Andrade, D. | Search bioRxiv

bioRxiv2026

Supporting Metadata Curation from Public Life Science Databases Using Open-Weight Large Language Models

Although the Gene Expression Omnibus and other public repositories are expanding rapidly, curation across these databases has not kept pace. Data reuse is often hindered by unstandardized metadata comprising unstructured text. To address this, we developed a workflow that combines retrieval via application programming interfaces with semantic filtering using large language models (LLMs) to support metadata screening as an initial step in broader curation workflows. As a focused pilot evaluation, we benchmarked multiple LLMs using metadata from 150 candidate Arabidopsis RNA-seq projects to classify projects containing exogenous ABA-treated samples and matched untreated controls. Simple keyword searches yielded many false positives (F1=0.59); classification using LLMs significantly improved performance. Several open-weight models achieved near-perfect classification performance in this defined task (F1>0.98), comparable to that of closed models. We also found that, for some high-performing models, self-reported confidence scores may help identify high-confidence cases that can be prioritized for automated processing. These results suggest that open-weight LLMs can support scalable metadata screening in local environments as an initial step in broader curation workflows, providing a foundation for accelerating public dataset reuse.

bioinformatics↗

bioRxiv2022

Energetic costs of bill heat exchange demonstrate contributions to thermoregulation at high temperatures in toco toucans (Ramphastos toco)

Body temperature regulation in the face of changes in ambient temperature and/or in metabolic heat production involves adjustments in heat exchange rates between the animal and the environment. One of those mechanisms include the modulation of the surface temperature of specific areas of the body through vasomotor adjustment and blood flow control, to change the thermal conductance of this region, thereby promoting dissipation or conservation of body heat. In homeotherms, this thermoregulatory adjustment is essential for the maintenance of body temperature over a moderate temperature range, known as the thermal neutral zone (TNZ), without increasing metabolic rate (MR). Thermal windows are poorly insulated body regions and highly vascularized that are particularly efficient for heat dissipation through that mechanism. The bill of the toco toucan (Ramphastos toco) has been described as a highly efficient thermal window and hypothesized to assist in the thermal homeostasis of this bird. Herein, we directly evaluated the contribution of heat exchange through the bill of the toco toucan and role of the bill in the delimitation of the TNZ. To do this, we measured metabolic rate, via oxygen consumption, over a range of ambient temperature from 0 to 35{degrees}C (every 5{degrees}C). MR measurements were made in birds with the bill intact (control group) and with the bill artificially insulated (experimental group). The limits of the TNZ, 10.9-25.0{degrees}C for the control group and 10.8-24.1{degrees}C for the experimental group, did not differ between the treatments. MR differed among treatments only at elevated temperatures (30 and 35{degrees}C), reaching values of 0.97 ml O2{middle dot}g-1{middle dot}h-1{middle dot}{degrees}C-1 ({+/-} 0.06) for the control group and 1.20 ml O2{middle dot}g-1{middle dot}h-1{middle dot}{degrees}C-1 ({+/-} 0.07) for the experimental group at 35{degrees}C. These results indicate that while heat dissipation through the bill does not contribute significantly to widening of the TNZ, it may well be critically important in assisting body temperature regulation at higher temperatures extending above the upper limit of the TNZ. We estimate that the contribution of the bill to total heat exchange approaches 31% of basal metabolic heat production, providing evidence of the substantial role of peripheral heat exchange and linking the role of appendage size as a key factor in the evolution of thermoregulatory responses in endotherms.

zoology↗