Biology subjects

Karimi, F.

Publications and source records attributed to Karimi, F..

3 recordsLinked to original sources

bioRxiv2025

Shaping a Collaborative, Sustainable, Accessible, and Reproducible Future for Computational Modeling

The o2S2PARC platform is an open-source, extensible, and scalable cloud-based platform developed in the context of the U.S. National Institutes of Health SPARC program to support collaborative, sustainable, FAIR (findable, accessible, interoperable, reusable) and reproducible computational modeling and analysis. This publication presents the main features of o2S2PARC, its underlying approaches and philosophy, innovative aspects of the developed technologies, while also drawing attention to its rapid adoption. The paper showcases a variety of applications and use cases enabled by the platform. These include hybrid electromagnetic-electrophysiology simulations of neural interfaces, personalized brain and spinal cord stimulation planning, in silico device safety assessments, the training and application of AI systems (e.g., for model-predictive control and medical image segmentation), hybridized surrogate modeling and multi-objective optimization in high-dimensional parameter spaces, sensitive and unbiased validation of measurement devices, and interactive data analysis as paper supplements.

neuroscience↗

bioRxiv2025

Evaluating Flow-Focused Microfluidic Device Fabrication Techniques for Silk Fibroin Microgel Production

Microgels, or micro-scale hydrogels, are versatile emerging biomaterials. They absorb large amounts of water and facilitate molecule transfer. Their tunable size and shape and the capacity to form 3D scaffolds with microscale porosity offer significant advantages over traditional bulk hydrogels. Various strategies exist for fabricating microgels with microfluidic techniques offering the most control of microgel properties. This study compares three microfluidic device fabrication techniques--maskless photolithography, laser engraving, and 3D printing--for making photo-crosslinked silk fibroin microgels. Silk microgels were fabricated via water-in-oil microfluidics and crosslinked through di-tyrosine bonds between native tyrosine residues in silk. Microfluidic devices with target channel depths of 50, 100, or 400 {micro}m were successfully fabricated, with each technique offering unique advantages and limitations. Maskless photolithography provided the highest channel patterning accuracy and smoothest profiles but was costly and required specialized facilities. Laser engraving was affordable but labor-intensive, with lower accuracy in the X-Y plane for deeper channels. 3D printing was user-friendly and affordable but resulted in low accuracy for 50 {micro}m channels and rougher channel profiles, leading to larger microgels and less efficient microgel formation than the other techniques. Spherical silk microgels with diameters between 50 {micro}m and > 400 {micro}m were produced by modulating channel depth and flow rates, while rod-shaped microgels were made by crosslinking in the outlet tubing. Silk molecular weight was adjusted to control surface porosity and compressive modulus, with lower molecular weight silk resulting in higher porosity and softer microgels (modulated between [~] 40 kPa and [~] 590 kPa) while maintaining consistent size. This study demonstrates the versatility and effectiveness of different microfluidic device fabrication techniques for producing photo-crosslinked silk microgels with tunable properties for biomedical applications.

bioengineering↗

bioRxiv2024

Safety of Non-invasive Brain Stimulation in Patients with Implants: A Computational Study

ObjectiveNon-invasive brain stimulation (NIBS) methodologies, such as transcranial electric (tES) and magnetic stimulation are increasingly employed for therapeutic, diagnostic, or research purposes. The concurrent presence of active or passive implants can pose safety risks, affect the NIBS delivery, or generate confounding signals. A systematic investigation is required to understand the interaction mechanisms, quantify exposure, assess safety, and establish guidance for NIBS applications. ApproachWe used measurements, simplified generic, and detailed anatomical modeling to: (i) systematically analyze exposure conditions with passive and active implants, considering local field enhancement, exposure dosimetry, tissue heating and neuromodulation, capacitive lead current injection, low-impedance pathways between electrode contacts, and insulation damage; (ii) identify safety metrics and efficient prediction strategies; (iii) quantify these metrics in relevant exposure cases and (iv) identify worst case conditions. Various aspects including implant design, positioning, scar tissue formation, anisotropy, and frequency were investigated. ResultsAt typical tES frequencies, local enhancement of dosimetric exposure quantities can reach up to one order of magnitude for DBS and SEEG implants (more for elongated passive implants), potentially resulting in unwanted neuromodulation that can confound results but is still 2-3 orders of magnitude lower than active DBS. Under worst-case conditions, capacitive current injection in the lead of active implants can produce local exposures of similar magnitude as the passive field enhancement, while capacitive pathways between contacts are negligible. Above 10 kHz, applied current magnitudes increase, necessitating consideration of tissue heating. Furthermore, capacitive effects become more prominent, leading to current injection that can reach DBS-like levels. Adverse effects from abandoned/damaged leads in direct electrode vicinity cannot be excluded. SignificanceSafety related concerns of tES application in the presence of implants are systematically identified and explored, resulting in specific and quantitative guidance and establishing a basis for safety standards. Furthermore, several methods for reducing risks are suggested.

bioengineering↗