Biology subjects

Avila, R.

Publications and source records attributed to Avila, R..

8 recordsLinked to original sources

bioRxiv2026

Convergent evolution of parrotfish beaks enables stress redistribution during high-force feeding

Convergent evolution is often interpreted as evidence that similar ecological challenges select for optimal functional solutions, yet the biomechanical mechanisms underlying such convergence remain poorly resolved. Parrotfishes independently evolved fused, beak-like dentition multiple times, a trait associated with feeding on hard substrates such as coral, but its advantage has not been quantified. Here, we combine finite element analysis with shockwave modeling to evaluate the performance of the beak during feeding. Across five species spanning independent evolutionary origins of beaked and non-beaked dentitions, we find that jaw opening is governed primarily by geometric scaling, with minimal influence from dentition morphology. In contrast, under stabilized biting, fused dentition reduces the rate of stress accumulation relative to discrete teeth, indicating a functional advantage under constrained loading. Shockwave modeling further shows that tooth geometry and stacking regulate stress propagation: smooth profiles reduce stress concentration, while stacked architectures localize stresses within the tooth material and limit transmission into the surrounding bone. These results suggest that convergent beak evolution in parrotfish reflects repeated optimization for stress management under constrained and impact loading, and reveals a general principle by which biological structures control internal force transmission during high-force feeding rather than maximize strength alone.

evolutionary biology↗

bioRxiv2026

Mechanics of Esophageal Retraction During Anterior Cervical Discectomy and Fusion

Dysphagia, difficulty swallowing due to irritation or damage to the esophagus, is one of the most common complications following anterior cervical discectomy and fusion (ACDF), the most frequently performed cervical spine procedure in the United States. Surgical retraction hardware imposes sustained compression on the esophagus during surgery, generating nonuniform stress and strain fields that may contribute to temporary postoperative soft tissue damage. Current intraoperative assessment relies on visual inspection and manual inspection by the surgical team and does not provide quantitative measures of esophageal deformation, strain, or retraction displacement. Here, we present a comprehensive mechanics analysis of esophageal compression during ACDF that integrates experiments on esophageal phantoms, nonlinear finite element modeling, and theoretical thick-wall scaling relationships. Modeling results quantify peak contact pressures and corresponding stress distributions, identifying conditions under which circumferential strain in the compressed esophageal wall increases sharply as localized pressures approach the upper physiological range ([~]6-17 kPa). Parametric investigation of retractor blade width, placement depth, and polymeric biocompatible coating properties demonstrates that targeted, yet mechanically simple, design modifications can help to attenuate strain concentrations. In particular, the introduction of compliant polymeric coatings redistributes contact loads and reduces peak wall stress by up to 20% relative to unbuffered blades (17 kPa to 13.5 kPa). Increasing blade width from 20 mm to 50 mm further decreases peak interface stress from 2.48 kPa to 0.45 kPa, corresponding to an 82% reduction. Reducing these stresses may help limit mechanically induced complications such as postoperative dysphagia. Experiments performed on esophageal phantoms with embedded pressure sensors replicate surgical ACDF retraction protocols under displacement-controlled conditions. This setup establishes physiologically relevant loading and enables quantitative validation of computational predictions by correlating measured voltage output with contact pressure and esophageal deformation. Measured relationships between applied retraction displacement, contact pressure, and tissue deformation govern stress amplification during ACDF retraction. Together, these results establish a predictive mechanics framework that links retractor blade design variables to esophageal stress fields, providing quantitative criteria to mitigate soft tissue damage during ACDF. HIGHLIGHTSO_LI2D and 3D finite element models quantify esophageal wall stress during anterior cervical discectomy and fusion (ACDF) retraction. C_LIO_LIRetractor blade geometry influences stress distribution, with wider blades reducing localized tissue loading by up to 82% likely associated with post-surgical dysphagia. C_LIO_LICompliant polymeric buffer layers attenuate pressure and smoothen stress gradients to reduce peak tissue loading by up to 20% during retraction. C_LI

bioengineering↗

bioRxiv2026

Bioabsorbable Magnesium Metal ScaffoldsImprove Dermal Wound Healing and Tissue Regeneration

ObjectiveEvaluate the effects of bioabsorbable magnesium wires on dermal wound healing and tissue regeneration in a murine full-thickness wound model. Approach6 mm diameter stented dorsal skin wounds were created in C57BL/6J mice and treated with implanted WE43B magnesium alloy wires or PBS control. Wound healing was evaluated on days 7 and 28 by histology, immunohistochemistry, and micro-CT. Finite element analysis modeled mechanical strain distribution due to wire degradation during healing. ResultsAt day 7, magnesium wire-treated wounds showed 100% improved granulation tissue formation, reduced inflammation (37% fewer CD45+ leukocytes and 37% fewer F4/80+ macrophages), increased neovascularization (91% more CD31+ lumens), and 74% more nerve bundles. Improved wound closure (mean difference -1.48 mm) did not reach statistical significance (d = 1.06). By day 28, magnesium-treated wounds showed improved collagen organization and normalized epidermal thickness. The increase in dermal appendages (247%), and vascular density (41%) did not reach statistical significance. Micro-CT confirmed progressive wire degradation. Modeling revealed that degrading wires dynamically altered strain gradients in healing tissue, thereby modulating the spatial mechanical cues that govern fibroblast migration and extracellular matrix (ECM) remodeling. InnovationMagnesium is an essential trace element involved in cellular processes critical to wound repair, including angiogenesis, nerve growth, inflammation modulation, and ECM remodeling. Previous magnesium delivery systems incorporated polymers or other confounding materials that degrade rapidly. We directly applied bioabsorbable pure magnesium metal to provide sustained ion release and favorable mechanical properties to support regenerative healing. ConclusionBioabsorbable magnesium wires support regenerative wound healing by reducing inflammation, enhancing neovascularization, and promoting favorable ECM remodeling without adverse inflammatory reactions. These findings provide a strong rationale to harness magnesium metal use in wound healing applications.

bioengineering↗

bioRxiv2025

Local optogenetic control of genome editing and tumorigenesis in vivo using wireless implantable optoelectronics

Precise spatial regulation of site-specific DNA recombination (SSR) in vivo remains a challenge due to limited tunability of current platforms. Here, we present an optogenetic approach that overcome these limitations by employing engineered light-regulated recombinase E-LightR-Cre and tunable wireless implantable optoelectronic devices. E-LightR-Cre meets the key criteria for spatial regulation of SSR in vivo, showing no detectable activity in the dark, while demonstrating robust activation upon blue-light illumination. To achieve local E-LightR-Cre activation in murine lungs, we developed wireless, fully-implantable optoelectronic devices enabling focal illumination with no discernible organ damage. By modulating illumination intensity and duration, we can control the size of the activated area. Local expression of oncogenic KRas-G12D in a photoactivated subpopulation of cells in vitro revealed rapid reprogramming of the mutant expressing cells and their non-activated neighbors. Light-guided activation of E-LightR-Cre in mouse lungs resulted in focal expression of a reporter gene and allowed us to induce local formation of oncogenic lesions in vivo.

bioengineering↗

bioRxiv2024

An Autonomous Implantable Device for the Prevention of Death from Opioid Overdose

Opioid overdose accounts for nearly 75,000 deaths per year in the United States, representing a leading cause of mortality amongst the prime working age population (25-54 years). At overdose levels, opioid-induced respiratory depression becomes fatal without timely administration of the rescue drug naloxone. Currently, overdose survival relies entirely on bystander intervention, requiring a nearby person to discover and identify the overdosed individual, and have immediate access to naloxone to administer. Government efforts have focused on providing naloxone in abundance but do not address the equally critical component for overdose rescue: a willing and informed bystander. To address this unmet need, we developed the Naloximeter: a class of life-saving implantable devices that autonomously detect and treat overdose, with the ability to simultaneously contact first-responders. We present three Naloximeter platforms, for both fundamental research and clinical translation, all equipped with optical sensors, drug delivery mechanisms, and a supporting ecosystem of technology to counteract opioid-induced respiratory depression. In small and large animal studies, the Naloximeter rescues from otherwise fatal opioid overdose within minutes. This work introduces life-changing, clinically translatable technologies that broadly benefit a susceptible population recovering from opioid use disorder.

bioengineering↗

bioRxiv2024

An integrated microfluidic and fluorescence platform for probing in vivo neuropharmacology

Neurotechnologies and genetic tools for dissecting neural circuit functions have advanced rapidly over the past decade, although the development of complementary pharmacological method-ologies has comparatively lagged. Understanding the precise pharmacological mechanisms of neuroactive compounds is critical for advancing basic neurobiology and neuropharmacology, as well as for developing more effective treatments for neurological and neuropsychiatric disorders. However, integrating modern tools for assessing neural activity in large-scale neural networks with spatially localized drug delivery remains a major challenge. Here, we present a dual microfluidic-photometry platform that enables simultaneous intracranial drug delivery with neural dynamics monitoring in the rodent brain. The integrated platform combines a wireless, battery-free, miniaturized fluidic microsystem with optical probes, allowing for spatially and temporally specific drug delivery while recording activity-dependent fluorescence using genetically encoded calcium indicators (GECIs), neurotransmitter sensors GRABNE and GRABDA, and neuropeptide sensors. We demonstrate the performance this platform for investigating neuropharmacological mechanisms in vivo and characterize its efficacy in probing precise mechanistic actions of neuroactive compounds across several rapidly evolving neuroscience domains.

neuroscience↗

bioRxiv2023

Multifunctional Materials Strategies for Enhanced Safety of Wireless, Skin-Interfaced Bioelectronic Devices

Many recently developed classes of wireless, skin-interfaced bioelectronic devices rely on conventional thermoset silicone elastomer materials, such as poly(dimethylsiloxane) (PDMS), as soft encapsulating structures around collections of electronic components, radio frequency antennas and, commonly, rechargeable batteries. In optimized layouts and device designs, these materials provide attractive features, most prominently in their gentle, noninvasive interfaces to the skin even at regions of high curvature and large natural deformations. Past work, however, overlooks opportunities for developing variants of these materials for multimodal means to enhance the safety of the devices against failure modes that range from mechanical damage to thermal runaway. This paper presents a self-healing PDMS dynamic covalent matrix embedded with chemistries that provide thermochromism, mechanochromism, strain-adaptive stiffening, and thermal insulation, as a collection of attributes relevant to safety. Demonstrations of this materials system and associated encapsulation strategy involve a wireless, skin-interfaced device that captures mechanoacoustic signatures of health status. The concepts introduced here can apply immediately to many other related bioelectronic devices.

bioengineering↗

bioRxiv2021

BioThings SDK: a toolkit for building high-performance data APIs in biomedical research

SummaryTo meet the increased need of making biomedical resources more accessible and reusable, Web APIs or web services have become a common way to disseminate knowledge sources. The BioThings APIs are a collection of high-performance, scalable, annotation as a service APIs that automate the integration of biological annotations from disparate data sources. This collection of APIs currently includes MyGene.info, MyVariant.info, and MyChem.info for integrating annotations on genes, variants, and chemical compounds, respectively. These APIs are used by both individual researchers and application developers to simplify the process of annotation retrieval and identifier mapping. Here, we describe the BioThings Software Development Kit (SDK), a generalizable and reusable toolkit for integrating data from multiple disparate data sources and creating high-performance APIs. This toolkit allows users to easily create their own BioThings APIs for any data type of interest to them, as well as keep APIs up-to-date with their underlying data sources. Availability and implementationThe BioThings SDK is built in Python and released via PyPI (https://pypi.org/project/biothings/). Its source code is hosted at its github repository (https://github.com/biothings/biothings.api).

bioinformatics↗