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Modeling and Simulation

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https://www.readbyqxmd.com/read/28743105/statistical-interactions-from-a-growth-curve-perspective
#1
Sean M Devlin, Jaya M Satagopan
Logistic regression is widely used to evaluate the association between risk factors and a binary outcome. The logistic curve is symmetric around its point of inflection. Alternative families of curves, such as the additive Gompertz or Guerrero-Johnson models, have been proposed in various scenarios due to their asymmetry: disease risk may initially increase rapidly and be followed by a longer period where the rate of growth slowly decreases. When modeling binary outcomes in relation to risk factors, an additive logistic model may not provide a good fit to the data...
July 26, 2017: Human Heredity
https://www.readbyqxmd.com/read/28743094/a-personalized-medicine-approach-to-the-design-of-dry-powder-inhalers-selecting-the-optimal-amount-of-bypass
#2
Thomas Kopsch, Darragh Murnane, Digby Symons
In dry powder inhalers (DPIs) the patient's inhalation manoeuvre strongly influences the release of drug. Drug release from a DPI may also be influenced by the size of any air bypass incorporated in the device. If the amount of bypass is high less air flows through the entrainment geometry and the release rate is lower. In this study we propose to reduce the intra- and inter-patient variations of drug release by controlling the amount of air bypass in a DPI. A fast computational method is proposed that can predict how much bypass is needed for a specified drug delivery rate for a particular patient...
July 22, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28743093/development-of-a-statistical-oil-spill-model-for-risk-assessment
#3
Weijun Guo
To gain a better understanding of the impacts from potential risk sources, we developed an oil spill model using probabilistic method, which simulates numerous oil spill trajectories under varying environmental conditions. The statistical results were quantified from hypothetical oil spills under multiple scenarios, including area affected probability, mean oil slick thickness, and duration of water surface exposed to floating oil. The three sub-indices together with marine area vulnerability are merged to compute the composite index, characterizing the spatial distribution of risk degree...
July 22, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28743074/coronary-perfusion-pressure-and-compression-quality-in-maternal-cardiopulmonary-resuscitation-in-supine-and-left-lateral-tilt-positions-a-prospective-crossover-study-using-mannequins-and-swine-models
#4
Satoshi Dohi, Kiyotake Ichizuka, Ryu Matsuoka, Kohei Seo, Masaaki Nagatsuka, Akihiko Sekizawa
OBJECTIVE: The risk of maternal and fetal mortality is high if cardiopulmonary arrest occurs during pregnancy. To assess the best position for maternal cardiopulmonary resuscitation (CPR), a prospective randomized crossover study was undertaken, involving basic life support mannequin-based simulation (BLS-MS) and a swine model of pulseless electrical activity (an unstable cardiac state) incorporating a fetal mannequin (PEA-FM). STUDY DESIGN: The BLS-MS (performed by certified rescuers) served to evaluate the quality of chest compressions in 30° left lateral tilt (LLT) and supine positions...
July 16, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28743072/molecular-modeling-and-molecular-dynamics-simulation-study-of-archaeal-leucyl-trna-synthetase-in-complex-with-different-mischarged-trna-in-editing-conformation
#5
A V Rayevsky, M Sharifi, M A Tukalo
Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNA(Leu) was modeled wherever tRNA's acceptor stem was oriented directly into the editing site...
July 18, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28743068/applying-monte-carlo-simulations-to-optimize-an-inelastic-neutron-scattering-system-for-soil-carbon-analysis
#6
Galina Yakubova, Aleksandr Kavetskiy, Stephen A Prior, H Allen Torbert
Computer Monte-Carlo (MC) simulations (Geant4) of neutron propagation and acquisition of gamma response from soil samples was applied to evaluate INS system performance characteristic [minimal detectible level (MDL), sensitivity] for soil carbon measurement. The INS system model with best performance characteristics was determined based on MC simulation results. Measurements of MDL using an experimental prototype based on this model demonstrated good agreement with simulated data. This prototype will be used as the base engineering design for a new INS system...
July 5, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28742964/conformational-flexibility-and-self-association-of-fibrinogen-in-concentrated-solutions
#7
Yuriy F Zuev, Rustem I Litvinov, Alexander E Sitnitsky, Bulat Z Idiyatullin, Dilyafruz R Bakirova, Dennis Galanakis, Artem Zhmurov, Valeri Barsegov, John W Weisel
We studied the hydrodynamic behavior of fibrinogen, a blood plasma protein involved in blood clotting, in a broad 0.3-60 mg/ml range of concentration and 5-42°C temperature using pulsed-field gradient 1H NMR-diffusometry. Arrhenius plots revealed the activation energy for fibrinogen diffusion Ed = 21.3 kJ/mol at 1.4 mg/ml and 28.4 kJ/mol at 38 mg/ml. We found a dramatic slowdown in fibrinogen self-diffusion with concentration beginning at 1.7-3.4 mg/ml, which deviated from the standard hard-particle behavior, suggesting a remarkable intermolecular entanglement...
July 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28742962/characterization-of-intramolecular-interactions-of-cytochrome-c-using-hydrogen-deuterium-exchange-trapped-ion-mobility-spectrometry-mass-spectrometry-and-molecular-dynamics
#8
Juan Camilo Molano-Arevalo, Kevin Jeanne Dit Fouque, Khoa N Pham, Jaroslava Miksovska, Mark E Ridgeway, Melvin A Park, Francisco Fernandez-Lima
Globular proteins, such as cytochrome c (cyt c), display an organized native conformation, maintained by a hydrogen bond interaction network. In the present work, the structural interrogation of kinetically trapped intermediates of cyt c was performed by correlating the ion-neutral collision cross section (CCS) and charge state with the starting solution conditions and time after desolvation using collision induced activation (CIA), time resolved hydrogen/deuterium back exchange (HDX) and trapped ion mobility spectrometry - mass spectrometry (TIMS-MS)...
July 25, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28742831/deterministic-stability-and-random-behavior-of-a-hepatitis-c-model
#9
Mehmet Merdan, Zafer Bekiryazici, Tulay Kesemen, Tahir Khaniyev
The deterministic stability of a model of Hepatitis C which includes a term defining the effect of immune system is studied on both local and global scales. Random effect is added to the model to investigate the random behavior of the model. The numerical characteristics such as the expectation, variance and confidence interval are calculated for random effects with two different distributions from the results of numerical simulations. In addition, the compliance of the random behavior of the model and the deterministic stability results is examined...
2017: PloS One
https://www.readbyqxmd.com/read/28742797/a-comparison-of-selective-aortic-arch-perfusion-and-resuscitative-endovascular-balloon-occlusion-of-the-aorta-for-the-management-of-hemorrhage-induced-traumatic-cardiac-arrest-a-translational-model-in-large-swine
#10
Ed B G Barnard, James E Manning, Jason E Smith, Jason M Rall, Jennifer M Cox, James D Ross
BACKGROUND: Survival rates remain low after hemorrhage-induced traumatic cardiac arrest (TCA). Noncompressible torso hemorrhage (NCTH) is a major cause of potentially survivable trauma death. Resuscitative Endovascular Balloon Occlusion of the Aorta (REBOA) at the thoracic aorta (Zone 1) can limit subdiaphragmatic blood loss and allow for IV fluid resuscitation when intrinsic cardiac activity is still present. Selective Aortic Arch Perfusion (SAAP) combines thoracic aortic balloon hemorrhage control with intra-aortic oxygenated perfusion to achieve return of spontaneous circulation (ROSC) when cardiac arrest has occurred...
July 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28742364/solvent-exchange-leading-to-nanobubble-nucleation-a-molecular-dynamics-study
#11
Qianxiang Xiao, Yawei Liu, Zhenjiang Guo, Zhiping Liu, Detlef Lohse, Xianren Zhang
The solvent exchange procedure has become the most-used protocol to produce surface nanobubbles, while the molecular mechanisms behind the solvent exchange are far from being fully understood. In this paper, we build a simple model and use molecular dynam- ics simulations to investigate the dynamic characteristics of solvent exchange for producing nanobubbles. We find that at the first stage of solvent exchange, there exists an interface between interchanging solvents of different gas solubility. This interface moves towards the substrate gradually as the exchange process proceeds...
July 25, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28742357/size-effect-in-the-ionization-energy-of-pah-clusters
#12
Christine Joblin, Léo Dontot, Gustavo A Garcia, Fernand Spiegelman, Mathias Rapacioli, Laurent Nahon, Pascal Parneix, Thomas Pino, Philippe Brechignac
We report the first experimental measurement of the near-threshold photo-ionization spectra of polycyclic aromatic hydrocarbon clusters made of pyrene C16H10 and coronene C24H12, obtained using imaging photoelectron photoion coincidence spectrometry with a VUV synchrotron beamline. The experimental results of the ionization energy are confronted to calculated ones obtained from simulations using dedicated electronic structure treatment for large ionized molecular clusters. Experiment and theory consistently find a decrease of the ionization energy with cluster size...
July 25, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28742353/a-dft-assessment-of-the-environment-polarity-effect-on-polyaniline-water-coupling
#13
Jasmina Nedkova Petrova, Anela N Ivanova, Alia V Tadjer
Crystallization water plays an important role for the self-organization of oligomer chains in conducting polyaniline - emeraldine. In order to quantify the interaction between the emeraldine salt and such a water, models containing a tetramer in bipolaronic or polaronic form, chloride counterions and an explicit water molecule are used. Different initial positions of water with respect to the oligomer chain - tangential and vertical, are considered. Various media are simulated by introducing implicit solvent continuum of decreasing polarity...
July 25, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28742267/profiling-the-effects-of-short-time-course-cold-ischemia-on-tumor-protein-phosphorylation-using-a-bayesian-approach
#14
You Wu, Jeremy Gaskins, Maiying Kong, Susmita Datta
Phosphorylated proteins provide insight into tumor etiology and are used as diagnostic, prognostic, and therapeutic markers of complex diseases. However, pre-analytic variations, such as freezing delay after biopsy acquisition, often occur in real hospital settings and potentially lead to inaccurate results. The objective of this work is to develop statistical methodology to assess the stability of phosphorylated proteins under short-time cold ischemia. We consider a hierarchical model to determine if phosphorylation abundance of a protein at a particular phosphorylation site remains constant or not during cold ischemia...
July 25, 2017: Biometrics
https://www.readbyqxmd.com/read/28742252/augmented-and-doubly-robust-g-estimation-of-causal-effects-under-a-structural-nested-failure-time-model
#15
Karl Mertens, Stijn Vansteelandt
Structural nested failure time models (SNFTMs) are models for the effect of a time-dependent exposure on a survival outcome. They have been introduced along with so-called G-estimation methods to provide valid adjustment for time-dependent confounding induced by time-varying variables. Adjustment for informative censoring in SNFTMs is possible via inverse probability of censoring weighting (IPCW). In the presence of considerable dropout, this can imply substantial information loss and consequently imprecise effect estimates...
July 25, 2017: Biometrics
https://www.readbyqxmd.com/read/28742219/model-free-scoring-system-for-risk-prediction-with-application-to-hepatocellular-carcinoma-study
#16
Weining Shen, Jing Ning, Ying Yuan, Anna S Lok, Ziding Feng
There is an increasing need to construct a risk-prediction scoring system for survival data and identify important risk factors (e.g., biomarkers) for patient screening and treatment recommendation. However, most existing methodologies either rely on strong model assumptions (e.g., proportional hazards) or only handle binary outcomes. In this article, we propose a flexible method that simultaneously selects important risk factors and identifies the optimal linear combination of risk factors by maximizing a pseudo-likelihood function based on the time-dependent area under the receiver operating characteristic curve...
July 25, 2017: Biometrics
https://www.readbyqxmd.com/read/28742159/%C3%AE-adrenergic-signaling-broadly-contributes-to-ltp-induction
#17
Joanna Jȩdrzejewska-Szmek, Vincent Luczak, Ted Abel, Kim T Blackwell
Long-lasting forms of long-term potentiation (LTP) represent one of the major cellular mechanisms underlying learning and memory. One of the fundamental questions in the field of LTP is why different molecules are critical for long-lasting forms of LTP induced by diverse experimental protocols. Further complexity stems from spatial aspects of signaling networks, such that some molecules function in the dendrite and some are critical in the spine. We investigated whether the diverse experimental evidence can be unified by creating a spatial, mechanistic model of multiple signaling pathways in hippocampal CA1 neurons...
July 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28742125/y-chromosomal-evidence-on-the-origin-of-northern-thai-people
#18
Andrea Brunelli, Jatupol Kampuansai, Mark Seielstad, Khemika Lomthaisong, Daoroong Kangwanpong, Silvia Ghirotto, Wibhu Kutanan
The Khon Mueang represent the major group of people present in today's northern Thailand. While linguistic and genetic data seem to support a shared ancestry between Khon Mueang and other Tai-Kadai speaking people, the possibility of an admixed origin with contribution from local Mon-Khmer population could not be ruled out. Previous studies conducted on northern Thai people did not provide a definitive answer and, in addition, have largely overlooked the distribution of paternal lineages in the area. In this work we aim to provide a comprehensive analysis of Y paternal lineages in northern Thailand and to explicitly model the origin of the Khon Mueang population...
2017: PloS One
https://www.readbyqxmd.com/read/28742083/long-time-analytic-approximation-of-large-stochastic-oscillators-simulation-analysis-and-inference
#19
Giorgos Minas, David A Rand
In order to analyse large complex stochastic dynamical models such as those studied in systems biology there is currently a great need for both analytical tools and also algorithms for accurate and fast simulation and estimation. We present a new stochastic approximation of biological oscillators that addresses these needs. Our method, called phase-corrected LNA (pcLNA) overcomes the main limitations of the standard Linear Noise Approximation (LNA) to remain uniformly accurate for long times, still maintaining the speed and analytically tractability of the LNA...
July 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28742063/demagnetization-harmonic-effects-on-the-magnetization-of-granular-systems-on-a-macroscopic-scale-the-superconducting-case
#20
Davide Mancusi, Armando Galluzzi, Sandro Pace, Massimiliano Polichetti
A model has been developed to determine the effective ac magnetic response of magnetic systems, taking into account the demagnetization effects arising from the sample geometry which determine out-of-phase components of the applied fundamental frequency and higher harmonic components. Indeed, demagnetization fields and their intermodulation can significantly affect the ac magnetic response. This approach provides a system of self-consistent linear equations relating the magnetic response to the external magnetic field by means of the nonlinear magnetic susceptibility...
July 25, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
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