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Real-Time Agent-Based Modeling Simulation with in-Situ Visualization of Complex Biological Systems: A Case Study on Vocal Fold Inflammation and Healing

Nuttiiya Seekhao, Caroline Shung, Joseph Jaja, Luc Mongeau, Nicole Y. K. Li-Jessen
2016 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)  
Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35x and 7x speedup in execution time over single-core and multi-core CPU respectively.  ...  We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms.  ...  The techniques proposed showed a speedup of 35x over an optimized sequential implementation when benchmarked with a complex biological modeling application of vocal folds inflammation and wound healing  ... 
doi:10.1109/ipdpsw.2016.20 pmid:27547508 pmcid:PMC4988409 dblp:conf/ipps/SeekhaoSJML16 fatcat:kwgncwoyufhfhphirnedluj3gm

In-Situ Visualization for 3D Agent-Based Vocal Fold Inflammation and Repair Simulation

2017 Supercomputing Frontiers and Innovations  
In this work, we present a novel high-performance scheme to couple in situ visualization with the simulation of the vocal fold inflammation and repair using little to no extra cost in execution time or  ...  A fast and insightful visualization is essential in modeling biological system behaviors and understanding underlying inter-cellular mechanisms.  ...  Sujal Bista for guidance in developing the visualization component. And UMIACS staff for assistance with VirtualGL and TurboVNC configuration.  ... 
doi:10.14529/jsfi170304 pmid:29177201 pmcid:PMC5701753 fatcat:6eh3zwpierf6flydpv66fkm5ju

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

Nuttiiya Seekhao, Caroline Shung, Joseph JaJa, Luc Mongeau, Nicole Y. K. Li-Jessen
2018 Frontiers in Physiology  
A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair.  ...  The case study model was simulated at the physiological scale of a human vocal fold.  ...  ACKNOWLEDGMENTS The authors would like to thank Yun (Yvonna) Li and Alireza Najafi Yazdi for their contributions to the development of the initial and base sequential model.  ... 
doi:10.3389/fphys.2018.00304 pmid:29706894 pmcid:PMC5906585 fatcat:brbpfu7tongjrgqwgfrcppnrw4

The 13th International Conference on Advances in Quantitative Laryngology, Voice and Speech Research (June 2–4, 2019, Montreal, Quebec, Canada)

Mongeau
2019 Applied Sciences  
The conference and workshops provide a unique opportunity for partnership and collaboration in the advancement of quantitative methods for the measurement and modelling of voice and speech.  ...  With a continued drive toward advancements in translational and clinical voice science, the AQL has rapidly expanded over the past 20 years, from a forum of 15 European member laboratories to a globally  ...  Acknowledgments: This study is partly supported by JSPS KAKENHI JP-17K02707. Acknowledgments: Financial support by CAPES, CNPq and FINEP is gratefully acknowledged.  ... 
doi:10.3390/app9132665 fatcat:xg47la5zkngzxaqe4cdeyv63rq

Passive and Active Microrheology for Biomedical Systems

Yating Mao, Paige Nielsen, Jamel Ali
2022 Frontiers in Bioengineering and Biotechnology  
Recently, there has been significant growth in using these minimally invasive techniques to investigate a wide range of biomedical systems both in vitro and in vivo.  ...  Microrheology can be characterized into either passive or active methods based on the driving force exerted on probe particles.  ...  HDR-2000202 and CMMI-2000330)  ... 
doi:10.3389/fbioe.2022.916354 pmid:35866030 pmcid:PMC9294381 fatcat:t27eh3shcnf7zplmm75jlqtsce

International Research Conference on Smart Computing and Systems Engineering SCSE 2020 Proceedings [Full Conference Proceedings]

2020 2020 International Research Conference on Smart Computing and Systems Engineering (SCSE)  
in the University of Kelaniya for their immense support and encouragement they gave throughout the development phase of the data sets.  ...  ACKNOWLEDGMENT The authors would like to thank the Department of Census and Department of Irrigation, Sri Lanka for providing the paddy yield and climate data for this study.  ...  Section (IV) discusses the testing and validation plan of the model with a set of case studies to be carried out with the system.  ... 
doi:10.1109/scse49731.2020.9313027 fatcat:gjk5az2mprgvrpallwh6uhvlfi

Three-dimensional point-cloud room model in room acoustics simulations

Milos Markovic, So/ren K. Olesen, Dorte Hammersho/i
2013 Journal of the Acoustical Society of America  
Time-domain simulations of wind instruments can, in principle, deal with non-linear oscillations and are also capable of modeling both the steady-state and the transient behavior of a system.  ...  Finally, a real time system using the control procedure is tested on a simplified musical instrument.  ...  We demonstrate that sequential methods are superior to solely iterative ones by linking estimates of times and amplitudes to propagation models and estimating source location and environmental parameters  ... 
doi:10.1121/1.4806371 fatcat:ln4w6j7cjvchrckf2gzfmeiwoi

Predicting and auralizing acoustics in classrooms

Claus Lynge Christensen
2005 Journal of the Acoustical Society of America  
A model of the human auditory system was implemented in the MATLAB platform based on two previous models ͓A. Härmä and K. Palomäki, HUTear, Espoo, Finland; and M. A. Akeroyd, A.  ...  The idea is illustrated in the case study of a plate on which polymer/aluminum thin patches have been bonded.  ...  In this talk, we focus on some recent advances in magnetic resonance imaging that allow us to perform near real-time investigations on the dynamics of vocal tract shaping during speech.  ... 
doi:10.1121/1.4787358 fatcat:xtcgzi3xrnay3eyww5uafbhtgy

2017 TERMIS - Americas Conference & Exhibition Charlotte, NC December 3–6, 2017

2017 Tissue Engineering. Part A  
In this study, we report on our efforts to recreate signaling conditions found in development to generate a model tissue-like system to study the co-development of vascular and neural networks in order  ...  In vitro clot collapse in the presence of fibrin-binding particles was visualized with confocal microscopy, and wound healing and inflammatory responses were assessed in vivo through analysis of wound  ...  Both cell types play unique roles during the inflammatory and wound healing response at the site of vocal fold injury.  ... 
doi:10.1089/ten.tea.2017.29003.abstracts pmid:29173019 fatcat:y5mu2h7aqjcy3cffg42ukwxwpm

24th Surgical Research Days

2021 European Surgical Research  
Fracture testing in this model allowed for a good estimate of rib fracture repair and handling of splints. The modell is recommend for further testing in experimental and training settings.  ...  Repair with single intramedullary splints and double-splints (3 mm splints) in a crossed K-wire techinque was feasible in the upper half of the hemithorax.  ...  The transhepatic puncture procedure was simulated in the liver phantom. A real-time and precise assessment system was established to improve the efficacy of training and competency evaluations.  ... 
doi:10.1159/000518793 pmid:34515110 fatcat:oermfeznkjc4fesa3ujcafqy5e

Advanced Functional Materials Based on Nanocellulose for Pharmaceutical/Medical Applications

Raluca Nicu, Florin Ciolacu, Diana E. Ciolacu
2021 Pharmaceutics  
A diversity of new functional materials with a wide range of biomedical applications has been designed based on the most desirable properties of NCs, such as biocompatibility, biodegradability, and their  ...  Nanocelluloses (NCs), with their remarkable characteristics, have proven to be one of the most promising "green" materials of our times and have received special attention from researchers in nanomaterials  ...  complex biological systems [218] .  ... 
doi:10.3390/pharmaceutics13081125 pmid:34452086 pmcid:PMC8399340 fatcat:a2r6taruofbbtmkefedqkhdbvq

Abstract

2021 European Journal of Clinical Investigation  
This presentation will review the technology and show examples of how it can inform basic and advanced cellular studies.  ...  SESSION 4 55ASM-0284 S1 PC2 | Measuring the impact of microbiome metabolites on mitochondrial function using the Agilent Seahorse XF analyser A.  ...  Wound-healing is a complex process in which mitochondria play a key role in regulating inflammation, skin cell proliferation, and synthesis of collagen.  ... 
doi:10.1111/eci.13567 fatcat:casumfo4afhklgo42swkednpya

Proceedings of the World Molecular Imaging Congress 2020, October 7-9, 2020: General Abstracts

2022 Molecular Imaging and Biology  
Results: In HGG xenografts, intratumoral distribution of pan800 correlated with the EGFR expression and the fluorescence signal.  ...  Age, combined with IDH-wildtype cerebral tumor, was predictive of positive EGFR protein expression in patients.  ...  become more correlated (D7-D9), and finally show a decrease of MC due to formation of abnormal blood vessels (D10-D15).  ... 
doi:10.1007/s11307-021-01691-0 pmid:34982363 pmcid:PMC8725637 fatcat:ipn7hwekzzh6nbsk6dr2mzuhhm

Nervous System [chapter]

Carlo Cantile, Sameh Youssef
2016 Jubb, Kennedy & Palmer's Pathology of Domestic Animals: Volume 1  
The outcome of fetal interactions with agents potentially teratogenic for the nervous system depends on the species and age of the fetus and the nature of the agent.  ...  In retrospective studies of malformations of unknown cause, it is only possible to identify the latest time at which the malformation may have been produced, based on the normal development of the nervous  ...  Based on the predominance of CD3+ T cells and major histocompatibility complex (MHC) class II antigen-positive macrophages, an immune-mediated mechanism has been proposed.  ... 
doi:10.1016/b978-0-7020-5317-7.00004-7 fatcat:v6yrgu7pw5a3dnd3ex6rovyefa

Proceedings_of_Measuring_Behavior_2014.pdf [article]

Andrew Spink, Egon Van Den Broek, Leanne Loijens, Marta Woloszynowska-Fraser, Lucas P. J. J. Noldus
2020 Figshare  
Proceedings of the 9th International Conference on Methods and Techniques in Behavioral Research  ...  Ethical statement All experiments reported here were performed with the permission of the Animal Ethics Committee ('Lely-DEC') and in full compliance with the legal requirements of Dutch legislation on  ...  FSL facilities are offered for evidence based research and education at Aalborg University, including Integrated Food Studies and PhD courses.  ... 
doi:10.6084/m9.figshare.11708187 fatcat:62o74kbgczf2tp2dk64jeszxr4
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