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Modeling and Simulation

Thorsten Tjardes, Markus Luecking
Introduction: To achieve the aim of zero preventable deaths on the battlefield a deeper understanding of uncontrolled hemorrhage from junctional or proximal extremity sources is mandatory. While tourniquet application to the extremities has drastically reduced morbidity and mortality, there is still room for improvement regarding the timing of tourniquet placement as the available evidence clearly points out a tight correlation between timing of tourniquet application and outcome. To save as many lives as possible the "point of no return" regarding the circulatory breakdown due to hemorrhage, colloquially addressed as platinum 5 min, needs to be determined...
March 14, 2018: Military Medicine
Rada M Savic, Prasanna Jagannathan, Richard Kajubi, Liusheng Huang, Nan Zhang, Moses Were, Abel Kakuru, Mary K Muhindo, Norah Mwebaza, Erika Wallender, Tamara D Clark, Bishop Opira, Moses Kamya, Diane V Havlir, Philip J Rosenthal, Grant Dorsey, Francesca T Aweeka
Background: Dihydroartemsinin-piperaquine is highly efficacious as intermittent preventive therapy for malaria during pregnancy (IPTp). Determining associations between piperaquine exposure, malaria risk, and adverse birth outcomes informs optimal dosing strategies. Methods: HIV-uninfected pregnant women were enrolled in a placebo-controlled trial of IPTp at 12-20 weeks gestation and randomized to: sulfadoxine-pyrimethamine every 8 weeks (n=106), dihydroartemsinin-piperaquine every 8 weeks (n=94), or dihydroartemsinin-piperaquine every 4 weeks (n=100) during pregnancy...
March 14, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
Deepak Reddy Gade, Amareswararao Makkapati, Rajesh Babu Yarlagadda, Godefridus J Peters, B S Sastry, V V S Rajendra Prasad
Overexpression of P-glycoprotein (P-gp) leads to the emergence of multidrug resistance (MDR) in cancer treatment. Acridones have the potential to reverse MDR and sensitize cells. In the present study, we aimed to elucidate the chemosensitization potential of acridones by employing various molecular modelling techniques. Pharmacophore modeling was performed for the dataset of chemosensitizing acridones earlier proved for cytotoxic activity against MCF7 breast cancer cell line. Gaussian-based QSAR studies also performed to predict the favored and disfavored region of the acridone molecules...
February 24, 2018: Computational Biology and Chemistry
X Bai, B Tie, J-H Schmitt, D Aubry
The correlation between ultrasonic wave propagation and polycrystalline microstructures has significant implications in nondestructive evaluation. An original numerical approach using the finite element method to quantify in both time and frequency domains the ultrasonic noise scattering due to the elastic heterogeneity of polycrystalline microstructures is presented. Based on the reciprocity theorem, it allows the scattering evaluation using mechanical data recorded only on the boundary of polycrystal instead of within its volume and is applicable to any polycrystalline aggregate regardless of its crystallographic or morphological characteristics...
February 14, 2018: Ultrasonics
Christine Prouty, Shima Mohebbi, Qiong Zhang
Given the increasing vulnerability of communities to the negative impacts of untreated wastewater, resource recovery (RR) systems provide a paradigm shift away from a traditional approach of waste separation and treatment towards a productive recovery of water, energy and nutrients. The aim of this research is to understand the relationships between factors that influence the adoption and sustainability of wastewater-based RR systems to inform technology implementation strategies. The study presents a theory-informed, community-influenced system dynamics (SD) model to provide decision-makers with an adaptable tool that simulates system-level responses to the strategies that are developed for the coastal town of Placencia, Belize...
March 7, 2018: Water Research
Alberto Perez, Florian Sittel, Gerhard Stock, Ken A Dill
The molecular actions of proteins occur along reaction coordinates. Current computer methods have limited ability to explore them. We describe a fast protocol called MELD-path that: (1) efficiently samples relevant conformational states via MELD, an accelerator of Molecular Dynamics (MD), (2) seeds multiple short MD trajectories from MELD states, then (3) constructs Markov State Models (MSM) that give the routes and kinetics. We tested the method against extensive (multi μs) MD simulations of the right-handed- to left-handed-helix transition of a 9-mer peptide of AIB, the symmetry of which allows us to establish convergence...
March 16, 2018: Journal of Chemical Theory and Computation
Harsha T Garimella, Reuben H Kraft, Andrzej J Przekwas
Subject-specific computer models (male and female) of the human head were used to investigate the possible axonal deformation resulting from the primary phase blast-induced skull flexures. The corresponding axonal tractography was explicitly incorporated into these finite element models using a recently developed technique based on the embedded finite element method. These models were subjected to extensive verification against experimental studies which examined their pressure and displacement response under a wide range of loading conditions...
2018: PloS One
Donghuan Liu, Jing Zhang
High-temperature thermal contact resistance (TCR) plays an important role in heat-pipe-cooled thermal protection structures due to the existence of contact interface between the embedded heat pipe and the heat resistive structure, and the reduction mechanism of thermal contact resistance is of special interests in the design of such structures. The present paper proposed a finite element model of the high-temperature thermal contact resistance based on the multi-point contact model with the consideration of temperature-dependent material properties, heat radiation through the cavities at the interface and the effect of thermal interface material (TIM), and the geometry parameters of the finite element model are determined by simple surface roughness test and experimental data fitting...
2018: PloS One
Min Liu, Qing-Xian Ma, Jian-Bin Luo
20Mn5 steel is widely used in the manufacture of heavy hydro-generator shaft forging due to its strength, toughness, and wear resistance. However, the hot deformation and recrystallization behaviors of 20Mn5 steel compressed under a high temperature were not studied. For this article, hot compression experiments under temperatures of 850-1200 °C and strain rates of 0.01 s-1 -1 s-1 were conducted using a Gleeble-1500D thermo-mechanical simulator. Flow stress-strain curves and microstructure after hot compression were obtained...
March 16, 2018: Materials
Martin Kornecki, Jochen Strube
Productivity improvements of mammalian cell culture in the production of recombinant proteins have been made by optimizing cell lines, media, and process operation. This led to enhanced titers and process robustness without increasing the cost of the upstream processing (USP); however, a downstream bottleneck remains. In terms of process control improvement, the process analytical technology (PAT) initiative, initiated by the American Food and Drug Administration (FDA), aims to measure, analyze, monitor, and ultimately control all important attributes of a bioprocess...
March 16, 2018: Bioengineering
Junbo Tie, Juliang Cao, Lubing Chang, Shaokun Cai, Meiping Wu, Junxiang Lian
Compensation of gravity disturbance can improve the precision of inertial navigation, but the effect of compensation will decrease due to the accelerometer bias, and estimation of the accelerometer bias is a crucial issue in gravity disturbance compensation. This paper first investigates the effect of accelerometer bias on gravity disturbance compensation, and the situation in which the accelerometer bias should be estimated is established. The accelerometer bias is estimated from the gravity vector measurement, and a model of measurement noise in gravity vector measurement is built...
March 16, 2018: Sensors
Jan Endrikat, Susan Dohanish, Nicolas Schleyer, Susanne Schwenke, Sheela Agarwal, Thomas Balzer
OBJECTIVES: The aim of this study was to critically assess the evaluation and categorization process for nephrogenic systemic fibrosis (NSF) based on reports received by Bayer from 2006 to 2016. MATERIALS AND METHODS: A total of 779 NSF reports received by Bayer globally from 2006 to 2016 were included in the analysis. Arlington Medical Resources provided gadolinium-based contrast agent (GBCA) market share. Reports were conservatively categorized based on the Cowper/Girardi criteria...
March 16, 2018: Investigative Radiology
Brodie Pearson, Baylor Fox-Kemper
Data from turbulent numerical simulations of the global ocean demonstrate that the dissipation of kinetic energy obeys a nearly log-normal distribution even at large horizontal scales O(10  km). As the horizontal scales of resolved turbulence are larger than the ocean is deep, the Kolmogorov-Yaglom theory for intermittency in 3D homogeneous, isotropic turbulence cannot apply; instead, the down-scale potential enstrophy cascade of quasigeostrophic turbulence should. Yet, energy dissipation obeys approximate log-normality-robustly across depths, seasons, regions, and subgrid schemes...
March 2, 2018: Physical Review Letters
Stéphanie Essafi, Jeremy N Harvey
For condensed-phase reactions, commonly used kinetic models assume that energy exchange from and to solvent molecules is much faster than any reactive steps. However, it is becoming increasingly evident that this does not always hold true. In this work, we use molecular dynamics simulations to explore the timescale for energy transfer between solvent and solute in some typical organic solvents. As a reference, energy transfer between solvent molecules is also considered. The timescale is found to depend most strongly on the identity of the solvent...
March 16, 2018: Journal of Physical Chemistry. A
Lucia Romero, Jordi Cano, Julio Gomis-Tena, Beatriz Trenor, Ferran Sanz, Manuel Pastor, Javier Saiz
Drug-induced proarrhythmicity is a major concern for regulators and pharmaceutical companies. For novel drug candidates, the standard assessment involves the evaluation of the potassium hERG channels block and the in vivo prolongation of the QT interval. However, this method is known to be too restrictive and to stop the development of potentially valuable therapeutic drugs. The aim of this work is to create an in silico tool for early detection of drug-induced proarrhythmic risk. The system is based on simulations of how different compounds affect the action potential duration (APD) of isolated endocardial, midmyocardial, and epicardial cells as well as the QT prolongation in a virtual tissue...
March 16, 2018: Journal of Chemical Information and Modeling
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
James Hope, Frederique Vanholsbeeck, A J McDaid
In neural interfaces for peripheral nerve a trade-off exists between the level of invasiveness and the selectivity of neural recordings. In this study, we implement electrical impedance tomography (EIT) in a nerve cuff with the aim to investigate the achievable level of selectivity.
 Approach: Established modelling approaches in neural-EIT are expanded on to be used, for the first time, on myelinated fibres which are abundant in mammalian peripheral nerves and transmit motor commands. The model is then used to evaluate the viability of using EIT with a nerve cuff to record neural activity in peripheral nerves...
March 16, 2018: Physiological Measurement
Xiaodi Niu, Yawen Gao, Yiding Yu, Yanan Yang, Guizhen Wang, Lin Sun, Hongsu Wang
Previous studies found that the activity of Sortase A, a bacterial surface protein from Staphylococcus aureus, was inhibited by curcumin and its analogues. To explore this inhibitory mechanism, Sortase A and its inhibitors in complex systems were studied by molecular docking, molecular modelling, binding energy decomposition calculation, and steered molecular dynamics simulations. Energy decomposition analysis indicated that PRO-163, LEU-169, GLN-172, ILE-182, and ILE-199 are key residues in Sortase A-inhibitor complexes...
March 16, 2018: Journal of Biomolecular Structure & Dynamics
Ilhem Bouderbala, Nadjia El Saadi, Alassane Bah, Pierre Auger
In this paper, we develop a 3D-individual-based model (IBM) to understand effect of various small-scale mechanisms in phytoplankton cells, on the cellular aggregation process. These mechanisms are: spatial interactions between cells due to their chemosensory abilities (chemotaxis), a molecular diffusion and a demographical process. The latter is considered as a branching process with a density-dependent death rate to take into account the local competition on resources. We implement the IBM and simulate various scenarios under real parameter values for phytoplankton cells...
March 15, 2018: Acta Biotheoretica
Barbara Wiśniowska, Sebastian Polak
The current study is an example of drug-disease interaction modeling where a drug induces a condition which can affect the pharmacodynamics of other concomitantly taken drugs. The electrophysiological effects of hypokaliemia and heart rate changes induced by the antiasthmatic drugs were simulated with the use of the cardiac safety simulator. Biophysically detailed model of the human cardiac physiology-ten Tusscher ventricular cardiomyocyte cell model-was employed to generate pseudo-ECG signals and QTc intervals for 44 patients from four clinical studies...
March 15, 2018: Journal of Pharmacokinetics and Pharmacodynamics
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