Bio Constraint Sweep

Biological responses to stress often exhibit path dependence: the trajectory during recovery may not retrace the trajectory during onset, even when the control parameter returns toward baseline. We operationalize this idea as a constraint-sweep hysteresis test on transcriptomic time series. Using GEO Series GSE74793 (rice leaf RNA-seq under heat and drought stress with recovery; Wilkins et al., 2016), we define a low-assumption “state” as PC1 of the submitter-provided processed expression matrix (DESeq2-normalized, variance-stabilized) and quantify hysteresis as the integral of the absolute separation between onset and recovery curves over their shared time window. A permutation null is constructed by shuffling phase labels within time bins, preserving temporal structure. In genotype-stratified analyses across four cultivars, heat stress exhibits strong hysteresis for Azucena and Pandan Wangi (permutation p = 1/20,001 ≈ 5.0×10⁻⁵, permutation floor, at 20,000 permutations), while drought serves as a negative comparator and does not show comparable signal. All code, inputs, and outputs are packaged as a one-command reproducible outsider packet (a self-contained archive designed for independent replication without prior project context).

**Keywords: **hysteresis; path dependence; time series; transcriptomics; stress response; permutation test; reproducibility; rice