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Immune system simulation online

N. Rapin, O. Lund, F. Castiglione
2011 Bioinformatics  
In current mesoscopic-scale simulators of the immune system, this crucial step has been modeled in a very approximated way.  ...  Results: We have equipped an agent-based model of the immune system with immuno-informatics methods to allow the simulation of the cardinal events of the antigenic recognition, going from single peptides  ...  The immune system simulation server presented here consists of a simple interface to the simulation method mentioned above where the user can specify the antigen injection schedule , the haplotype of the  ... 
doi:10.1093/bioinformatics/btr335 pmid:21685045 fatcat:yfpulxapo5attnaizmkrq2nbse

Novel Control Scheme for Helicopter Flight: Fuzzy Immune Adaptive Model Inversion Control

Zhao Jia, Chen Shenggong, Shen Gongzhang
2008 IFAC Proceedings Volumes  
Simulation results comparing with the neural network adaptive control method show the system based on the proposed scheme has better real-time performance.  ...  It could achieve effective control throughout large flight envelope curve via the design of fuzzy immune online-compensation element, only needing a static inverse model on the basis of a single flight  ...  FIOCE DESIGN As the core of whole system, FIOCE will simulate biology immune response mechanism and counteract the inversion error brought by RDIP in time.  ... 
doi:10.3182/20080706-5-kr-1001.02546 fatcat:yrjtblzj6bd37izbbgzz4jumh4

Two-Way Mutual-Structure-Based Public Opinion Communication System: An Analysis with Simulation

2019 Tehnički Vjesnik  
The multi-agent simulation platform Netlogo is used to simulate a constructed public opinion evolution model, and the law of public opinion evolution under the resonance path is analyzed.  ...  Taking Stephen Hawking's death in 2018 as a sample case, simulation results are verified through data collection and collation; additionally, the law of the evolution of public opinion in the two-way mutual  ...  The state of online media outlet k (whether concerning a diffuser or immunizer) depends on clique, denoting the number of distributors in the system space at time t.  ... 
doi:10.17559/tv-20181122070039 fatcat:brvabpqpujgo7mxlaoawrizgju

Page 1991 of International Pharmaceutical Abstracts Vol. 35, Issue 18 [page]

1998 International Pharmaceutical Abstracts  
3511202 IMPACT OF A SIMULATED IMMUNIZATION REGISTRY ON PERCEIVED CHILDHOOD IMMUNIZATION STATUS Yawn, B. P. (Dept. of Res., Olmsted Med. Ctr., 210 Ninth St.  ...  The perceived rate was compared to the rate obtained by combining all recorded immunizations from all facilities (simulated registry).  ... 

Integrated Systems View on Networking by Hormones in Arabidopsis Immunity Reveals Multiple Crosstalk for Cytokinin

M. Naseem, N. Philippi, A. Hussain, G. Wangorsch, N. Ahmed, T. Dandekar
2012 The Plant Cell  
Our dynamic simulation is instrumental in predicting system effects of individual components in complex hormone disease networks and synergism or antagonism between pathways.  ...  Dynamic modeling and system analysis identified multiple cytokinin-mediated regulatory interactions in plant disease networks.  ...  Table 2 online for simulation validation).  ... 
doi:10.1105/tpc.112.098335 pmid:22643121 pmcid:PMC3442570 fatcat:vbolq5by3jhvha6vvohphvadru

Immune Signaling Networks: Sources of Robustness and Constrained Evolvability during Coevolution

Edward C Schrom, Joaquín M Prada, Andrea L Graham
2017 Molecular biology and evolution  
Here, we use a theoretical simulation model to examine how underlying network architectures constrain the evolution of immune strategies, and how these network architectures account for desirable immune  ...  This is because evolution proceeds via mutational changes to the protein interaction networks underlying immune responses, not by changes to an immune strategy directly.  ...  immune systems.  ... 
doi:10.1093/molbev/msx321 pmid:29294066 fatcat:i62e2tc4s5aubbx5wttu6crvx4

Systems biology model repository for macrophage pathway simulation

M. Nagasaki, A. Saito, A. Fujita, G. Tremmel, K. Ueno, E. Ikeda, E. Jeong, S. Miyano
2011 Bioinformatics  
The Macrophage Pathway Knowledgebase (MACPAK) is a computational system that allows biomedical researchers to query and study the dynamic behaviors of macrophage molecular pathways.  ...  MACPAK comprises a total of 24 009 entities and 12 774 processes and is described in the Cell System Markup Language (CSML), an XML format that runs on the Cell Illustrator platform and can be visualized  ...  INTRODUCTION The immune system has evolved as a defense mechanism against pathogenic microbes.  ... 
doi:10.1093/bioinformatics/btr173 pmid:21505034 fatcat:vxxnphdk5zcutam4f2sv6dwpou

Immune Loss as a Driver of Coexistence During Host-Phage Coevolution [article]

Jake L Weissman, Rayshawn Holmes, Rodolphe Barrangou, Sylvain Moineau, William F Fagan, Bruce R Levin, Philip LF Johnson
2017 bioRxiv   pre-print
We pair a general model of immunity with an experimental and theoretical case study of the CRISPR-Cas immune system to contrast the behavior of tradeoff and loss mechanisms in well-mixed systems.  ...  Despite this prediction, in many systems host and pathogen coexist with minimal coevolution even when well-mixed.  ...  402 of spacers (Semenova et al., 2016) . 403 While we conclude that immune loss plays a key role in our system, it is not 404 immediately clear why bacterial immune systems would lose functionality  ... 
doi:10.1101/105908 fatcat:dyqrxurysnenripc6s3v2qz4wa

Rational design of chimeric Multiepitope Based Vaccine (MEBV) against human T-cell lymphotropic virus type 1: An integrated vaccine informatics and molecular docking based approach

Muhammad Hamza Tariq, Rashid Bhatti, Nida Fatima Ali, Usman Ali Ashfaq, Farah Shahid, Ahmad Almatroudi, Mohsin Khurshid, Muhammad Younas Khan Barozai
2021 PLoS ONE  
Repeated-exposure simulations and Immune simulations ensured the rapid antigen clearance and higher levels of cell-mediated immunity, respectively.  ...  Additionally, Molecular docking analysis and Molecular Dynamics (MD) simulations confirmed the strong association between MEBV construct and human pathogenic immune receptor TLR-3.  ...  systems were simulated for 20ns.  ... 
doi:10.1371/journal.pone.0258443 pmid:34705829 pmcid:PMC8550388 fatcat:pnxh6zxterc6xalvlj6aejpfxq

A Hybrid Algorithm Between the Artificial Immunological Network and the ANFIS Technique with Application

Omar Kasim, Israa Alkhayyat
2018 Al-Kitab Journal for Pure Sciences  
the Artificial Immune Network, was developed using the Adaptive Neuro Fuzzy Inference System (ANFIS) by using the Immune Memory, The immunological network as an input to ANFIS technology to increase the  ...  The proposed algorithm proved to have better and more efficient results rack on the patterns compared with the usual artificial immune system.  ...  EFF (Decision Boundary) Efficiency Scale ANFIS ANFIS Artificial Immune System Ag Clonal If Then) MSE Selection ANFIS 5 Time Artificial Immune Systems (Ab Triangular Function (Affinity Degree AIN_ANFIS  ... 
doi:10.32441/kjps.02.02.p22 fatcat:pyl3fsuwpbge5oylvu7kk6vage

Progress Towards an Open Source PhysiCell Ecosystem [article]

Paul Macklin
2019 Figshare  
of systems (e.g., immune system) In cancer, these systems become dysregulated.  ...  Treatments target parts of these systems. Cancer is a complex system: changing one part can have surprising effects! Modeling can help understand this system. This is multicellular systems biology.  ... 
doi:10.6084/m9.figshare.9934469.v1 fatcat:b6n6wc7nsnepthm26yy2tfbx4q

Immune loss as a driver of coexistence during host-phage coevolution

Jake L Weissman, Rayshawn Holmes, Rodolphe Barrangou, Sylvain Moineau, William F Fagan, Bruce Levin, Philip L F Johnson
2018 The ISME Journal  
We pair a general model of immunity with an 9 experimental and theoretical case study of the CRISPR-Cas immune system to contrast 10 the behavior of tradeoff and loss mechanisms in well-mixed systems.  ...  Despite this prediction, in many systems host and pathogen coexist with 5 minimal coevolution even when well-mixed.  ...  402 of spacers (Semenova et al., 2016) . 403 While we conclude that immune loss plays a key role in our system, it is not 404 immediately clear why bacterial immune systems would lose functionality  ... 
doi:10.1038/ismej.2017.194 pmid:29328063 pmcid:PMC5776473 fatcat:s4b3dyhq5rbjxfqv35vn52zqkq

A tipping point in cancer-immune dynamics leads to divergent immunotherapy responses and hampers biomarker discovery

Jeroen H A Creemers, W Joost Lesterhuis, Niven Mehra, Winald R Gerritsen, Carl G Figdor, I Jolanda M de Vries, Johannes Textor
2021 Journal for ImmunoTherapy of Cancer  
and molecular approaches, only a limited number of candidate biomarkers eventually enter clinical practice.MethodsA computational modeling approach based on ordinary differential equations was used to simulate  ...  the fundamental mechanisms that dictate tumor-immune dynamics and to investigate its implications on responses to immune checkpoint inhibition (ICI) and patient survival.  ...  To illustrate this, we simulated twenty patients with identical immune systems (ie, identical T cell killing rates).  ... 
doi:10.1136/jitc-2020-002032 pmid:34059522 pmcid:PMC8169479 fatcat:yqegut6fv5bfxopjhx3zakq34q

Toward computational modelling on immune system function

Francesco Pappalardo, Giulia Russo, Pedro A. Reche
2020 BMC Bioinformatics  
AbstractThe 3rd edition of the computational methods for the immune system function workshop has been held in San Diego, CA, in conjunction with the IEEE International Conference on Bioinformatics and  ...  System Function (CMISF 2019).  ...  About this supplement This article has been published as part of BMC Bioinformatics Volume 21 Supplement 17 2020: Selected papers from the 3rd International Workshop on Computational Methods for the Immune  ... 
doi:10.1186/s12859-020-03897-5 pmid:33308137 fatcat:nkcsqmolsjholihix7ajahg2ry

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow [article]

Jonathan Ozik, Nicholson Collier, Justin Wozniak, Charles Macal, Chase Cockrell, Samuel Friedman, Ahmadreza Ghaffarizadeh, Randy Heiland, Gary An, Paul Macklin
2017 bioRxiv   pre-print
Cancer is a complex, multiscale dynamical system, with interactions between tumor cells and non-cancerous host systems.  ...  Therapies act on this combined cancer-host system, sometimes with unexpected results.  ...  The copyright holder for this preprint . http://dx.doi.org/10.1101/196709 doi: bioRxiv preprint first posted online Sep. 30, 2017; Figure 1 Sample 3-D cancer-immune simulation. 3-D simulation of adaptive  ... 
doi:10.1101/196709 fatcat:uk4522iosraf5mlthxpkodnnym
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