High-Performance Agent-Based Modeling Applied to Vocal Fold Inflammation and Repair

Unraveling the Relevance of Tissue-Specific Decellularized Extracellular Matrix Hydrogels for Vocal Fold Regenerative Biomaterials: A Comprehensive Proteomic and In Vitro Study

Decellularized extracellular matrix (dECM) is a promising material for tissue engineering applications. Tissue-specific dECM is often seen as a favorable material that recapitulates a native-like microenvironment for cellular remodeling. However, the minute quantity of dECM derivable from small organs like the vocal fold (VF) hampers manufacturing scalability. Small intestinal submucosa (SIS), a commercial product with proven regenerative capacity, may be a viable option for VF applications. This study aims to compare dECM hydrogels derived from SIS or VF tissue with respect to protein content and functionality using mass spectrometry-based proteomics and in vitro studies. Proteomic analysis reveals that VF and SIS dECM share 75% of core matrisome proteins. Although VF dECM proteins have greater overlap with native VF, SIS dECM shows less cross-sample variability. Following decellularization, significant reductions of soluble collagen (61%), elastin (81%), and hyaluronan (44%) are noted in VF dECM. SIS dECM contains comparable elastin and hyaluronan but 67% greater soluble collagen than VF dECM. Cells deposit more neo-collagen on SIS than VF-dECM hydrogels, whereas neo-elastin (~50 μg/scaffold) and neo-hyaluronan (~ 6 μg/scaffold) are comparable between the two hydrogels. Overall, SIS dECM possesses reasonably similar proteomic profile and regenerative capacity to VF dECM. SIS dECM is considered a promising alternative for dECM-derived biomaterials for VF regeneration.

Progress in Vocal Fold Regenerative Biomaterials: An Immunological Perspective

Vocal folds, housed in the upper respiratory tract, are important to daily breathing, speech and swallowing functions. Irreversible changes to the vocal fold mucosae, such as scarring and atrophy, require a regenerative medicine approach to promote a controlled regrowth of the extracellular matrix (ECM)-rich mucosa. Various biomaterial systems have been engineered with an emphasis on stimulating local vocal fold fibroblasts to produce new ECM. At the same time, it is imperative to limit the foreign body reaction and associated immune components that can hinder the integration of the biomaterial into the host tissue. Modern biomaterial designs have become increasingly focused on actively harnessing the immune system to accelerate and optimize the process of tissue regeneration. An array of physical and chemical biomaterial parameters have been reported to effectively modulate local immune cells, such as macrophages, to initiate tissue repair, stimulate ECM production, promote biomaterial-tissue integration, and restore the function of the vocal folds. In this perspective paper, the unique immunological profile of the vocal folds will first be reviewed. Key physical and chemical biomaterial properties relevant to immunomodulation will then be highlighted and discussed. A further examination of the physicochemical properties of recent vocal fold biomaterials will follow to generate deeper insights into corresponding immune-related outcomes. Lastly, a perspective will be offered on the opportunity of integrating material-led immunomodulatory strategies into future vocal fold tissue engineering therapies.

Agent-based models of inflammation in translational systems biology: A decade later

Agent-based modeling is a rule-based, discrete-event, and spatially explicit computational modeling method that employs computational objects that instantiate the rules and interactions among the individual components ("agents") of system. Agent-based modeling is well suited to translating into a computational model the knowledge generated from basic science research, particularly with respect to translating across scales the mechanisms of cellular behavior into aggregated cell population dynamics manifesting at the tissue and organ level. This capacity has made agent-based modeling an integral method in translational systems biology (TSB), an approach that uses multiscale dynamic computational modeling to explicitly represent disease processes in a clinically relevant fashion. The initial work in the early 2000s using agent-based models (ABMs) in TSB focused on examining acute inflammation and its intersection with wound healing; the decade since has seen vast growth in both the application of agent-based modeling to a wide array of disease processes as well as methodological advancements in the use and analysis of ABM. This report presents an update on an earlier review of ABMs in TSB and presents examples of exciting progress in the modeling of various organs and diseases that involve inflammation. This review also describes developments that integrate the use of ABMs with cutting-edge technologies such as high-performance computing, machine learning, and artificial intelligence, with a view toward the future integration of these methodologies. This article is categorized under: Translational, Genomic, and Systems Medicine > Translational Medicine Models of Systems Properties and Processes > Mechanistic Models Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models Models of Systems Properties and Processes > Organismal Models.

Towards a Physiological Scale of Vocal Fold Agent-Based Models of Surgical Injury and Repair: Sensitivity Analysis, Calibration and Verification

Agent based models (ABM) were developed to numerically simulate the biological response to surgical vocal fold injury and repair at the physiological level. This study aimed to improve the representation of existing ABM through a combination of empirical and computational experiments. Empirical data of vocal fold cell populations including neutrophils, macrophages and fibroblasts were obtained using flow cytometry up to four weeks following surgical injury. Random Forests were used as a sensitivity analysis method to identify model parameters that were most influential to ABM outputs. Statistical Parameter Optimization Tool for Python was used to calibrate those parameter values to match the ABM-simulation data with the corresponding empirical data from Day 1 to Day 5 following surgery. Model performance was evaluated by verifying if the empirical data fell within the 95% confidence intervals of ABM outputs of cell quantities at Day 7, Week 2 and Week 4. For Day 7, all empirical data were within the ABM output ranges. The trends of ABM-simulated cell populations were also qualitatively comparable to those of the empirical data beyond Day 7. Exact values, however, fell outside of the 95% statistical confidence intervals. Parameters related to fibroblast proliferation were indicative to the ABM-simulation of fibroblast dynamics in final stages of wound healing.

High-Performance Host-Device Scheduling and Data-Transfer Minimization Techniques for Visualization of 3D Agent-Based Wound Healing Applications

High-fidelity numerical simulations produce massive amounts of data. Analyzing these numerical data sets as they are being generated provides useful insights into the processes underlying the modeled phenomenon. However, developing real-time in-situ visualization techniques to process large amounts of data can be challenging since the data does not fit on the GPU, thus requiring expensive CPU-GPU data copies. In this work, we present a scheduling scheme that achieve real-time simulation and interactivity through GPU hyper-tasking. Furthermore, the CPU-GPU communications were minimized using an activity-aware technique to reduce redundant copies. Our simulation platform is capable of visualizing 1.7 billion protein data points in situ, with an average frame rate of 42.8 fps. This performance allows users to explore large data sets on remote server with real-time interactivity as they are performing their simulations.