Additional file 1 of Epidemiology and genetic diversity of circulating dengue viruses in Medellin, Colombia: a fever surveillance study
Bibliographic record
Abstract
Additional file 1: S1. Checklist: STROBE Checklist. Figure S1. DENV-1 Maximum Likelihood tree and root-to-tip regression. A) Linear regression of root-to-tip divergence and dates of isolation indicating the slope and R-squared value for temporal signal evaluation. Each datapoint is color-coded based on the corresponding genotype within DENV-1. B) Maximum likelihood tree with 954 full-length E-gene sequences (1485 nt) representing the five genotypes reported for DENV-1. Tips are colored by corresponding genotype and labelled tip indicate the strain obtain in this study. The tree was rooted with the sequence DENV2-NGC strain as outgroup (GenBank: KM204118) and the sequence names are coded as GenBank accession|ISO-3166 Alpha-3 country code|Date of isolation. Figure S2. DENV-3 Maximum Likelihood tree and root-to-tip regression. A) Linear regression of root-to-tip divergence and dates of isolation indicating the slope and R-squared value for temporal signal evaluation. Each datapoint is color-coded based on the corresponding genotype within DENV-3. B) Maximum likelihood tree with 553 full-length E-gene sequences (1479 nt) representing the five genotypes reported for DENV-3. Tips are colored by corresponding genotype and labelled tips indicate the strains obtain in this study. The tree was rooted with the sequence DENV-1-Hawaii strain as outgroup (GenBank: KM204119) and the sequence names are coded as GenBank accession|ISO-3166 Alpha-3 country code|Date of isolation. Figure S3. DENV-4 Maximum Likelihood tree and root-to-tip regression. A) Linear regression of root-to-tip divergence and dates of isolation indicating the slope and R-squared value for temporal signal evaluation. Each datapoint is color-coded based on the corresponding genotype within DENV-4. B) Maximum likelihood tree with 867 full-length E-gene sequences (1485 nt) representing the four genotypes reported for DENV-4. Tips are colored by corresponding genotype and labelled tips indicate the strains obtain in this study. The tree was rooted with the sequence DENV2-NGC strain as outgroup (GenBank: KM204118) and the sequence names are coded as GenBank accession|ISO-3166 Alpha-3 country code|Date of isolation. Figure S4. Root-to-tip analysis for identified genotypes. Linear regression of root-to-tip divergence and date of isolation for the E-gene of DENV-1 (GV), DENV-3 (GIII) and DENV-4 (GIIb) to evaluate the temporal structure of datasets. Each plot shows the R-squared value and slope of the black dashed regression line which indicate the substitution rate for these viruses. The linear regression supports the use of these data for molecular clock inferences. Each datapoint is color-coded based on the geographic area of origin. Table S1. Nucleotide Substitution model selection. Results for the statistical best fit model selection process with jModelTest for each serotype. Table S2. Molecular clock and demographic growth model selection. Marginal likelihoods calculated with path-sampling (PS) and stepping-stone sampling (SS) methods for the combinations of four demographic growth models (constant size, exponential, Bayesian Skyline and Bayesian SkyGrid) and two molecular clock models (strict clock and uncorrelated relaxed clock with log-normal distribution). Bayes factors were calculated against the model combination with the lower marginal likelihood estimation which in all three cases was the constant tree prior and strict clock.
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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 | 0.021 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.761 | 0.071 |
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".