Additional file 2 of Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers
Bibliographic record
Abstract
Additional file 2: Supplementary Table 1. Total relative abundance, alpha diversity,definition of bacterial communities in the samples, positive controls and ASV count tables luminal and tissue. Supplementary Table 2. Sociodemographic and clinical characteristics per study participant. Supplementary Table 3. Metabolic profile of the luminal microbiome. Supplementary Table 4. Sociodemographic and clinical characteristics of study participants included in the transcriptomic profiling at time of tissue sample collection, grouped based on their tissue microbiome. Supplementary Table 5. Differentially expressed genes between the luminal study groups. Supplementary Table 6. Pathway enrichment analysis for the differentially expressed genes across the luminal samples. Supplementary Table 7. Pathway enrichment analysis for the differentially expressed genes by pairwise comparisons between the luminal samples. Supplementary Table 8. Transcription factor protein-protein interaction (TF-PPI) network analysis by pairwise comparisons between the luminal samples. Supplementary Table 9. Differentially expressed genes between the tissue study groups. Supplementary Table 10. Pathway enrichment analysis for the differentially expressed genes across the tissue samples. Supplementary Table 11. Pathway enrichment analysis for the differentially expressed genes by pairwise comparisons between the tissue samples. Supplementary Table 12. Transcription factor protein-protein interaction (TF-PPI) network analysis by pairwise comparisons between the tissue samples. Supplementary Table 13. Differentially expressed genes and pathway enrichment analysis for the comparison of sample groups defined as L2T2 and L2T3. Supplementary Table 14. Characterization of proteins and antibodies included in the protein profiling assay, cytokine data and cytokine results. Supplementary Table 15. Sociodemographic and clinical characteristics of study participants included in the protein profiling at time of luminal sample collection. Supplementary Table 16. Comparisons of protein levels between the luminal study groups. Supplementary Table 17. Comparisons of protein levels between the tissue study groups.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.022 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.834 | 0.096 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".