Additional file 1 of Epidemiology and genetic diversity of circulating dengue viruses in Medellin, Colombia: a fever surveillance study
Notice bibliographique
Résumé
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.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,002 | 0,021 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,000 |
| Méta-épidémiologie (sens large) | 0,001 | 0,001 |
| Bibliométrie | 0,003 | 0,005 |
| Études des sciences et des technologies | 0,001 | 0,000 |
| Communication savante | 0,001 | 0,001 |
| Science ouverte | 0,001 | 0,001 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,761 | 0,071 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».