Additional file 2: Figure S1. of Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America
Bibliographic record
Abstract
Maximum Likelihood phylogeny depicting the inferred relationship among fusion gene sequences for APMV-1 class I isolates available on The National Center for Biotechnology Information GenBank as of 26 August 2016 (n = 211). The tree with the highest log likelihood (−14761.8677) is shown. Bootstrap support values ≥ 60 are shown. The tree is drawn to scale, with branch lengths depicting the number of substitutions per site. All positions containing gaps and missing data were eliminated. There were a total of 1662 positions in the final dataset. Branch tips include sub-genotypes assigned to major clades meeting criteria described by Diel et al. (2012; U = unclassified), followed by the GenBank accession number, host name, country of isolation, strain designation and year of isolation (if available). Sequences generated for this study are indicated with asterisks (***). Figure S2. Maximum Likelihood phylogeny depicting the inferred relationship among fusion gene sequences for APMV-1 class II isolates available on The National Center for Biotechnology Information GenBank as of 26 August 2016 (n = 1272). The tree with the highest log likelihood (−82565.4161) is shown. Bootstrap support values > 60 are shown. The tree is drawn to scale, with branch lengths depicting the number of substitutions per site. All positions containing gaps and missing data were eliminated. There were a total of 1644 positions in the final dataset. Branch tips include sub-genotypes assigned to major clades meeting criteria described by Diel et al. (2012; U = unclassified), followed by the GenBank accession number, host name, country of isolation, strain designation and year of isolation (if available). Sequences generated for this study are indicated with asterisks (***). Figure S3. Maximum Likelihood phylogenetic tree depicting the inferred genetic relationship among fusion gene sequences for 180 APMV-1 isolates originating from samples collected from wild birds in North America. Bootstrap support values for major clades are shown. Sequences generated for this study are indicated with asterisks (***). Taxonomic order of host (Anseriformes = square, Charadriiformes = triangle, Suliformes = circle, Pelecaniformes = star) and region of sample collection (Alaska = red, Canada = yellow, West = orange, Midwest = blue, Gulf Coast = black, East = green) are indicated. (PDF 1177 kb)
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.022 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.006 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.841 | 0.165 |
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".