Additional file 1 of Microbial dysbiosis and the host airway epithelial response: insights into HIV-associated COPD using multi’omics profiling
Bibliographic record
Abstract
Additional file 1. Figure S1: Multi ‘omic integration study design. Figure S2: 16S RNA gene copies/μL measured in airway epithelial cells. Figure S3: Principal coordinate plot by smoking status. Figure S4: Plot showing potential interactive effects of COPD and HIV status on Shannon Index, Faith PD, Bray Curtis PC1, and Bray Curtis PC2. Figure S5: Shannon Diversity Index differences between the COPD and HIV groups after removing 4 COPD- subjects administered with inhaled corticosteroids from the analysis. Figure S6: Principal coordinate plot showing microbial community structures among subject groups based on the Bray-Curtis metric, after removing 4 COPD- subjects administered with inhaled corticosteroids from the analysis. Figure S7: 16S RNA gene copies/μL measured in bronchial brushings and control specimens of HIV+ subjects. Table S1 Relative taxa abundance comparisons at the phylum level between the COPD+ and COPD-,HIV+ and HIV-, andCOPD-HIV-, COPD-HIV+, COPD+HIV- and COPD+HIV+ groups in AEC samples. Table S2: Relative taxa abundance comparisons at the genus level between the COPD+ and COPD-, HIV+ and HIV-, and COPD-HIV-, COPD-HIV+, COPD+HIV- and COPD+HIV+ groups in AEC samples. Table S3: Pairwise PERMANOVA comparisons between the different specimen types obtained from HIV+ subjects.
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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 | 0.002 | 0.032 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.864 | 0.140 |
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; the direct Gemma label and the distilled Codex classifier agree on what is shown here.
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".