scholarly journals PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

2022 ◽  
Author(s):  
Miguel Ponce-de-Leon ◽  
Arnau Montagud ◽  
Vincent Noel ◽  
Gerard Pradas ◽  
Annika Meert ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Multiple Scales ◽  
Spatial Scales ◽  
Cell Signalling ◽  
Boolean Model ◽  
Computational Framework ◽  
Agent Based ◽  
Modelling Framework ◽  
Underlying Mechanisms ◽  
Set Up

Motivation: Cancer progression is a complex phenomenon that spans multiple scales from molecular to cellular and intercellular. Simulations can be used to perturb the underlying mechanisms of those systems and to generate hypotheses on novel therapies. We present a new version of PhysiBoSS, a multiscale modelling framework designed to cover multiple temporal and spatial scales, that improves its integration with PhysiCell, decoupling the cell agent simulations with the internal Boolean model in an easy-to-maintain computational framework. Results: PhysiBoSS 2.0 is a redesign and reimplementation of PhysiBoSS, conceived as an add-on that expands the PhysiCell agent-based functionalities with intracellular cell signalling using MaBoSS having a decoupled, maintainable and model-agnostic design. PhysiBoSS 2.0 successfully reproduces simulations reported in the former PhysiBoSS and expands its functionalities such as using user-defined models and cells' specifications, having mechanistic submodels of substrate internalisation with ODEs and enabling the study of drug synergies. Availability and implementation: PhysiBoSS 2.0 is open-source and publicly available on GitHub (https://github.com/PhysiBoSS/PhysiBoSS) under the BSD 3-clause license. Additionally, a nanoHUB tool has been set up to ease the use of PhysiBoSS 2.0 (https://nanohub.org/tools/pba4tnf/).

Fostering International Collaboration Through a Unified Verification, Validation, and Diagnostics Framework - METplus 

2021 ◽  
Author(s):  
Tara Jensen ◽  
Marion Mittermaier ◽  
Paul Kucera ◽  
Barbara Brown
Keyword(s):  
Multiple Scales ◽  
Spatial Scales ◽  
System Modeling ◽  
The United States ◽  
Verification And Validation ◽  
Current Status ◽  
United States Department ◽  
Earth System Modeling ◽  
Dynamic Framework ◽  
Set Up

<p>Verification and validation activities are critical for the success of modeling and prediction efforts at organizations around the world.  Having reproducible results via a consistent framework is equally important for model developers and users alike.  The Model Evaluation Tools (MET) was developed over a decade ago and expanded to the METplus framework with a view towards providing a consistent platform delivering reproducible results.   </p><p>The METplus system is an umbrella verification, validation and diagnostic framework for use by thousands of users from both US and international organizations.  These tools are designed to be highly flexible to allow for quick adaption to meet additional evaluation and diagnostic needs.  A suite of python wrappers have been implemented to facilitate a quick set-up and implementation of the system, and to enhance the pre-existing plotting capabilities.  Recently, several organizations within the National Oceanic and Atmospheric Adminstration (NOAA), the United States Department of Defense (DOD), and international partnerships such as Unified Model (UM) Partnership led by the Met Office have adopted the tools for their use both operationally and for research purposes.  Many of these organizations are also now contributing to METplus development, leading to a more robust and dynamic framework for the entire earth system modeling community to use.</p><p>This presentation will provide an update on the current status of METplus and how it is being used in across multiple scales and applications.  It will highlight examples of METplus applied to verification and validation efforts throughout the international community to address a range of temporal (hourly forecasts to subseasonal-to-seasonal) and spatial scales (convection allowing to mesoscale, regional to global, tropical to cryosphere to space).</p>

scholarly journals PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling

2018 ◽  
Vol 35 (7) ◽  
pp. 1188-1196 ◽  
Author(s):  
Gaelle Letort ◽  
Arnau Montagud ◽  
Gautier Stoll ◽  
Randy Heiland ◽  
Emmanuel Barillot ◽  
...  
Keyword(s):  
Cell Signalling ◽  
Agent Based ◽  
Agent Based Modelling ◽  
Multi Scale ◽  
Modelling Framework

Targeting Tumour Metastasis: The Emerging Role of Nanotechnology

2020 ◽  
Vol 27 (8) ◽  
pp. 1367-1381 ◽  
Author(s):  
Sarah Visentin ◽  
Mirela Sedić ◽  
Sandra Kraljević Pavelić ◽  
Krešimir Pavelić
Keyword(s):  
Cancer Progression ◽  
Metastatic Cancer ◽  
Treatment Strategies ◽  
Metastatic Progression ◽  
Therapeutic Concept ◽  
Molecular Alterations ◽  
Tumour Metastasis ◽  
Metastatic Cells ◽  
Metastatic Process ◽  
Underlying Mechanisms

The metastatic process has still not been completely elucidated, probably due to insufficient knowledge of the underlying mechanisms. Here, we provide an overview of the current findings that shed light on specific molecular alterations associated with metastasis and present novel concepts in the treatment of the metastatic process. In particular, we discuss novel pharmacological approaches in the clinical setting that target metastatic progression. New insights into the process of metastasis allow optimisation and design of new treatment strategies, especially in view of the fact that metastatic cells share common features with stem cells. Nano- and micro-technologies are herein elaborated in details as a promising therapeutic concept in targeted drug delivery for metastatic cancer. Progression in the field could provide a more efficient way to tackle metastasis and thus bring about advancements in the treatment and management of patients with advanced cancer.

Exploring PLAC1 Structure and Underlying Mechanisms to Design a Derivative Vaccine Against Breast Cancer Progression; In-Silico Study

2020 ◽  
Vol 17 (5) ◽  
pp. 379-391
Author(s):  
Farzaneh Afzali ◽  
Parisa Ghahremanifard ◽  
Mohammad Mehdi Ranjbar ◽  
Mahdieh Salimi
Keyword(s):  
Breast Cancer ◽  
Cancer Progression ◽  
In Silico ◽  
Tertiary Structure ◽  
Specific Antigen ◽  
Docking Simulation ◽  
Post Translational Modification ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Underlying Mechanisms

Background: The tolerogenic homeostasis in Breast Cancer (BC) can be surpassed by rationally designed immune-encouraging constructs against tumor-specific antigens through immunoinformatics approach. Objective: Availability of high throughput data providing the underlying concept of diseases and awarded computational simulations, lead to screening the potential medications and strategies in less time and cost. Despite the extensive effects of Placenta Specific 1 (PLAC1) in BC progression, immune tolerance, invasion, cell cycle regulation, and being a tumor-specific antigen the fundamental mechanisms and regulatory factors were not fully explored. It is also worth to design an immune response inducing construct to surpass the hurdles of traditional anti-cancer treatments. Methods and Result: The study was initiated by predicting and modelling the PLAC1 secondary and tertiary structures and then engineering the fusion pattern of PLAC1 derived immunodominant predicted CD8+ and B-cell epitopes to form a multi-epitope immunogenic construct. The construct was analyzed considering the physiochemical characterization, safety, antigenicity, post-translational modification, solubility, and intrinsically disordered regions. After modelling its tertiary structure, proteinprotein docking simulation was carried out to ensure the attachment of construct with Toll-Like Receptor 4 (TLR4) as an immune receptor. To guarantee the highest expression of the designed construct in E. coli k12 as an expressional host, the codon optimization and in-silico cloning were performed. The PLAC1 related miRNAs in BC were excavated and validated through TCGA BC miRNA-sequencing and databases; the common pathways then were introduced as other probable mechanisms of PLAC1 activity. Conclusion: Regarding the obtained in-silico results, the designed anti-PLAC1 multi-epitope construct can probably trigger humoral and cellular immune responses and inflammatory cascades, therefore may have the potential of halting BC progression and invasion engaging predicted pathways.

Novel Findings of Anti-cancer Property of Propofol

2018 ◽  
Vol 18 (2) ◽  
pp. 156-165 ◽  
Author(s):  
Jiaqiang Wang ◽  
Chien-shan Cheng ◽  
Yan Lu ◽  
Xiaowei Ding ◽  
Minmin Zhu ◽  
...  
Keyword(s):  
General Anesthesia ◽  
Cancer Progression ◽  
Molecular Mechanisms ◽  
Intravenous Anesthetic ◽  
The Past ◽  
Anti Cancer ◽  
Underlying Mechanisms ◽  
Recent Attention

Background: Propofol, a widely used intravenous anesthetic agent, is traditionally applied for sedation and general anesthesia. Explanation: Recent attention has been drawn to explore the effect and mechanisms of propofol against cancer progression in vitro and in vivo. Specifically, the proliferation-inhibiting and apoptosis-inducing properties of propofol in cancer have been studied. However, the underlying mechanisms remain unclear. Conclusion: This review focused on the findings within the past ten years and aimed to provide a general overview of propofol's malignance-modulating properties and the potential molecular mechanisms.

scholarly journals Active control of liquid film flows: beyond reduced-order models

2021 ◽  
Vol 104 (1) ◽  
pp. 267-287
Author(s):  
Radu Cimpeanu ◽  
Susana N. Gomes ◽  
Demetrios T. Papageorgiou
Keyword(s):  
Liquid Film ◽  
Information Transfer ◽  
Analytical Models ◽  
Feedback Controls ◽  
Reduced Order ◽  
Modelling Framework ◽  
Theoretical Approaches ◽  
Active Feedback ◽  
Feedback Strategies ◽  
Set Up

AbstractThe ability to robustly and efficiently control the dynamics of nonlinear systems lies at the heart of many current technological challenges, ranging from drug delivery systems to ensuring flight safety. Most such scenarios are too complex to tackle directly, and reduced-order modelling is used in order to create viable representations of the target systems. The simplified setting allows for the development of rigorous control theoretical approaches, but the propagation of their effects back up the hierarchy and into real-world systems remains a significant challenge. Using the canonical set-up of a liquid film falling down an inclined plane under the action of active feedback controls in the form of blowing and suction, we develop a multi-level modelling framework containing both analytical models and direct numerical simulations acting as an in silico experimental platform. Constructing strategies at the inexpensive lower levels in the hierarchy, we find that offline control transfer is not viable; however, analytically informed feedback strategies show excellent potential, even far beyond the anticipated range of applicability of the models. The detailed effects of the controls in terms of stability and treatment of nonlinearity are examined in detail in order to gain understanding of the information transfer inside the flows, which can aid transition towards other control-rich frameworks and applications.

scholarly journals Agent-Based Coordinated Control of Power Electronic Converters in a Microgrid

Electronics ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1031
Author(s):  
Maryam Nasri ◽  
Herbert L. Ginn ◽  
Mehrdad Moallem
Keyword(s):  
Hash Table ◽  
Power Sharing ◽  
Distributed Hash Table ◽  
Power Electronic ◽  
Power Electronic Converters ◽  
Agent Based ◽  
Development Framework ◽  
Study Results ◽  
Set Up ◽  
Microgrid Control

This paper presents the implementation of an agent-based architecture suitable for the coordination of power electronic converters in stand-alone microgrids. To this end, a publish-subscribe agent architecture was utilized as a distributed microgrid control platform. Over a distributed hash table (DHT) searching overlay, the publish-subscribe architecture was identified based on a numerical analysis as a scalable agent-based technology for the distributed real-time coordination of power converters in microgrids. The developed framework was set up to deploy power-sharing distributed optimization algorithms while keeping a deterministic time period of a few tens of milliseconds for a system with tens of converters and when multiple events might happen concurrently. Several agents participate in supervisory control to regulate optimum power-sharing for the converters. To test the design, a notional shipboard system, including several converters, was used as a case study. Results of implementing the agent-based publish-subscribe control system using the Java Agent Development Framework (JADE) are presented.

Implications of temporal and spatial scale for Atlantic salmon (Salmo salar) research

1998 ◽  
Vol 55 (S1) ◽  
pp. 9-21 ◽  
Author(s):  
Carol L Folt ◽  
Keith H Nislow ◽  
Mary E Power
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Multiple Scales ◽  
Spatial Scales ◽  
Effective Means ◽  
Research Strategies ◽  
Atlantic Salmon Salmo Salar ◽  
Temporal And Spatial ◽  
And Migration ◽  
Dependent Processes

The Atlantic salmon (Salmo salar) is a model species for studying scale issues (i.e., the extent, duration, and resolution of a study or natural process) in ecology. Major shifts in behavior and habitat use over ontogeny, along with a relatively long life span and large dispersal and migration distances, make scale issues critical for effective conservation, management, and restoration of this species. The scale over which a process occurs must be linked to the research design and we illustrate this with a discussion of resource tracking by Atlantic salmon. Identifying scale inconsistencies (e.g., when a process is evident at one scale but not another) is shown to be an effective means by which some scale-dependent processes are understood. We review the literature to assess the temporal and spatial scales used in Atlantic salmon research and find most current studies appear to sacrifice spatial and temporal extent for increased resolution. Finally, we discuss research strategies for expanding the temporal and spatial scales in salmon research, such as conducting multiple scales studies to elucidate scale inconsistencies, identifying mechanisms, and using techniques and approaches to generalize across studies and over time and space.

scholarly journals Nrf2 Signaling Pathway in Chemoprotection and Doxorubicin Resistance: Potential Application in Drug Discovery

Antioxidants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 349
Author(s):  
Sepideh Mirzaei ◽  
Ali Zarrabi ◽  
Farid Hashemi ◽  
Amirhossein Zabolian ◽  
Hossein Saleki ◽  
...  
Keyword(s):  
Cancer Therapy ◽  
Adverse Effects ◽  
Cancer Progression ◽  
Related Factor ◽  
Pharmacological Agents ◽  
Nrf2 Signaling Pathway ◽  
High Concentrations ◽  
Genetic Interventions ◽  
Underlying Mechanisms ◽  
In Cells

Doxorubicin (DOX) is extensively applied in cancer therapy due to its efficacy in suppressing cancer progression and inducing apoptosis. After its discovery, this chemotherapeutic agent has been frequently used for cancer therapy, leading to chemoresistance. Due to dose-dependent toxicity, high concentrations of DOX cannot be administered to cancer patients. Therefore, experiments have been directed towards revealing underlying mechanisms responsible for DOX resistance and ameliorating its adverse effects. Nuclear factor erythroid 2-related factor 2 (Nrf2) signaling is activated to increase levels of reactive oxygen species (ROS) in cells to protect them against oxidative stress. It has been reported that Nrf2 activation is associated with drug resistance. In cells exposed to DOX, stimulation of Nrf2 signaling protects cells against cell death. Various upstream mediators regulate Nrf2 in DOX resistance. Strategies, both pharmacological and genetic interventions, have been applied for reversing DOX resistance. However, Nrf2 induction is of importance for alleviating side effects of DOX. Pharmacological agents with naturally occurring compounds as the most common have been used for inducing Nrf2 signaling in DOX amelioration. Furthermore, signaling networks in which Nrf2 is a key player for protection against DOX adverse effects have been revealed and are discussed in the current review.

scholarly journals How model paradigms affect our representation of future land-use change

2020 ◽  
Author(s):  
Calum Brown ◽  
Ian Holman ◽  
Mark Rounsevell
Keyword(s):  
Land Use ◽  
Land Use Change ◽  
System Development ◽  
Active Management ◽  
Integrated Modelling ◽  
Agent Based Model ◽  
Agent Based ◽  
Modelling Framework ◽  
Land Use Models ◽  
Landscape Scales

Abstract. Land use models operating at regional to global scales are almost exclusively based on the single paradigm of economic optimisation. Models based on different paradigms are known to produce very different results, but these are not always equivalent or attributable to particular assumptions. In this study, we compare two pan-European land use models that are based on the same integrated modelling framework and utilise the same climatic and socio-economic scenarios, but which adopt fundamentally different model paradigms. One of these is a constrained optimising economic-equilibrium model and the other is a stochastic agent-based model. We run both models for a range of scenario combinations and compare their projections of spatial and aggregate land use change and ecosystem service supply. We find that the agent-based model projects more multifunctional and heterogeneous landscapes in most scenarios, providing a wider range of ecosystem services at landscape scales, as agents make individual, time-dependent decisions that reflect economic and non-economic motivations. This tendency also results in food shortages under certain scenario conditions. The optimisation model, in contrast, maintains food supply through intensification of agricultural production in the most profitable areas, sometimes at the expense of active management in large, contiguous parts of Europe. We relate the principal differences observed to underlying model assumptions, and hypothesise that optimisation may be appropriate in scenarios that allow for coherent political and economic control of land systems, but not in scenarios where economic and other scenario conditions prevent the normal functioning of price signals and responses. In these circumstances, agent-based modelling allows explicit consideration of behavioural processes, but in doing so provides a highly flexible account of land system development that is harder to link to underlying assumptions. We suggest that structured comparisons of parallel, transparent but paradigmatically distinct models are an important method for better understanding the potential scope and uncertainties of future land use change.

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