Additional file 6 of Identification of the distribution of human endogenous retroviruses K (HML-2) by PCR-based target enrichment sequencing
Bibliographic record
Abstract
Additional file 6: Fig. S4. Verification of polymorphic loci. Selected polymorphic loci detected by PTESHK were verified using specific primers (Additional file 5: Table S2) and separated on a 1.5% agarose gel. Primer pairs F1/R1 were used for the primary PCR performed as follows: 95 °C for 3 min; 30 cycles of 95 °C for 30 s, 52 °C for 30 s, 72 °C for 1 min per kb of the product, and a final extension step at 72 °C for 10 min. Primer pairs F2/R2 were used for the nested PCR, except 4 loci using 5LTR2 as one of the nested PCR primers (Additional file 5: Table S2). The PCR procedure was performed as follows: 95 °C for 3 min; 6 cycles of 95 °C for 30 s, 60 °C for 30 s, decreasing of 1 °C every cycle, 72 °C for 1 min per kb of the product; 30 cycles of 95 °C for 30 s, 58 °C for 30 s, 72 °C for 1 min per kb of the product, and a final extension step at 72 °C for 10 min. Among all 14 polymorphic loci, 12 loci could be verified, except for 12p12d and 6p21.32a, which may be caused by either their location in a repeat element or a provirus integration where the length of the products were too long to amplify. For 6p21.32b and 19p12b, the results were partly confirmed, as 6p21.32b of Y and 19p12b of W were not amplified. This may be caused by the difference in DNA or experimental error.
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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 | 0.003 | 0.032 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.864 | 0.209 |
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".