Bibliographic record
Abstract
Flow cytometry data on a mock community of bacterial isolates originating from the human body (Escherichia coli K12 (ATCC 25404), Enterococcus faecalis (SF24397), Prevotella intermedia (ATCC 25611), Bacteroides fragilis (32-6-I 11 MRS AN), and Bifidobacterium longum subsp. infantis (ATCC 15697), grown together or separately. The mock community was created by adding OD600 0.05 of the overnight cultures of each isolate to autoclaved reduced Bovine Heart Infusion broth (rBHI). The mock community was incubated for 1 hour, followed by another three hours with (or without) 20 uM 5-ethnyl-2'-deoxyuridine (EdU), a thymidine analogue, to capture the actively replicating cells. The bacterial cells underwent a click reaction with Alexa Fluor 647 azide (APC channel) to make newly replicated bacteria fluoresece. They were also stained with Sybr Green I nucleic acid stain (FITC channel) to capture all bacteria. In the file names: BI = Bifidobacterium longum subsp. infantis BF = Bacteroides fragilis EC = Escherichia coli K12 EF = Enterococcus faecalis PI = Prevotella intermedia
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 | 0.001 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.001 | 0.003 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.234 | 0.111 |
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".