Additional file 7 of The BAF chromatin remodeling complex licenses planarian stem cells access to ectodermal and mesodermal cell fates
Bibliographic record
Abstract
Additional file 7. Chromatin accessibility and gene expression changes are correlated in planarian X1s. (A) FISH for pooled primer probe soxP-1/soxP-2and piwi-1 marking s- neoblasts. Planarians were imaged in the boxed region indicated by the diagram on the left. soxP-1/soxP-2+piwi-1+ cells to total piwi-1+ cells are quantified in the graph to the right. (B) DA peaks associated by proximity to gene loci that cause changes in that transcript abundance. (C) Average change in transcript abundance based on location of DA peaks relative to gene loci of dysregulated genes with associated DA peaks. (D) DA peaks associated with unique transcripts based on proximity to gene loci compared with dysregulated transcripts. Quantifications are mean 1 S.D Significance levels in plots: *p<0.05,**p<0.01, ***p<0.001, each “n” is a representative region from 1 planarian.
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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 | 0.016 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.887 | 0.315 |
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".