Circadian Rhythms in <i>Neurospora</i> Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations
Bibliographic record
Abstract
Circadian rhythms are endogenous cycles of approximately 24 hours reinforced by external cues such as light. These cycles are typically modeled as harmonic oscillators with fixed amplitude peaks. Using experimental data measuring global gene transcription in Neurospora crassa over 48 hours in the dark (i.e. with external queues removed), we demonstrate that many circadian genes frequently exhibit either damped harmonic oscillations, in which the peak amplitudes decrease each day, or driven harmonic oscillations, in which the peak amplitudes increase each day. By fitting extended harmonic oscillator models which include a damping ratio coefficient, we detected additional circadian genes that were not identified by the current standard tools that use fixed amplitude waves as reference, e.g. JTK_CYCLE. Functional Catalogue analysis confirms that our identified damped or driven genes exhibit distinct biological functions. The application of extended damped/driven harmonic oscillator models thus can elucidate, not only previously unidentified circadian genes, but also characterize gene subsets with expression patterns of biological relevance. Thus, expanded harmonic oscillators provide a powerful new tool for circadian system biology.
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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 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".