Biology subjects

Davila, D.

Publications and source records attributed to Davila, D..

3 recordsLinked to original sources

bioRxiv2021

FlywheelTools: Data Curation and Manipulation on the Flywheel Platform

The recent and growing focus on reproducibility in neuroimaging studies has led many major academic centers to use cloud-based imaging databases for storing, analyzing, and sharing complex imaging data. Flywheel is one such database platform that offers easily accessible, large-scale data management, along with a framework for reproducible analyses through containerized pipelines. The Brain Imaging Data Structure (BIDS) is a data storage specification for neuroimaging data, but curating neuroimaging data into BIDS can be a challenging and time-consuming task. In particular, standard solutions for BIDS curation are not designed for use on cloud-based systems such as Flywheel. To address these challenges, we developed "FlywheelTools", a software toolbox for reproducible data curation and manipulation on Flywheel. FlywheelTools includes two elements: fw-heudiconv, for heuristic-driven curation of data into BIDS, and flaudit, which audits and inventories projects on Flywheel. Together, these tools accelerate reproducible neuroscience research on the widely used Flywheel platform.

bioinformatics↗

bioRxiv2019

Accelerated Cortical Thinning within Structural Brain Networks is Associated with Irritability in Youth

BackgroundIrritability is an important dimension of psychopathology that spans multiple clinical diagnostic categories, yet its relationship to patterns of brain development remains sparsely explored. Here, we examined how trans-diagnostic symptoms of irritability relate to the development of structural brain networks.\n\nMethodsAll participants (n=144, 87 females) completed structural brain imaging with 3 Tesla MRI at two timepoints (mean age at follow-up: 20.9 years, mean inter-scan interval: 5.1 years). Irritability at follow-up was assessed using the Affective Reactivity Index, and cortical thickness was quantified using Advanced Normalization Tools software. Structural covariance networks were delineated using non-negative matrix factorization, a multivariate analysis technique. Both cross-sectional and longitudinal associations with irritability at follow-up were evaluated using generalized additive models with penalized splines. The False Discovery Rate (q<0.05) was used to correct for multiple comparisons.\n\nResultsCross-sectional analysis of follow-up data revealed that 11 of the 24 covariance networks were associated with irritability, with higher levels of irritability being associated with thinner cortex. Longitudinal analyses further revealed that accelerated cortical thinning within 9 networks was related to irritability at follow-up. Effects were particularly prominent in brain regions implicated in emotion regulation, including the orbitofrontal, lateral temporal, and medial temporal cortex.\n\nConclusionsCollectively, these findings suggest that irritability is associated with widespread cortical thickness reductions and accelerated cortical thinning, particularly within frontal and temporal cortex. Aberrant structural maturation of regions important for emotional regulation may in part underlie symptoms of irritability.

neuroscience↗

bioRxiv2017

Hypoosmolar dose-dependent swelling occurs in both pyramidal neurons and astrocytes in acute hippocampal slices

Normal nervous system function is critically dependent on the balance of water and ions in the extracellular space. Pathological reduction in brain interstitial osmolarity results in osmotically-driven flux of water into cells, causing cellular edema which reduces the extracellular space and increases neuronal excitability and risk of seizures. Astrocytes are widely considered to be particularly susceptible to cellular edema due to selective expression of the water channel aquaporin-4 (AQP4). The apparent resistance of pyramidal neurons to osmotic swelling has been attributed to lack of functional water channels. In this study we report rapid volume changes in CA1 pyramidal cells in hypoosmolar ACSF (hACSF) that are equivalent to volume changes in astrocytes across a variety of conditions. Astrocyte and neuronal swelling was significant within 1 minute of exposure to 17 or 40% hACSF, was rapidly reversible upon return to normosmolar ACSF, and repeatable upon re-exposure to hACSF. Neuronal swelling was not an artifact of patch clamp, occurred deep in tissue, was similar at physiological vs. room temperature, and occurred in both juvenile and adult hippocampal slices. Neuronal swelling was neither inhibited by TTX, nor by antagonists of NMDA or AMPA receptors, suggesting that it was not occurring as a result of excitotoxicity. Surprisingly, genetic deletion of AQP4 did not inhibit, but rather augmented, astrocyte swelling in severe hypoosmolar conditions. Taken together, our results indicate that neurons are not osmoresistant as previously reported, and that osmotic swelling is driven by an AQP4-independent mechanism.

neuroscience↗