Factors influencing the detection of bacterial cells using fluorescence in situ hybridization (FISH): A quantitative review of published reports
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
Abstract Fluorescence in situ hybridization (FISH) is widely used to describe bacterial community composition and, to a lesser extent, to describe the physiological state of cells. One of the limitations of the technique is that the effectiveness of the detection of target cells appears to vary widely. Here, we present a quantitative review of published reports on the percentage of cells detected using the common EUB338 probe (%Eub) in aquatic ecosystems. The %Eub varies from 1 to 100% in the different published reports, with an average of 56%. There is a methodological component in this variation, with a significant effect of the fluorochrome type and the stringency conditions of the reaction. But there is also a strong environmental component, and the type of ecosystem and dominant phylogenetic group significantly influence %Eub. We argue that the optimization of the FISH protocol to describe the phylogenetic composition of bacterial assemblages will probably lead to techniques that are not effective to describe the physiological state of cells.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.002 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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 it