Biology subjects

Marques, D.

Publications and source records attributed to Marques, D..

4 recordsLinked to original sources

bioRxiv2026

Introducing circStudio, a Python package for preprocessing, analyzing and modeling actigraphy data

Actigraphy is a non-invasive and cost-effective method for monitoring behavioral rhythms under real-world conditions by collecting time-resolved measurements of locomotor activity, light exposure, and temperature. Although several open-source packages support specific aspects of actigraphy analysis, aspects such as preprocessing, metric calculation, and mathematical modeling are often distributed across separate software packages, limiting interoperability and increasing programming overhead. Here we introduce circStudio, a Python package that unifies actigraphy data processing and mathematical modeling of circadian rhythms within a single framework. Built from the pyActigraphy codebase and integrating circadian models from the Arcascope circadian package, circStudio provides flexible preprocessing tools, support for multiple actigraphy file formats through adaptor classes, standalone functions for computing commonly used actigraphy metrics, and implementations of several mathematical models of circadian rhythms. The package enables users to move efficiently from raw wearable data to physiologically interpretable circadian outputs. Ultimately, circStudio aims to facilitate reproducible workflows and to provide a flexible foundation for research applications across circadian biology, sleep science, and digital health.

bioinformatics↗

bioRxiv2025

Circadian disruption beneath the surface: a screening approach to identify actigraphy-based markers of split shift work in submariners

Identifying behavioral markers of disease risk associated with circadian disruption remains challenging due to reproducibility concerns, as human studies are often under-powered to detect the effects of interest. Submarines provide an extreme example of cir-cadian disruption, depriving individuals of natural light-dark cycles and limiting oppor-tunities for physical activity. To address these challenges, we developed an effect size-based method to robustly screen potential actigraphy-derived markers of the submarine environment. Actigraphy data was collected across the pre-mission, mission and post-mission periods. During the mission, crew members followed a 6-hours-on/6-hours-off split shift schedule, except for submariners with on-call duty or extended hours. Forty-one actigraphy variables were screened for their ability to differentiate between study periods and shifts. A Monte Carlo permutation test was used for this initial screening, followed by receiver operating characteristic (ROC) curve analysis for pairwise compar-isons. Light-related features, the slopes of regression lines fitted to the daily predicted dim light melatonin onset (DLMO) trajectories, and Pearson correlation coefficients be-tween each recording day and its corresponding predicted DLMO demonstrated the great-est potential to distinguish between study periods. Most high-performing features dis-criminated between split shift work schedules and on-call or extended-hours schedules. Only the relative amplitude (RA) and the average light intensity during the five least-illuminated hours of the day (L5) reliably distinguished between the shift performing the bulk of nighttime work and its counterpart. Although submarine settings offer an oppor-tunity to study a healthy population living under confined movement and dim light, de-tecting biological signals through actigraphy in this environment is inherently challeng-ing. Demonstrating robust effects under these conditions supports the use of actigraphy in dimly-lit, isolated, confined, and extreme (DICE) environments, but also its applica-bility to study other operational or clinical populations with reduced activity levels.

bioinformatics↗

bioRxiv2024

Circulating (poly)phenol metabolites in the brain: unveiling in vitro and in vivo blood-brain barrier transport

Circulating metabolites resulting from colonic metabolism of dietary (poly)phenols are highly abundant in the bloodstream, though still marginally explored, particularly concerning their brain accessibility. Our goal is to disclose (poly)phenol metabolites blood-brain barrier (BBB) transport, in vivo and in vitro, as well as their role at BBB level. For three selected metabolites, benzene-1,2-diol-3-sulfate/benzene-1,3-diol-2-sulfate (pyrogallol-sulfate - Pyr-sulf), benzene-1,3-diol-6-sulfate (phloroglucinol-sulfate - Phlosulf), and phenol-3-sulfate (resorcinol-sulfate - Res-sulf), BBB transport was assessed in human brain microvascular endothelial cells (HBMEC). Their potential in modulating in vitro BBB properties at circulating concentrations was also studied. Metabolites fate towards the brain, liver, kidney, urine, and blood was disclosed in Wistar rats upon injection. Transport kinetics in HBMEC highlighted different BBB permeability rates, where Pyr-sulf emerged as the most in vitro BBB permeable metabolite. Pyr-sulf was also the most potent regarding BBB properties improvement, namely increased beta({beta})-catenin membrane expression and reduction of zonula occludens-1 membrane gaps. Whereas no differences were observed for transferrin, increased expression of caveolin-1 upon Pyr-sulf and Res-sulf treatments was found. Pyrsulf was also capable of modulating gene and protein expression of some solute carrier transporters. Notably, each of the injected metabolites exhibited a unique tissue distribution in vivo, with the remarkable ability to almost immediately reach the brain.

biochemistry↗

bioRxiv2020

Genomic approach for conservation and the sustainable management of endangered species of the Amazon

A broad panel of potentially amplifiable microsatellite loci and a multiplex system were developed for the Amazonian symbol fish species Arapaima gigas, which is currently in high danger of extinction due to the disorderly fishing exploitation. Several factors have contributed to the increase of this threat, among which we highlight the lack of genetic information about the structure and taxonomic status of the species, as well as the lack of accurate tools for evaluation of the effectivity of current management programs. Based on Arapaima gigas whole genome, available at the NCBI database (ID: 12404), a total of 95,098 unique perfect microsatellites were identified, including their proposed primers. From this panel, a multiplex system containing 12 tetranucleotide microsatellite markers was validated. These tools are valuable for research in as many areas as bioinformatics, ecology, genetics, evolution and comparative studies, since they are able to provide more accurate information for fishing management, conservation of wild populations and genetic management of aquaculture.

genomics↗