Additional file 3 of The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes
Bibliographic record
Abstract
Additional file 3: Survey of candidate genes for epithelia, multicilliogenesis, signaling pathways, transcription factors, neuro-sensory functions, biosilicification. Table S9. Blastp search of proteins involved in bilaterian epithelial functions. Figure S7. Domain prediction of integrins and of laminins. Table S10. Blastp search concerning proteins involved in bilaterian multiciliogenesis. Table S11. Blast Search of core genes involved in three main ancestral signalling pathways. Table S12. Blastp search results concerning G-proteins. Table S13. Blastp search and protein domain analyses concerning basic Helix Loop Helixtranscription factors. Figure S8. Phylogenetic relationships among bHLH Transcription factors. Figure S9. Phylogenetic position of Oopsacas bHLH-PAS Transcription factors. Table S14. Blastp search, domain and phylogenetic analyses performed on various transcription factor types. Figure S10. Domain Prediction of HD transcription factors. Figure S11. Phylogenetic positions of Oopsacas Homeobox Transcription factors of the ANTP class. Table S15. Survey of candidate genes for photoreception. Table S16. Blastp search for proteins involved in chemical signaling. Table S17. HHMER searches in O. minuta for voltage gated ion channels. Figure S12. Diversity and phylogenetic positions of Oopsacas calcium channels. Figure S13. Phylogenetic positions of Oopsacas potassium channels. Table S18. Blastp search of proteins involved in bilaterian synapses. Table S19. Results of HMMER searches for SNARES proteins. Table S20. Blast P search of proteins involved in silica biogenesis. Table S21. List of sequences used for phylogenetic analyses of silicatein and cathepsin.
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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 | 0.006 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| 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) | 0.712 | 0.151 |
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".