Additional file 5 of Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor
Bibliographic record
Abstract
Supplementary Material 5: Figure 4. A library of early childhood gut bacterial isolates. Bacterial strains from the fecal-derived chemostat community of NS0 or NS1 individuals were isolated by axenic culture using a variety of media formulations (Suppl. Table 2 ). 80 unique bacterial strains were archived, constituting a library of NS0 sample (Suppl. Table 14 ), and 118 unique bacterial strains were archived, constituting a library of NS1 sample (Suppl. Table 15). (a) Phylogenetic tree of all gut bacterial isolates (species-level) identified by 16S rRNA gene sequencing of NS0 and NS1 libraries. Colored squares indicate phylum. (b) The relative abundance distribution of each isolate species in the fecal samples of CHILD cohort infants at 12 months old is shown (n=842 samples). 16S rRNA gene sequencing dataset from CHILD cohort was obtained at the Sequence Read Archive of NCBI via accession number PRJNA657821.
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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 | 0.015 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.799 | 0.206 |
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".