Biology subjects

Salas, R.

Publications and source records attributed to Salas, R..

3 recordsLinked to original sources

bioRxiv2026

PINN-ing the Balloon: A Physically Informed Neural Network Modelling the Nonlinear Haemodynamic Response Function in MRI

Accurate characterisation of the haemodynamic response function (HRF) is central to interpreting blood-oxygen-level-dependent (BOLD) signals in functional magnetic resonance imaging, yet standard estimation approaches remain centred around phenomenological formulations lacking biophysical grounding. We present a proof-of-concept methodological study: a physics-informed neural network (PINN) framework that bridges these paradigms by embedding the Balloon-Windkessel model directly into the training objective of a multi-headed neural network. Our approach simultaneously estimates probable latent neurovascular state variables such as cerebral blood inflow, metabolic rate of oxygen consumption, blood volume, and deoxyhaemoglobin content, through an indirect optimisation scheme in which the predicted BOLD signal is obtained via convolution of the estimated HRF with experimental stimuli. Training is governed by a composite loss, balancing differential-equation residuals, hard physics regularisation term, physiological initial conditions and data fidelity. In simulations with temporal signal-to-noise ratios representative of clinical acquisitions, the framework recovered ground-truth state variables with coefficients of determination exceeding 0.95 and mean squared errors below 10-3, at a physics-to-data weighting of 0.40:0.60. Application to 1.5 T block-design clinical data from an ischaemic stroke patient provides feasibility testing, yielding physiologically plausible, subject-specific HRF estimates, establishing feasibility of single-subject, physics-constrained HRF inference without reliance on fixed gamma basis assumptions. To our knowledge, this constitutes the first deployment of a single PINN incorporating the full Balloon-Windkessel model within an indirect training objective, reconstructing full BOLD observations, thereby positioning PINN-based haemodynamic modelling as a principled and personalised route towards more interpretable and patient-specific biomarkers.

neuroscience↗

bioRxiv2026

Imminent invasion of the chytrid fungus threatens the last naive amphibian biodiversity hotspots

While the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is driving catastrophic biodiversity loss worldwide, some amphibian communities persist seemingly unaffected despite occurring in climates conducive to pathogen establishment. These amphibian communities may remain epidemiologically naive. As mitigation of Bd is rarely successful after establishment, identifying remaining Bd-free refuges is imperative. Presently, the only known large-scale Bd-free refuge is the island of New Guinea (NG), safeguarding Australasias amphibian phylogenetic diversity otherwise devastated by Bd. Following extensive multi-year disease surveillance, we here uncover a second large-scale Bd-free refuge in the Sierra Nevada de Santa Marta (SNSM), a Neotropical biodiversity hotspot in northern Colombia. We detected no evidence of Bd in SNSM-wide screening, while we uncovered the presence of hypervirulent Bd-GPL in adjacent areas of the tropical Andes. Population genomic analyses in an SNSM-endemic anuran found no evidence for demographic bottlenecks indicative of cryptic epizootic decline. Niche modelling highlights the high risk for Bd establishment and Bd-induced declines in both the SNSM and NG, and the important role of lowland environmental barriers in restricting Bd invasion. Infection trials using three SNSM-endemic amphibians reveal varying disease susceptibility. Together, these data identify the SNSM as an epidemiologically naive refuge likely facing imminent Bd invasion, which could result in the loss of at least 25 endemic amphibian species. We highlight the urgent need for proactive conservation action and strict implementation of biosecurity to safeguard the unique and vast amphibian diversity of the worlds last major Bd-free refuges. Significance StatementAmphibian chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) has driven unprecedented global biodiversity loss. The Neotropics and Australasia comprise epicenters of declines. Identifying remaining Bd-free refuges is crucial to curb further amphibian extinctions, but so far contemporary absence of Bd has only been demonstrated for New Guinea. Here we identify the last known major Bd-free biodiversity hotspot in the Neotropics: the Sierra Nevada de Santa Marta (SNSM) in Colombia. Our results show that amphibian communities in this hotspot are immunologically naive despite occurrence of hypervirulent Bd lineages nearby and climatic conditions within the SNSM conducive to Bd-induced declines. This creates an imminent risk for Bd-driven declines and highlights the urgent need for preventive actions to avert another wave of biodiversity loss.

ecology↗

bioRxiv2024

Light exposure induces phenotypic plasticity of the upside-down jellyfish Cassiopea and its endosymbiotic dinoflagellates

The upside-down jellyfish, Cassiopea, is an increasingly popular model organism gaining prominence for both its endosymbiotic dinoflagellates from the family Symbiodiniaceae and its behavioral changes of bell pulsations associated with environmental cues. Pulsation provides a unique window into the hosts response to environmental conditions, a typically difficult to access component of other symbiotic cnidarians. Pulsation has also been hypothesized to play a regulatory role on the endosymbiotic assemblage, but the magnitude of this regulatory effect is not well understood. Here, we used two light-acclimation experiments to help disentangle the complex phenotypic responses of the cnidarian host and its endosymbiotic dinoflagellates. The first experiment examined the phenotypic plasticity (size, behavior, color) of Cassiopea sp. in response to repeated ambient light acclimation trials to determine the rate and magnitude of phenotypic plasticity. The second experiment compared the acclimation response of jellyfish across three experimental groups to test whether a variable environment and resulting short acclimation times destabilized the host-endosymbiont relationship. Our goal was to identify covarying host-endosymbiont phenotypes to gain new insights into the dynamics of this relationship. We employed flow cytometric phenotypic profiling for high-throughput phenotypic characterization of endosymbiotic dinoflagellates in addition to pulse-amplitude modulated (PAM) fluorometry to characterize photosynthetic efficiency (Fv/Fm). Host phenotypes responded predictably to light-dark cycles, and stabilized after nine to twelve days of exposure to consistent light conditions. However, disruption of this acclimation period affected both the hosts circadian rhythm and the endosymbionts phenotypic profile. We also found evidence that phenotypic responses of the host and endosymbionts were generally decoupled, indicating a stronger regulatory response of light conditions on phenotypes than possible host-regulatory strategies on the endosymbiotic assemblage. This study provides unique insights into the acclimation strategies of upside-down jellyfish, an emerging model for the study of cnidarian-dinoflagellate symbiosis. HighlightsO_LICassiopea behavior and color respond predictably to changing light conditions C_LIO_LIInadequate acclimation time destabilizes the hosts circadian rhythm and causes unique phenotypic characteristics of the endosymbionts C_LIO_LILight may be a stronger influence on host and endosymbiont phenotypes than host-endosymbiont relationships C_LI

ecology↗