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Systems dynamics model

Ben Serrien, Naaike Verhaeghe, Silke Verhaeghe, Bruno Tassignon, Jean-Pierre Baeyens
Hysteresis in the coordination of movement can be described in the language of coordination dynamics as an asymmetrical response of a system's order parameter with respect to opposite changes in a control parameter. For movement tasks involving a large number of active degrees-of-freedom, the order parameter can be modelled with a pattern recognition approach like Self-Organizing Maps (SOM). This study explored this method in a rope-skipping task, which involves the coordinated oscillation of several segments in the lower and upper limb and trunk and we compared the results to a classical order parameter like continuous relative phase...
June 15, 2018: Human Movement Science
Xianli Chen, Xiaoguang Li, Wei Zhao, Tiejun Li, Qi Ouyang
Understanding how gene alterations induce oncogenesis plays an important role in cancer research and may be instructive for cancer prevention and treatment. We conducted a parameter sensitivity analysis to the mitochondrial apoptosis model. Both a nonlinear bifurcation analysis of the deterministic dynamics and energy barrier analysis of the corresponding stochastic models were performed. We found that the parameter sensitivity ranking according to the change of the bifurcation-point locations in deterministic models and the change of the barrier heights from a living to death state of the cell in stochastic models are highly correlated...
2018: PloS One
Ksenya Kveler, Elina Starosvetsky, Amit Ziv-Kenet, Yuval Kalugny, Yuri Gorelik, Gali Shalev-Malul, Netta Aizenbud-Reshef, Tania Dubovik, Mayan Briller, John Campbell, Jan C Rieckmann, Nuaman Asbeh, Doron Rimar, Felix Meissner, Jeff Wiser, Shai S Shen-Orr
Cytokines are signaling molecules secreted and sensed by immune and other cell types, enabling dynamic intercellular communication. Although a vast amount of data on these interactions exists, this information is not compiled, integrated or easily searchable. Here we report immuneXpresso, a text-mining engine that structures and standardizes knowledge of immune intercellular communication. We applied immuneXpresso to PubMed to identify relationships between 340 cell types and 140 cytokines across thousands of diseases...
June 18, 2018: Nature Biotechnology
Caroline Desgranges, Jerome Delhommelle
Using molecular dynamics simulation, we study the impact of the degree of supercooling on the crystal nucleation of ultra-soft particles, modeled with the Gaussian core potential. Focusing on systems with a high number density, our simulations reveal dramatically different behaviors as the degree of supercooling is varied. In the moderate supercooling regime, crystal nucleation proceeds as expected from classical nucleation theory, with a decrease in the free energy of nucleation, as well as in the size of the critical nucleus, as supercooling is increased...
June 18, 2018: Soft Matter
Bright N Okine, Clare Spicer, Paul Millns, Andrew Bennett, Victoria Chapman
Background and aims The clinical management of chronic neuropathic pain remains a global health challenge. Current treatments are either ineffective, or associated with unwanted side-effects. The development of effective, safe therapies requires the identification of novel therapeutic targets using clinically relevant animal models of neuropathic pain. Peroxisome proliferator activated receptor alpha (PPARα), is a member of the nuclear hormone family of transcription factors, which is widely distributed in the peripheral and central nervous systems...
December 29, 2017: Scandinavian Journal of Pain
Benjamin Owen, Nicholas Bojdo, Andrey Jivkov, Bernard Keavney, Alistair Revell
Computational modelling of the cardiovascular system offers much promise, but represents a truly interdisciplinary challenge, requiring knowledge of physiology, mechanics of materials, fluid dynamics and biochemistry. This paper aims to provide a summary of the recent advances in cardiovascular structural modelling, including the numerical methods, main constitutive models and modelling procedures developed to represent cardiovascular structures and pathologies across a broad range of length and timescales; serving as an accessible point of reference to newcomers to the field...
June 18, 2018: Biomechanics and Modeling in Mechanobiology
Jae Im Choi, Hee Kyung Lee, Hae Su Kim, So Young Park, Tong Young Lee, Kyoung-Hye Yoon, Jin I Lee
Animals sense an enormous number of cues in their environments, and, over time, can form learned associations and memories with some of these. The nervous system remarkably maintains the specificity of learning and memory to each of the cues. Here we asked whether the nematode Caenorhabditis elegans adjusts the temporal dynamics of adaptation and aversive learning depending on the specific odor sensed. C. elegans senses a multitude of odors, and adaptation and learned associations to many of these odors requires activity of the cGMP-dependent protein kinase EGL-4 in the AWC sensory neuron...
2018: PeerJ
Noureldin Saleh, Gunnar Kleinau, Nicolas Heyder, Timothy Clark, Peter W Hildebrand, Patrick Scheerer
The melanocortin-4 receptor (MC4R) is a potential drug target for treatment of obesity, anxiety, depression, and sexual dysfunction. Crystal structures for MC4R are not yet available, which has hindered successful structure-based drug design. Using microsecond-scale molecular-dynamics simulations, we have investigated selective binding of the non-peptide antagonist MCL0129 to a homology model of human MC4R (hMC4R). This approach revealed that, at the end of a multi-step binding process, MCL0129 spontaneously adopts a binding mode in which it blocks the agonistic-binding site...
2018: Frontiers in Pharmacology
Aashish N Patel, Michael D Howard, Shane M Roach, Aaron P Jones, Natalie B Bryant, Charles S H Robinson, Vincent P Clark, Praveen K Pilly
Mental state monitoring is a critical component of current and future human-machine interfaces, including semi-autonomous driving and flying, air traffic control, decision aids, training systems, and will soon be integrated into ubiquitous products like cell phones and laptops. Current mental state assessment approaches supply quantitative measures, but their only frame of reference is generic population-level ranges. What is needed are physiological biometrics that are validated in the context of task performance of individuals...
2018: Frontiers in Human Neuroscience
Vishal Metri, Ameur Louhichi, Jiajun Yan, Guilhem P Baeza, Krzysztof Matyjaszewski, Dimitris Vlassopoulos, Wim J Briels
The equilibrium mechanical properties of a cross-linked gel of telechelic star polymers are studied by rheology and Brownian dynamics simulations. The Brownian dynamics model consists of cores to which Rouse arms are attached. Forces between the cores are obtained from a potential of mean force model developed by Likos and co-workers. Both experimentally and in the simulations, networks were created by attaching sticker groups to the ends of the arms of the polymers, which were next allowed to form bonds among them in a one to one fashion...
April 24, 2018: Macromolecules
Skylar R Hopkins, Cari M McGregor, Lisa K Belden, Jeremy M Wojdak
All dynamic species interaction models contain an assumption that describes how contact rates scale with population density. Choosing an appropriate contact-density function is important, because different functions have different implications for population dynamics and stability. However, this choice can be challenging, because there are many possible functions, and most are phenomenological and thus difficult to relate to underlying ecological processes. Using one such phenomenological function, we described a nonlinear relationship between field transmission rates and host density in a common snail-oligochaete symbiosis...
June 16, 2018: Oecologia
R-Cs Begy, H Simon, Sz Kelemen, L Preoteasa
Being a dynamic environment associated with complex costal, fluvial and marine processes, only a few studies regarding the evolution of the Danube Delta and the human impacts on its ecosystem have been carried out. Being a sensible to all processes occurring in its catchment area, information is stored in the deposited sediments, which can be used as tracers for natural and anthropogenic processes. The aim of this study is to determine a detailed reconstruction of the sedimentation rates in the last century by applying the 210 Pb dating method validated by 137 Cs profiles...
June 14, 2018: Journal of Environmental Radioactivity
Sandra Peherstorfer, Hans Henning Brewitz, Ajay Abisheck Paul George, Amelie Wißbrock, Jana Maria Adam, Lutz Schmitt, Diana Imhof
BACKGROUND: Tight regulation of heme homeostasis is a critical mechanism in pathogenic bacteria since heme functions as iron source and prosthetic group, but is also toxic at elevated concentrations. Hemolysin-activating lysine-acyltransferase (HlyC) from Escherichia coli is crucial for maturation of hemolysin A, which lyses several mammalian cells including erythrocytes liberating large amounts of heme for bacterial uptake. A possible impact and functional consequences of the released heme on events employing bacterial HlyC have remained unexplored...
June 14, 2018: Biochimica et Biophysica Acta
Daoxi Zhang, Samantha Lavender, Jan-Peter Muller, David Walton, Xi Zou, Fang Shi
The historical data from the MEdium Resolution Imaging Spectrometer (MERIS) is an invaluable archive for studying global waters from inland lakes to open oceans. Although the MERIS sensor ceased to operate in April 2012, the data capacities are now re-established through the recently launched Sentinel-3 Ocean and Land Colour Instrument (OLCI). The development of a consistent time series for investigating phytoplankton phenology features is crucial if the potential of MERIS and OLCI data is to be fully exploited for inland water monitoring...
June 13, 2018: Science of the Total Environment
Daniel P Otto, Melgardt M de Villiers
Improvement of problematic dissolution and solubility properties of a model drug, furosemide, was investigated for poly(amidoamine) (PAMAM) dendrimer complexes of the drug. Full and half generation dendrimers with amino and ester terminals respectively, were studied. In vitro release performance of these complexes was investigated at drug loads ranging 5-60% using simulated gastric fluids. Full generation dendrimers accommodated higher drug loads, outperformed half-generation complexes, and free drug. Pharmacokinetic studies in rats indicated that the dendrimer complexes markedly improved in the bioavailability of the drug compared to the unformulated drug...
June 13, 2018: International Journal of Pharmaceutics
Victor J Barranca, George Zhu
The center-surround receptive field structure, ubiquitous in the visual system, is hypothesized to be evolutionarily advantageous in image processing tasks. We address the potential functional benefits and shortcomings of spatial localization and center-surround antagonism in the context of an integrate-and-fire neuronal network model with image-based forcing. Utilizing the sparsity of natural scenes, we derive a compressive-sensing framework for input image reconstruction utilizing evoked neuronal firing rates...
June 13, 2018: Journal of Theoretical Biology
Bryce Morsky, Dervis Can Vural
Much research has focused on the deleterious effects of free-riding in public goods games, and a variety of mechanisms that suppress cheating behavior. Here we argue that under certain conditions cheating can be beneficial to the population. In a public goods game, cheaters do not pay for the cost of the public goods, yet they receive the benefit. Although this free-riding harms the entire population in the long run, the success of cheaters may aid the population when there is a common enemy that antagonizes both cooperators and cheaters...
June 13, 2018: Journal of Theoretical Biology
David M Devilbiss
Flexible and adaptive behaviors have evolved with increasing complexity and numbers of neuromodulator systems. The neuromodulatory locus coeruleus-norepinephrine (LC-NE) system is central to regulating cognitive function in a behaviorally-relevant and arousal-dependent manner. Through its nearly ubiquitous efferent projections, the LC-NE system acts to modulate neuron function on a cell-by-cell basis and exert a spectrum of actions across different brain regions to optimize target circuit function. As LC neuron activity, NE signaling, and arousal level increases, cognitive performance improves over an inverted-U shaped curve...
June 13, 2018: Brain Research
Subhas Khajanchi, Sandip Banerjee
We present a mathematical model which describes the growth of malignant gliomas in presence of immune responses by considering the role of immunotherapeutic agent T11 target structure (T11TS). The model consider five populations, namely, glioma cells, macrophages, cytotoxic T-lymphocytes, TGF - β and IFN - γ. The model system has highly nonlinear terms with four discrete time lags, but remains tractable. The goal of this work is to better understand the effect of multiple delays on the interaction between gliomas and immune components in conjunction with an administration of T11 target structure...
June 13, 2018: Mathematical Biosciences
Dimitrios Stamovlasis, Sofia-Eleftheria N Gonida
The present study used achievement goal theory (AGT) as a theoretical framework and examined the role of mastery and performance goals, both performance-approach and performance-avoidance, on school achieve-ment within the nonlinear dynamical systems (NDS) perspective. A series of cusp catastrophe models were applied on students' achievement in a number of school subjects, such as mathematics and language for elementary school and algebra, geometry, ancient and modern Greek language for high school, using achievement goal orientations as control variables...
July 2018: Nonlinear Dynamics, Psychology, and Life Sciences
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