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Modeling and Simulation

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https://www.readbyqxmd.com/read/28109179/quantitative-and-integrative-analysis-of-paracrine-hepatocyte-activation-by-non-parenchymal-cells-upon-lipopolysaccharide-induction
#1
Katharina Beuke, Frank A Schildberg, Federico Pinna, Ute Albrecht, Roman Liebe, Michaela Bissinger, Peter Schirmacher, Steven Dooley, Johannes G Bode, Percy A Knolle, Ursula Kummer, Kai Breuhahn, Sven Sahle
Gut-derived bacterial lipopolysaccharides (LPS) stimulate the secretion of tumor necrosis factor (TNF) from liver macrophages (MCs), liver sinusoidal endothelial cells (LSECs), and hepatic stellate cells (HSCs), which control the acute phase response in hepatocytes through activation of the NF-κB pathway. The individual and cooperative impact of non-parenchymal cells on this clinically relevant response has not been analysed in detail due to technical limitations. To gain an integrative view on this complex inter- and intracellular communication, we combined a multi-scale mathematical model with quantitative, time-resolved experimental data of different primary murine liver cell types...
January 21, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28109135/assessing-the-hydroxyl-radical-and-volatilization-roles-in-the-aquatic-fate-estimations-of-sulfur-heterocycles-dibenzothiophene-derivatives
#2
Parichehr Saranjampour, Kevin L Armbrust, Brian D Marx
Polycyclic aromatic sulfur heterocycles (PASHs) and their alkyl derivatives can be released into aquatic systems via crude oil spills or via runoff from petroleum treated areas such as asphalt. Dibenzothiophene (DBT) and its derivatives, C1-DBT, C2-DBT, and C4-DBT were chosen as model compounds to investigate the relative impact of volatilization and hydroxyl radical degradation on estimates of their overall dissipation after entry into aquatic ecosystems as a function of depth using the Exposure Analysis Modeling System (EXAMS)...
January 21, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28109130/identification-of-promising-dna-gyrb-inhibitors-for-tuberculosis-using-pharmacophore-based-virtual-screening-molecular-docking-and-molecular-dynamics-studies
#3
Md Ataul Islam, Tahir S Pillay
In the current study, we searched for potential DNA GyrB inhibitors using pharmacophore-based virtual screening followed by molecular docking and molecular dynamics simulation approaches. For this purpose, a set of 248 DNA GyrB inhibitors were collected from the literature and a well-validated pharmacophore model was generated. The best pharmacophore model explained that two each of hydrogen bond acceptor and hydrophobicity were critical for inhibition of DNA GyrB. Good statistical results of the pharmacophore model indicated that the model was robust in nature...
January 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28109128/population-pharmacokinetics-and-pharmacodynamics-of-benralizumab-in-healthy-volunteers-and-patients-with-asthma
#4
B Wang, L Yan, Z Yao, L K Roskos
Benralizumab is a humanized, afucosylated, anti-interleukin-5 receptor α, immunoglobulin G (IgG) 1 κ monoclonal antibody. We developed a population pharmacokinetic (PK)/pharmacodynamic (PD) model for benralizumab by analyzing PK and blood eosinophil count data from two healthy volunteer studies (N = 48) and four studies in patients with asthma (N = 152). Benralizumab PK was dose-proportional and adequately described by a two-compartment model with first-order elimination from the central compartment and first-order absorption from the subcutaneous dosing site...
January 21, 2017: CPT: Pharmacometrics & Systems Pharmacology
https://www.readbyqxmd.com/read/28108975/3d-printed-soft-tissue-physical-models-of-renal-malignancies-for-individualized-surgical-simulation-a-feasibility-study
#5
Michael M Maddox, Allison Feibus, James Liu, Julie Wang, Raju Thomas, Jonathan L Silberstein
To construct patient-specific physical three-dimensional (3D) models of renal units with materials that approximates the properties of renal tissue to allow pre-operative and robotic training surgical simulation, 3D physical kidney models were created (3DSystems, Rock Hill, SC) using computerized tomography to segment structures of interest (parenchyma, vasculature, collection system, and tumor). Images were converted to a 3D surface mesh file for fabrication using a multi-jet 3D printer. A novel construction technique was employed to approximate normal renal tissue texture, printers selectively deposited photopolymer material forming the outer shell of the kidney, and subsequently, an agarose gel solution was injected into the inner cavity recreating the spongier renal parenchyma...
January 20, 2017: Journal of Robotic Surgery
https://www.readbyqxmd.com/read/28108942/compartmentalized-culture-of-perivascular-stroma-and-endothelial-cells-in-a-microfluidic-model-of-the-human-endometrium
#6
Juan S Gnecco, Virginia Pensabene, David J Li, Tianbing Ding, Elliot E Hui, Kaylon L Bruner-Tran, Kevin G Osteen
The endometrium is the inner lining of the uterus. Following specific cyclic hormonal stimulation, endometrial stromal fibroblasts (stroma) and vascular endothelial cells exhibit morphological and biochemical changes to support embryo implantation and regulate vascular function, respectively. Herein, we integrated a resin-based porous membrane in a dual chamber microfluidic device in polydimethylsiloxane that allows long term in vitro co-culture of human endometrial stromal and endothelial cells. This transparent, 2-μm porous membrane separates the two chambers, allows for the diffusion of small molecules and enables high resolution bright field and fluorescent imaging...
January 20, 2017: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/28108886/phase-behaviour-in-complementary-dna-coated-gold-nanoparticles-and-fd-viruses-mixtures-a-numerical-study
#7
Massimiliano Chiappini, Erika Eiser, Francesco Sciortino
A new gel-forming colloidal system based on a binary mixture of fd-viruses and gold nanoparticles functionalized with complementary DNA single strands has been recently introduced. Upon quenching below the DNA melt temperature, such a system results in a highly porous gel state, that may be developed in a new functional material of tunable porosity. In order to shed light on the gelation mechanism, we introduce a model closely mimicking the experimental one and we explore via Monte Carlo simulations its equilibrium phase diagram...
January 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/28108595/identification-of-the-adpr-binding-pocket-in-the-nudt9-homology-domain-of-trpm2
#8
Peilin Yu, Xiwen Xue, Jianmin Zhang, Xupang Hu, Yan Wu, Lin-Hua Jiang, Hongwei Jin, Jianhong Luo, Liangren Zhang, Zhenming Liu, Wei Yang
Activation of the transient receptor potential melastatin 2 (TRPM2) channel occurs during the response to oxidative stress under physiological conditions as well as in pathological processes such as ischemia and diabetes. Accumulating evidence indicates that adenosine diphosphate ribose (ADPR) is the most important endogenous ligand of TRPM2. However, although it is known that ADPR binds to the NUDT9 homology (NUDT9-H) domain in the intracellular C-terminal region, the molecular mechanism underlying ADPR binding and activation of TRPM2 remains unknown...
January 20, 2017: Journal of General Physiology
https://www.readbyqxmd.com/read/28108588/inferring-recent-demography-from-isolation-by-distance-of-long-shared-sequence-blocks
#9
Harald Ringbauer, Graham Coop, Nicholas H Barton
Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes...
January 20, 2017: Genetics
https://www.readbyqxmd.com/read/28108586/fluctuating-selection-in-the-moran
#10
Antony M Dean, Clarence Lehman, Xiao Yi
Contrary to classical population genetics theory, experiments demonstrate that fluctuating selection can protect a haploid polymorphism in the absence of frequency dependent effects on fitness. Using forward simulations with the Moran model we confirm our analytical results showing that a fluctuating selection regime, with a mean selection coefficient of zero, promotes polymorphism. We find that increases in heterozygosity over neutral expectations are especially pronounced when fluctuations are rapid, mutation is weak, the population size is large and the variance in selection is big...
January 20, 2017: Genetics
https://www.readbyqxmd.com/read/28108450/netland-quantitative-modeling-and-visualization-of-waddington-s-epigenetic-landscape-using-probabilistic-potential
#11
Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng
: Waddington's epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks. Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington's landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of gene regulatory networks (GRNs), and visualizing the corresponding Waddington's epigenetic landscape in three dimensions without restriction on the number of genes in a GRN...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108361/development-and-characterization-of-new-functionalized-polyurethanes-for-sustained-and-site-specific-drug-release-in-the-gastrointestinal-tract
#12
María Dolores Campiñez, Elena Benito, Lucía Romero-Azogil, Ángela Aguilar-de-Leyva, María de Gracia García-Martín, Juan Antonio Galbis, Isidoro Caraballo
The main objective of the present paper has been the development and study of two new biodegradable polyurethanes, PU(dithiodiethanol-DTDI) and PU[((i)Pr)Man-DTDI], to be used as sustained matrix forming excipients. Furthermore, their capacity to act as excipient for colon drug delivery systems has been evaluated. Thus, SeDeM diagrams have been obtained to investigate their suitability to be processed through a direct compression process. Matrices containing 10-30% w/w of the polymers and theophylline anhydrous as model drug have been manufactured...
January 17, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28108306/bone-remodeling-as-a-spatial-evolutionary-game
#13
Marc D Ryser, Kevin A Murgas
Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location in the bone. Several spatial extensions of these models have been proposed, but they generally suffer from two limitations: first, they are not amenable to analysis and are computationally expensive, and second, they neglect the role played by bone-embedded osteocytes. To address these issues, we developed a novel model of spatial remodeling based on the principles of evolutionary game theory...
January 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28108202/evaluation-of-coronary-flow-conditions-in-complex-coronary-artery-bifurcations-stenting-using-computational-fluid-dynamics-impact-of-final-proximal-optimization-technique-on-different-double-stent-techniques
#14
Gianluca Rigatelli, Marco Zuin, Fabio Dell'Avvocata, Dobrin Vassilev, Ramesh Daggubati, Thach Nguyen, Nguyen Van Viet Thang, Nicolas Foin
BACKGROUND/PURPOSE: Computational fluid dynamics (CFD) have been recently adopted in many fields of cardiovascular medicine and in interventional cardiology. Using CFD analysis we compared the use of different PCI procedures, with and without the utilization of a proximal optimization technique (POT), on a complex coronary artery bifurcation. METHODS/MATERIALS: For the analysis, we considered a hypothetic model of a left anterior descending artery-diagonal Medina 1,1,1 bifurcation type with a diameter of the proximal main branch (MB) and the side branch (SB) set at 3...
January 9, 2017: Cardiovascular Revascularization Medicine: Including Molecular Interventions
https://www.readbyqxmd.com/read/28108168/joint-refinement-of-fret-measurements-using-spectroscopic-and-computational-tools
#15
Alexander Kyrychenko, Mykola V Rodnin, Chiranjib Ghatak, Alexey S Ladokhin
The variability of the orientation factor is a long-standing challenge in converting FRET efficiency measurements into donor-acceptor distances. We propose the use of molecular dynamics (MD) simulations to characterize orientation distributions and thus improve the accuracy of distance measurements. Here, we test this approach by comparing experimental and simulated FRET efficiencies for a model donor-acceptor pair of enhanced cyan and enhanced yellow FPs connected by a flexible linker. Several spectroscopic techniques were used to characterize FRET in solution...
January 17, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28108101/development-of-a-high-resolution-voxelised-head-phantom-for-medical-physics-applications
#16
REVIEW
V Giacometti, S Guatelli, M Bazalova-Carter, A B Rosenfeld, R W Schulte
Computational anthropomorphic phantoms have become an important investigation tool for medical imaging and dosimetry for radiotherapy and radiation protection. The development of computational phantoms with realistic anatomical features contribute significantly to the development of novel methods in medical physics. For many applications, it is desirable that such computational phantoms have a real-world physical counterpart in order to verify the obtained results. In this work, we report the development of a voxelised phantom, the HIGH_RES_HEAD, modelling a paediatric head based on the commercial phantom 715-HN (CIRS)...
January 17, 2017: Physica Medica: PM
https://www.readbyqxmd.com/read/28108092/the-analysis-and-application-of-a-new-hybrid-pollutants-forecasting-model-using-modified-kolmogorov-zurbenko-filter
#17
Peizhi Li, Yong Wang, Qingli Dong
Cities in China suffer from severe smog and haze, and a forecasting system with high accuracy is of great importance to foresee the concentrations of the airborne particles. Compared with chemical transport models, the growing artificial intelligence models can simulate nonlinearities and interactive relationships and getting more accurate results. In this paper, the Kolmogorov-Zurbenko (KZ) filter is modified and firstly applied to construct the model using an artificial intelligence method. The concentration of inhalable particles and fine particulate matter in Dalian are used to analyze the filtered components and test the forecasting accuracy...
January 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28108064/stent-and-leaflet-stresses-in-a-26-mm-first-generation-balloon-expandable-transcatheter-aortic-valve
#18
Yue Xuan, Kapil Krishnan, Jian Ye, Danny Dvir, Julius M Guccione, Liang Ge, Elaine E Tseng
OBJECTIVE: Transcatheter aortic valve replacement is established therapy for high-risk and inoperable patients with severe aortic stenosis, but questions remain regarding long-term durability. Valve design influences durability. Increased leaflet stresses in surgical bioprostheses have been correlated with degeneration; however, transcatheter valve leaflet stresses are unknown. From 2007 to 2014, a majority of US patients received first-generation balloon-expandable transcatheter valves...
December 23, 2016: Journal of Thoracic and Cardiovascular Surgery
https://www.readbyqxmd.com/read/28108037/a-semi-analytical-method-for-simulating-matrix-diffusion-in-numerical-transport-models
#19
Ronald W Falta, Wenwen Wang
A semi-analytical approximation for transient matrix diffusion is developed for use in numerical contaminant transport simulators. This method is an adaptation and extension of the heat conduction method of Vinsome and Westerveld (1980) used to simulate heat losses during thermally enhanced oil recovery. The semi-analytical method is used in place of discretization of the low permeability materials, and it represents the concentration profile in the low permeability materials with a fitting function that is adjusted in each element at each time-step...
January 11, 2017: Journal of Contaminant Hydrology
https://www.readbyqxmd.com/read/28108002/reduced-order-model-based-active-disturbance-rejection-control-of-hydraulic-servo-system-with-singular-value-perturbation-theory
#20
Chengwen Wang, Long Quan, Shijie Zhang, Hongjun Meng, Yuan Lan
Hydraulic servomechanism is the typical mechanical/hydraulic double-dynamics coupling system with the high stiffness control and mismatched uncertainties input problems, which hinder direct applications of many advanced control approaches in the hydraulic servo fields. In this paper, by introducing the singular value perturbation theory, the original double-dynamics coupling model of the hydraulic servomechanism was reduced to a integral chain system. So that, the popular ADRC (active disturbance rejection control) technology could be directly applied to the reduced system...
January 17, 2017: ISA Transactions
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