Engineering a colorimetric yeast-based assay to detect small molecules in the gastrointestinal system
Bibliographic record
Abstract
The procedures involved in diagnoses of intestinal diseases are often costly, invasive, expensive and dependent on specific technical expertise; these factors can hinder clinicians’ efforts to monitor and treat inflammatory bowel disease and other conditions. Simpler, less expensive and more widely accessible methods could help evaluate the efficacy of treatments and assess the risk of relapse. Yeast, including the probiotic strain Saccharomyces boulardii, can access the gastrointestinal tract, coming into contact with otherwise difficult-to-access disease biomarkers. These yeast cells can be recovered from patient stool samples after ingestion and used to report on prevailing conditions within the gastrointestinal tract during their passage. Here, we report a yeast-based assay offering a simple output based on colour change of colonies plated from recovered stool samples and demonstrate that the reporter can respond to an externally-supplied small-molecule signal while passing through the gastrointestinal system of mice.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".