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Modeling and Simulation

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https://www.readbyqxmd.com/read/28645090/the-impact-of-tidal-and-mesoscale-eddy-advection-on-the-long-term-dispersion-of-99-tc-from-sellafield
#1
Magne Simonsen, Øyvind Saetra, Pål Erik Isachsen, Ole Christian Lind, Hilde Kristin Skjerdal, Brit Salbu, Hilde Elise Heldal, Justin P Gwynn
In the present work, numerical models are used to study the fate of the (99)Tc discharges from Sellafield with a specific focus on the role of mesoscale eddy and tidal advection on the transport and dispersion of this radionuclide. Transport estimates are made with an ocean model that resolves a large part of the ocean mesoscale eddy field and also includes tides. Equivalent estimates are also computed with another model in which these processes are either absent or parametrized. Comparison with field observations shows that the coarse-resolution model can reproduce the general features of the observed time-space (99)Tc distribution if the diffusivity in its eddy parametrization scheme is suitably chosen...
June 20, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28644920/genome-scale-metabolic-models-applied-to-human-health-and-disease
#2
REVIEW
Daniel J Cook, Jens Nielsen
Advances in genome sequencing, high throughput measurement of gene and protein expression levels, data accessibility, and computational power have allowed genome-scale metabolic models (GEMs) to become a useful tool for understanding metabolic alterations associated with many different diseases. Despite the proven utility of GEMs, researchers confront multiple challenges in the use of GEMs, their application to human health and disease, and their construction and simulation in an organ-specific and disease-specific manner...
June 23, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28644865/test-designs-and-modeling-under-the-general-nominal-diagnosis-model-framework
#3
Jinsong Chen, Hui Zhou
Most psychological questionnaires face issues of response bias in respondent-reported scales, inadequacy for criterion-reference testing, or difficulty in estimating a large number of latent traits. Situational tests together with the general nominal diagnosis model framework provide a viable alternative to alleviate these concerns. Under this framework, there are different ways to design situationally nominal items, which can offer more flexibility for test development. Any response bias remaining with respondent-reported questionnaires may be addressed with appropriate test designs...
2017: PloS One
https://www.readbyqxmd.com/read/28644856/estimating-psychopathological-networks-be-careful-what-you-wish-for
#4
Sacha Epskamp, Joost Kruis, Maarten Marsman
Network models, in which psychopathological disorders are conceptualized as a complex interplay of psychological and biological components, have become increasingly popular in the recent psychopathological literature (Borsboom, et. al., 2011). These network models often contain significant numbers of unknown parameters, yet the sample sizes available in psychological research are limited. As such, general assumptions about the true network are introduced to reduce the number of free parameters. Incorporating these assumptions, however, means that the resulting network will lead to reflect the particular structure assumed by the estimation method-a crucial and often ignored aspect of psychopathological networks...
2017: PloS One
https://www.readbyqxmd.com/read/28644808/esim-edge-similarity-for-screen-content-image-quality-assessment
#5
Zhangkai Ni, Lin Ma, Huanqiang Zeng, Jing Chen, Canhui Cai, Kai-Kuang Ma
In this paper, an accurate full-reference image quality assessment (IQA) model developed for assessing screen content images (SCIs), called the edge similarity (ESIM), is proposed. It is inspired by the fact that the human visual system (HVS) is highly sensitive to edges that are often encountered in SCIs; therefore, essential edge features are extracted and exploited for conducting IQA for the SCIs. The key novelty of the proposed ESIM lies in the extraction and use of three salient edge features-i.e., edge contrast, edge width, and edge direction...
June 21, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28644803/cardiac-strain-imaging-with-coherent-compounding-of-diverging-waves
#6
Julien Grondin, Vincent Sayseng, Elisa E Konofagou
Current methods of cardiac strain imaging at high frame rate suffer from motion matching artifacts or poor lateral resolution. Coherent compounding has been shown to improve echocardiographic image quality while maintaining high frame rate but has never been used to image cardiac strain. However, myocardial velocity can have an impact on coherent compounding due to displacements between frames. The objective of this study was to investigate the feasibility and performance of coherent compounding for cardiac strain imaging at a low and a high myocardial velocity...
June 20, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28644798/joint-alignment-of-multiple-point-sets-with-batch-and-incremental-expectation-maximization
#7
Dimitrios Georgios Evangelidis, Radu Horaud
This paper addresses the problem of registering multiple point sets. Solutions to this problem are often approximated by repeatedly solving for pairwise registration, which results in an uneven treatment of the sets forming a pair: a model set and a data set. The main drawback of this strategy is that the model set may contain noise and outliers, which negatively affects the estimation of the registration parameters. In contrast, the proposed formulation treats all the point sets on an equal footing. Indeed, all the points are drawn from a central Gaussian mixture, hence the registration is cast into a clustering problem...
June 21, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28644672/topological-fractional-pumping-with-alkaline-earth-like-atoms-in-synthetic-lattices
#8
Luca Taddia, Eyal Cornfeld, Davide Rossini, Leonardo Mazza, Eran Sela, Rosario Fazio
Alkaline-earth(-like) atoms, trapped in optical lattices and in the presence of an external gauge field, can form insulating states at given fractional fillings. We will show that, by exploiting these properties, it is possible to realize a topological fractional pump. Our analysis is based on a many-body adiabatic expansion, on simulations with time-dependent matrix product states, and, for a specific form of atom-atom interaction, on an exactly solvable model of fractional pump. The numerical simulations allow us to consider a realistic setup amenable of an experimental realization...
June 9, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28644624/extensive-assessment-of-various-computational-methods-for-aspartate-s-pka-shift
#9
Zhaoxi Sun, Xiaohui Wang, Jianing Song
A series of computational methods for pKa shift prediction are extensively tested on a set of benchmark protein systems, aiming at identifying pitfalls and evaluating their performance on high variants. Including 19 ASP residues in 10 protein systems, the benchmark set consists of both residues with highly shifted pKa values as well as those varying little from the reference value, with an experimental RMS free energy differences of 2.49 kcal/mol with respect to blocked amino acid, namely the RMS pKa shift being 1...
June 23, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28644579/pairing-field-methods-to-improve-inference-in-wildlife-surveys-while-accommodating-detection-covariance
#10
John Clare, Shawn T McKinney, John E DePue, Cynthia S Loftin
It is common to use multiple field sampling methods when implementing wildlife surveys to compare method efficacy or cost-efficiency, integrate distinct pieces of information provided by separate methods, or evaluate method-specific biases and misclassification error. Existing models that combine information from multiple field methods or sampling devices permit rigorous comparison of method-specific detection parameters, enable estimation of additional parameters such as false-positive detection probability, and improve occurrence or abundance estimates, but with the assumption that the separate sampling methods produce detections independently of one another...
June 23, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28644546/-18-f-fluoromisonidazole-uptake-in-advanced-stage-non-small-cell-lung-cancer-a-voxel-by-voxel-pet-kinetics-study
#11
Daniel R McGowan, Ruth E Macpherson, Sara L Hackett, Dan Liu, Fergus V Gleeson, W Gillies McKenna, Geoff S Higgins, John D Fenwick
PURPOSE: To determine the relative abilities of compartment models to describe time-courses of 18F-fluoromisonidazole (FMISO) uptake in tumor voxels of patients with non-small cell lung cancer (NSCLC) imaged using dynamic positron emission tomography. Also to use fits of the best-performing model to investigate changes in fitted rate-constants with distance from the tumor edge. METHODS: Reversible and irreversible two- and three-tissue compartment models were fitted to 24,662 individual voxel time activity curves (TACs) obtained from tumors in 9 patients, each imaged twice...
June 23, 2017: Medical Physics
https://www.readbyqxmd.com/read/28644421/antibacterial-effect-of-a-4x-cu-tio%C3%A2-coating-simulating-acute-periprosthetic-infection-an-animal-model
#12
Andreas Mauerer, Stefanie Stenglein, Stefan Schulz-Drost, Christoph Schörner, Dominic Taylor, Sebastian Krinner, Frank Heidenau, Werner Adler, Raimund Forst
The purpose of our study was to investigate the antibacterial effect of a spacer (Ti6Al4V) coated with 4x Cu-TiO₂ in an animal model simulating an acute periprosthetic infection by Staphylococcus aureus. Ti6Al4 bolts contaminated with Staphylococcus aureus were implanted into the femoral condyle of rabbits (n = 36) divided into 3 groups. After one week in group 1 (control) the bolts were removed without any replacement. In group2 Ti6Al4V bolts with a 4x Cu-TiO₂ coating and in group 3 beads of a gentamicin-PMMA chain were imbedded into the borehole...
June 23, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28644410/enhanced-antibacterial-activity-of-ent-labdane-derivatives-of-salvic-acid-7%C3%AE-hydroxy-8-17-ent-labden-15-oic-acid-effect-of-lipophilicity-and-the-hydrogen-bonding-role-in-bacterial-membrane-interaction
#13
Javier Echeverría, Alejandro Urzúa, Loreto Sanhueza, Marcela Wilkens
In the present study, the antibacterial activity of several ent-labdane derivatives of salvic acid (7α-hydroxy-8(17)-ent-labden-15-oic acid) was evaluated in vitro against the Gram-negative bacterium Escherichia coli and the Gram-positive bacteria Staphylococcus aureus and Bacillus cereus. For all of the compounds, the antibacterial activity was expressed as the minimum inhibitory concentration (MIC) in liquid media and minimum inhibitory amount (MIA) in solid media. Structure activity relationships (SAR) were employed to correlate the effect of the calculated lipophilicity parameters (logPow) on the inhibitory activity...
June 23, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28644375/gaden-a-3d-gas-dispersion-simulator-for-mobile-robot-olfaction-in-realistic-environments
#14
Javier Monroy, Victor Hernandez-Bennets, Han Fan, Achim Lilienthal, Javier Gonzalez-Jimenez
This work presents a simulation framework developed under the widely used Robot Operating System (ROS) to enable the validation of robotics systems and gas sensing algorithms under realistic environments. The framework is rooted in the principles of computational fluid dynamics and filament dispersion theory, modeling wind flow and gas dispersion in 3D real-world scenarios (i.e., accounting for walls, furniture, etc.). Moreover, it integrates the simulation of different environmental sensors, such as metal oxide gas sensors, photo ionization detectors, or anemometers...
June 23, 2017: Sensors
https://www.readbyqxmd.com/read/28644152/incorporating-hypr-de-noising-within-iterative-pet-reconstruction-hypr-osem
#15
Ju-Chieh Kevin Cheng, Julian C Matthews, Vesna Sossi, Jose Anton-Rodriguez, Andre Salomon, Ronald Boellaard
HighlY constrained back-PRojection (HYPR) is a post-processing de-noising technique originally developed for time-resolved Magnetic Resonance Imaging. It has been recently applied to dynamic imaging for Positron Emission Tomography (PET) and shown promising results. In this work, we have developed an iterative reconstruction algorithm (HYPR-OSEM) which improves the signal-to-noise ratio (SNR) in static imaging (i.e. single frame reconstruction) by incorporating HYPR de-noising directly within the ordered subsets expectation maximization (OSEM) algorithm...
June 23, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28644151/ecg-based-4d-dose-reconstruction-of-cardiac-arrhythmia-ablation-with-carbon-ion-beams-application-in-a-porcine-model
#16
Daniel Richter, H Immo Lehmann, Anna Eichhorn, Anna M Constantinescu, Robert Kaderka, Matthias Prall, Patrick Lugenbiel, Mitsuru Takami, Dierk Thomas, Christoph Bert, Marco Durante, Douglas L Packer, Christian Graeff
Noninvasive ablation of cardiac arrhythmia by scanned particle radiotherapy is highly promising, but especially challenging due to cardiac and respiratory motion. Irradiations for catheter-free ablation in intact pigs were carried out at the GSI Helmholtz Center in Darmstadt using scanned carbon ions. Here, we present real-time electrocardiogram (ECG) data to estimate time-resolved (4D) delivered dose. For 11 animals, surface ECGs and temporal structure of beam delivery were acquired during irradiation. R waves were automatically detected from surface ECGs...
June 23, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28644150/rapid-fluorescence-lifetime-estimation-with-modified-phasor-approach-and-laguerre-deconvolution-a-comparative-study
#17
Farzad Fereidouni, Dimitris Gorpas, Dinglong Ma, Hussain Fatakdawala, Laura Marcu
Fluorescence lifetime imaging has been shown to serve as a valuable tool for interrogating and diagnosis of biological tissue at mesoscopic level. The ability to analyze fluorescence decay curves to extract lifetime values in real-time is crucial for clinical translation and applications such as tumor margin delineation or intracoronary imaging of atherosclerotic plaques. In this work, we compare the performance of two popular non-parametric (fit-free) methods for determining lifetime values from fluorescence decays in real-time -Phasor approach and Laguerre deconvolution...
June 23, 2017: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28643926/fluid-pressurization-and-tractional-forces-during-tmj-disc-loading-a-biphasic-finite-element-analysis
#18
Y Wu, S E Cisewski, F Wei, X She, T S Gonzales, L R Iwasaki, J C Nickel, H Yao
OBJECTIVES: To investigate the ploughing mechanism associated with tractional force formation on the temporomandibular joint (TMJ) disc surface. SETTING AND SAMPLE POPULATION: Ten left TMJ discs were harvested from 6- to 8-month-old male Yorkshire pigs. MATERIALS AND METHODS: Confined compression tests characterized mechanical TMJ disc properties, which were incorporated into a biphasic finite element model (FEM). The FEM was established to investigate load carriage within the extracellular matrix (ECM) and the ploughing mechanism during tractional force formation by simulating previous in vitro plough experiments...
June 2017: Orthodontics & Craniofacial Research
https://www.readbyqxmd.com/read/28643868/the-potassium-battery-a-mobile-energy-source-for-transport-processes-in-plant-vascular-tissues
#19
REVIEW
Ingo Dreyer, Judith Lucia Gomez-Porras, Janin Riedelsberger
Contents I. II. III. IV. V. VI. VII. VIII. References SUMMARY: Plant roots absorb potassium ions from the soil and transport them in the xylem via the transpiration stream to the shoots. There, in source tissues where sufficient chemical energy (ATP) is available, K(+) is loaded into the phloem and then transported with the phloem stream to other parts of the plant; in part, transport is also back to the roots. This, at first sight, futile cycling of K(+) has been uncovered to be part of a sophisticated mechanism that (1) enables the shoot to communicate its nutrient demand to the root, (2) contributes to the K(+) nutrition of transport phloem tissues and (3) transports energy stored in the K(+) gradient between phloem cytosol and the apoplast...
June 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28643833/modelling-critical-casimir-force-induced-self-assembly-experiments-on-patchy-colloidal-dumbbells
#20
Arthur C Newton, T Anh Nguyen, Sandra J Veen, Daniela J Kraft, Peter Schall, Peter G Bolhuis
Colloidal particles suspended in a binary liquid mixture can interact via solvent mediated interactions, known as critical Casimir forces. For anisotropic colloids this interaction becomes directional, which leads to rich phase behavior. While experimental imaging and particle tracking techniques allow determination of isotropic effective potentials via Boltzmann inversion, the modeling of effective interaction in anisotropic systems is non-trivial precisely because of this directionality. Here we extract effective interaction potentials for non-spherical dumbbell particles from observed radial and angular distributions, by employing reference interaction site model (RISM) theory and direct Monte Carlo simulations...
June 23, 2017: Soft Matter
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