Gokhale, P. | bioRxiv Science

bioRxiv2026

SpectroBird: Event-Level Vocalization Detection and Curation for Avian Ecology

Passive acoustic monitoring often summarizes long recordings as fixed-window presence predictions, but many ecological questions require records of individual vocal events: how many occurred, when they occurred, whether they overlapped, how long they lasted, what frequency band they occupied, and whether each event was complete enough for structural measurement. We address this event-level measurement problem with SpectroBird, a spectrogram-based method for localizing and curating avian vocalizations in noisy field recordings. SpectroBird first applies a detection-localization model to identify candidate vocalizations as time-frequency boxes. An event-consolidation step merges repeated detections from overlapping windows while preserving overlapping vocalizations as separate events. A completeness-curation model then classifies each consolidated event as complete or incomplete before downstream event-level analysis. We demonstrate SpectroBird on breeding-season Hume's Leaf Warbler buzz vocalizations recorded in the Himalaya across a 3,200-3,800 m elevational gradient. Under shared window-level scoring, the detection-localization model remained competitive with AST and YOLOv11-cls baselines while retaining event timing and frequency bounds; event-level evaluation achieved AP > 0.999 for complete buzzes. Applied to two field seasons, the resulting event records showed that duration of complete buzzes declined with elevation, complete-buzz occurrence showed no simple elevation trend, and relative day-of-year occurrence patterns were strongly correlated between years. These results show how event-level detection and curation can support ecological analyses that depend on individual vocalizations rather than fixed-window presence alone.

bioinformatics↗

bioRxiv2019

Nucleosides rescue replication-mediated genome instability of human pluripotent stem cells

Human pluripotent stem cells (PSC) often acquire genetic changes on prolonged culture, which pose concerns for their use in research and regenerative medicine (Amps et al., 2011, Seth et al., 2011). The acquisition of these changes during culture necessarily first requires mutation and then selection of those mutations that provide a growth advantage. Whilst selection accounts for the recurrent nature of the variants commonly reported (Draper et al., 2004, Olariu et al., 2010), the mechanisms of mutation in PSC remain largely elusive. Here we show that, in contrast to somatic cells, human PSC have an increased susceptibility to DNA damage and mitotic errors, both of which are caused by heightened replication stress in PSC and this can be alleviated by culture with exogenous nucleosides. These results reflect the requirement for rapid replication of human PSC enabled by a truncated G1 (Becker et al., 2006, Becker et al., 2010) that impairs the preparation of these cells for the ensuing DNA replication. A similar relationship has been shown in relation to chromosomal instability in cancer cells (Burrell et al., 2013, Wilhelm et al., 2019) but PSC differ by replication stress triggering apoptosis (Desmarais et al., 2012, Desmarais et al., 2016). Nevertheless, evasion of this response still leads to the appearance of genetic variants that are of concern for regenerative medicine. The inclusion of nucleosides into culture media greatly improves the efficiency of human PSC culture and minimises the acquisition of genomic damage.

cell biology↗