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Israr Bin M Ibrahim, Ramana M Pidaparti, Kevin R Ward
Ventilation-induced lung injury is a common problem faced by patients with respiratory problems who require mechanical ventilation (MV). This injury may lead to a greater chance of developing or exacerbating the acute respiratory distress syndrome which further complicates the therapeutic use of MV. The chain of events begins with the MV initiating an immune response that leads to inflammation induced tissue material alteration (stiffening) and eventually the loss of lung resistance. It is clear from this sequence of events that the phenomenon of ventilation induced injury is multi-scale by nature and, hence, requires holistic analysis involving simulations and informatics...
2018: IEEE Journal of Translational Engineering in Health and Medicine
Pingyu Nan, Darragh M Walsh, Kerry A Landman, Barry D Hughes
Motivated by in vitro time-lapse images of ovarian cancer spheroids inducing mesothelial cell clearance, the traditional agent-based model of cell migration, based on simple volume exclusion, was extended to include the possibility that a cell seeking to move into an occupied location may push the resident cell, and any cells neighbouring it, out of the way to occupy that location. In traditional discrete models of motile cells with volume exclusion such a move would be aborted. We introduce a new shoving mechanism which allows cells to choose the direction to shove cells that expends the least amount of shoving effort (to account for the likely resistance of cells to being pushed)...
2018: PloS One
Eunjung Kim, Jae-Young Kim, Matthew A Smith, Eric B Haura, Alexander R A Anderson
During the last decade, our understanding of cancer cell signaling networks has significantly improved, leading to the development of various targeted therapies that have elicited profound but, unfortunately, short-lived responses. This is, in part, due to the fact that these targeted therapies ignore context and average out heterogeneity. Here, we present a mathematical framework that addresses the impact of signaling heterogeneity on targeted therapy outcomes. We employ a simplified oncogenic rat sarcoma (RAS)-driven mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase-protein kinase B (PI3K-AKT) signaling pathway in lung cancer as an experimental model system and develop a network model of the pathway...
March 2018: PLoS Biology
Behnaz Moradabadi, Mohammad Reza Meybodi
This paper proposes a new cellular learning automaton, called a wavefront cellular learning automaton (WCLA). The proposed WCLA has a set of learning automata mapped to a connected structure and uses this structure to propagate the state changes of the learning automata over the structure using waves. In the WCLA, after one learning automaton chooses its action, if this chosen action is different from the previous action, it can send a wave to its neighbors and activate them. Each neighbor receiving the wave is activated and must choose a new action...
February 2018: Chaos
E Estevez-Rams, D Estevez-Moya, B Aragón-Fernández
A recently introduced model of coupled nonlinear oscillators in a ring is revisited in terms of its information processing capabilities. The use of Lempel-Ziv based entropic measures allows to study thoroughly the complex patterns appearing in the system for different values of the control parameters. Such behaviors, resembling cellular automata, have been characterized both spatially and temporally. Information distance is used to study the stability of the system to perturbations in the initial conditions and in the control parameters...
February 2018: Chaos
Rifat Sipahi, Günther K H Zupanc
Neural stem and progenitor cells isolated from the central nervous system form, under specific culture conditions, clonal cell clusters known as neurospheres. The neurosphere assay has proven to be a powerful in vitro system to study the behavior of such cells and the development of their progeny. However, the theory of neurosphere growth has remained poorly understood. To overcome this limitation, we have, in the present paper, developed a cellular automata model, with which we examined the effects of proliferative potential, contact inhibition, cell death, and clearance of dead cells on growth rate, final size, and composition of neurospheres...
February 22, 2018: Journal of Theoretical Biology
Takeshi Osawa, Kazuhisa Yamasaki, Ken Tabuchi, Akira Yoshioka, Mayura B Takada
Detecting dispersal pathways is important both for understanding species range expansion and for managing nuisance species. However, direct detection is difficult. Here, we propose detecting these crucial pathways using a virtual ecology approach, simulating species dynamics using models, and virtual observations. As a case study, we developed a dispersal model based on cellular automata for the pest insect Stenotus rubrovittatus and simulated its expansion. We tested models for species expansion based on four landscape parameters as candidate pathways; these are river density, road density, area of paddy fields, and area of abandoned farmland, and validated their accuracy...
February 23, 2018: Ambio
Zhenwei Yao
Various lattice gas automata have been proposed in the past decades to simulate physics and address a host of problems on collective dynamics arising in diverse fields. In this work, we employ the lattice gas model defined on the sphere to investigate the curvature-driven dynamic structures and analyze the statistical behaviors in equilibrium. Under the simple propagation and collision rules, we show that the uniform collective movement of the particles on the sphere is geometrically frustrated, leading to several nonequilibrium dynamic structures not found in the planar lattice, such as the emergent bubble and vortex structures...
December 2017: Physical Review. E
Richard J Carter, Karoline Wiesner, Stephen Mann
As a step towards understanding pre-evolutionary organization in non-genetic systems, we develop a model to investigate the emergence and dynamics of proto-autopoietic networks in an interacting population of simple information processing entities (automata). Our simulations indicate that dynamically stable strongly connected networks of mutually producing communication channels emerge under specific environmental conditions. We refer to these distinct organizational steady states as information niches In each case, we measure the information content by the Shannon entropy, and determine the fitness landscape, robustness and transition pathways for information niches subjected to intermittent environmental perturbations under non-evolutionary conditions...
January 2018: Journal of the Royal Society, Interface
Tao Zhang, Lei Li, Shi-Hong Lu, Hai Gong, Yun-Xin Wu
Asymmetrical shear rolling with velocity asymmetry and geometry asymmetry is beneficial to enlarge deformation and refine grain size at the center of the thick plate compared to conventional symmetrical rolling. Dynamic recrystallization (DRX) plays a vital role in grain refinement during hot deformation. Finite element models (FEM) coupled with microstructure evolution models and cellular automata models (CA) are established to study the microstructure evolution of plate during asymmetrical shear rolling. The results show that a larger DRX fraction and a smaller average grain size can be obtained at the lower layer of the plate...
January 17, 2018: Materials
Milad Yousefi, Moslem Yousefi, F S Fogliatto, R P M Ferreira, J H Kim
The objective of this study was to develop an agent based modeling (ABM) framework to simulate the behavior of patients who leave a public hospital emergency department (ED) without being seen (LWBS). In doing so, the study complements computer modeling and cellular automata (CA) techniques to simulate the behavior of patients in an ED. After verifying and validating the model by comparing it with data from a real case study, the significance of four preventive policies including increasing number of triage nurses, fast-track treatment, increasing the waiting room capacity and reducing treatment time were investigated by utilizing ordinary least squares regression...
January 11, 2018: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
Travis Gagie, Giovanni Manzini, Jouni Sirén
The famous Burrows-Wheeler Transform (BWT) was originally defined for a single string but variations have been developed for sets of strings, labeled trees, de Bruijn graphs, etc. In this paper we propose a framework that includes many of these variations and that we hope will simplify the search for more. We first define Wheeler graphs and show they have a property we call path coherence. We show that if the state diagram of a finite-state automaton is a Wheeler graph then, by its path coherence, we can order the nodes such that, for any string, the nodes reachable from the initial state or states by processing that string are consecutive...
October 25, 2017: Theoretical Computer Science
Mohammed Bensalah, Ouardia Bouayadi, Nawal Rahmani, Amina Lyagoubi, Somiya Lamrabat, Mohammed Choukri
Parathormone (PTH) is the main hormone of phosphocalcic homeostasis. It is synthesized and secreted by the parathyroid glands. PTH has become a routine test in the medical biology laboratory. However, its measurement presents analytical difficulties with the various marketed kits. The aim of this work is to present the results of a comparative study between the PTH measurment on Abbott architect ci8200 and on Roche's Cobas e411 automaton. It is a prospective study carried out for 252 hospitalized patients in the various departments of the University Hospital Center Mohammed VI of Oujda...
December 15, 2017: Annales de Biologie Clinique
Koen Degeling, Stefano Schivo, Niven Mehra, Hendrik Koffijberg, Rom Langerak, Johann S de Bono, Maarten J IJzerman
BACKGROUND: With the advent of personalized medicine, the field of health economic modeling is being challenged and the use of patient-level dynamic modeling techniques might be required. OBJECTIVES: To illustrate the usability of two such techniques, timed automata (TA) and discrete event simulation (DES), for modeling personalized treatment decisions. METHODS: An early health technology assessment on the use of circulating tumor cells, compared with prostate-specific antigen and bone scintigraphy, to inform treatment decisions in metastatic castration-resistant prostate cancer was performed...
December 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
J M Nava-Sedeño, H Hatzikirou, R Klages, A Deutsch
Many diffusion processes in nature and society were found to be anomalous, in the sense of being fundamentally different from conventional Brownian motion. An important example is the migration of biological cells, which exhibits non-trivial temporal decay of velocity autocorrelation functions. This means that the corresponding dynamics is characterized by memory effects that slowly decay in time. Motivated by this we construct non-Markovian lattice-gas cellular automata models for moving agents with memory...
December 5, 2017: Scientific Reports
Randall D Beer
Computing properties of the set of precursors of a given configuration is a common problem underlying many important questions about cellular automata. Unfortunately, such computations quickly become intractable in dimension greater than one. This paper presents an algorithm-incremental aggregation-that can compute aggregate properties of the set of precursors exponentially faster than naïve approaches. The incremental aggregation algorithm is demonstrated on two problems from the two-dimensional binary Game of Life cellular automaton: precursor count distributions and higher-order mean field theory coefficients...
November 2017: Chaos
M Nassar, A Gromer, D Favier, F Thalmann, P Hébraud, Y Holl
The origin and time evolution of heterogeneities in drying colloidal films is still a matter of debate. In this work, we studied the behaviour of horizontal drying fronts in a 1D configuration. The effects of hydrostatic pressure and collective diffusion of charged particles, neglected so far, were introduced. We made use of the new simulation tool based on cellular automata we recently presented (Langmuir 2015 & 2017). To check the simulation results, measurements of film profiles in the wet state and drying front velocities were performed with silica colloids...
December 13, 2017: Soft Matter
Peter Dittrich
The organic code concept and its operationalization by molecular codes have been introduced to study the semiotic nature of living systems. This contribution develops further the idea that the semantic capacity of a physical medium can be measured by assessing its ability to implement a code as a contingent mapping. For demonstration and evaluation, the approach is applied to a formal medium: elementary cellular automata (ECA). The semantic capacity is measured by counting the number of ways codes can be implemented...
February 2018: Bio Systems
Jan Egger, Christopher Nimsky, Xiaojun Chen
Objectives: Spinal diseases are very common; for example, the risk of osteoporotic fracture is 40% for White women and 13% for White men in the United States during their lifetime. Hence, the total number of surgical spinal treatments is on the rise with the aging population, and accurate diagnosis is of great importance to avoid complications and a reappearance of the symptoms. Imaging and analysis of a vertebral column is an exhausting task that can lead to wrong interpretations. The overall goal of this contribution is to study a cellular automata-based approach for the segmentation of vertebral bodies between the compacta and surrounding structures yielding to time savings and reducing interpretation errors...
2017: SAGE Open Medicine
Peer Zahoor Ahmad, S M K Quadri, Firdous Ahmad, Ali Newaz Bahar, Ghulam Mohammad Wani, Shafiq Maqbool Tantary
Quantum-dot cellular automata, is an extremely small size and a powerless nanotechnology. It is the possible alternative to current CMOS technology. Reversible QCA logic is the most important issue at present time to reduce power losses. This paper presents a novel reversible logic gate called the F-Gate. It is simplest in design and a powerful technique to implement reversible logic. A systematic approach has been used to implement a novel single layer reversible Full-Adder, Full-Subtractor and a Full Adder-Subtractor using the F-Gate...
December 2017: Data in Brief
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