plot were calculated using a chi-squared test. The horizontal dashed gray line indicates an adjusted P value of 0.05 while the vertical dashed gray line indicates an urban/rural fold change of 1. See Additional file 13: Table S5H-I for all KEGG functions tested and the model results, including mean and standard deviation, P values, effect sizes (as measured by model R 2), and Spearman correlation. (TIFF 9521 kb

Additional file 7: Figure S5. of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

Prevalence across the data set. Urban and rural prevalence vs. unadjusted P value for the null hypothesis that the OTU had the same distribution in rural and urban populations. Each point represents the average Human Microbiome Project prevalence of a 25 OTU windows. (TIFF 4218 kb

Additional file 22: of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

Supplementary Text. Detailed Methods. (DOCX 324 kb

Additional file 23: Table S9. of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

Data that were significantly different between urban and rural subjects using linear model results were generally also significant when using nonparametric models. The columns indicate the type of data, the phylogenetic, or gene level (or NA if no level is applicable), the number of values significantly different between urban and rural subjects (adjusted P value < 0.05) using a linear model, the number significantly different between urban and rural subjects using a nonparametric model, the number of values significant in both models, and then whether MDS1 was significantly different between urban and rural subjects using a linear model, nonparametric model, and in both models. 16S rRNA sequencing data was not included, as we had multiple samples from the same individual at two timepoints, which cannot be captured with a nonparametric test without splitting our data. (XLSX 10 kb

Additional file 5: Figure S4. of Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes

Differences in microbial diversity based on 16S rRNA sequencing are driven by differences in evenness and are opposite differences in richness. Comparison of (A) inverse Simpson diversity index, (B) richness, or (C) evenness for each taxonomic level, based on 16S rRNA sequencing. P values indicate the significance of the difference between urban and rural subjects. Microbial composition was determined using RDP (phylum-genus) or AbundantOTU+ (OTU). (TIFF 34218 kb