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Modeling and Simulation

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https://www.readbyqxmd.com/read/27923202/structure-based-optimization-of-salt-bridge-network-across-the-complex-interface-of-ptpn4-pdz-domain-with-its-peptide-ligands-in-neuroglioma
#1
Xian Xiao, Qiang-Hua He, Li-Yan Yu, Song-Qing Wang, Yang Li, Hua Yang, Ai-Hua Zhang, Xiao-Hong Ma, Yu-Jie Peng, Bing Chen
The PTP non-receptor type 4 (PTPN4) is an important regulator protein in learning, spatial memory and cerebellar synaptic plasticity; targeting the PDZ domain of PTPN4 has become as attractive therapeutic strategy for human neuroglioma. Here, we systematically examined the complex crystal structures of PTPN4 PDZ domain with its known peptide ligands; a number of charged amino acid residues were identified in these ligands and in the peptide-binding pocket of PDZ domain, which can constitute a complicated salt-bridge network across the complex interface...
November 30, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27923179/structural-dynamics-of-casein-kinase-i-cki-from-malarial-parasite-plasmodium-falciparum-isolate-3d7-insights-from-theoretical-modelling-and-molecular-simulations
#2
Budheswar Dehury, Santosh Kumar Behera, Namita Mahapatra
The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation...
November 21, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27922831/comprehensive-monte-carlo-study-of-patient-doses-from-cone-beam-ct-imaging-in-radiotherapy
#3
T E Marchant, K D Joshi
Accurate knowledge of ionizing radiation dose from cone-beam CT (CBCT) imaging in radiotherapy is important to allow concomitant risks to be estimated and for justification of imaging exposures. This study uses a Monte Carlo CBCT model to calculate imaging dose for a wide range of imaging protocols for male and female patients. The Elekta XVI CBCT system was modeled using GATE and simulated doses were validated against measurements in a water tank and thorax phantom. Imaging dose was simulated in the male and female ICRP voxel phantoms for a variety of anatomical sites and imager settings (different collimators, filters, full and partial rotation)...
December 6, 2016: Journal of Radiological Protection: Official Journal of the Society for Radiological Protection
https://www.readbyqxmd.com/read/27922825/model-of-turnover-kinetics-in-the-lamellipodium-implications-of-slow-and-fast-diffusing-capping-protein-and-arp2-3-complex
#4
Laura M McMillen, Dimitrios Vavylonis
Cell protrusion through polymerization of actin filaments at the leading edge of motile cells may be influenced by spatial gradients of diffuse actin and regulators. Here we study the distribution of two of the most important regulators, capping protein and Arp2/3 complex, which regulate actin polymerization in the lamellipodium through capping and nucleation of free barbed ends. We modeled their kinetics using data from prior single molecule microscopy experiments on XTC cells. These experiments have provided evidence for a broad distribution of diffusion coefficients of both capping protein and Arp2/3 complex...
December 6, 2016: Physical Biology
https://www.readbyqxmd.com/read/27922735/virtual-cell-imaging-a-review-on-simulation-methods-employed-in-image-cytometry
#5
REVIEW
Vladimír Ulman, David Svoboda, Matti Nykter, Michal Kozubek, Pekka Ruusuvuori
The simulations of cells and microscope images thereof have been used to facilitate the development, selection, and validation of image analysis algorithms employed in cytometry as well as for modeling and understanding cell structure and dynamics beyond what is visible in the eyepiece. The simulation approaches vary from simple parametric models of specific cell components-especially shapes of cells and cell nuclei-to learning-based synthesis and multi-stage simulation models for complex scenes that simultaneously visualize multiple object types and incorporate various properties of the imaged objects and laws of image formation...
December 6, 2016: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/27922719/markov-mixed-effects-modeling-using-electronic-adherence-monitoring-records-identifies-influential-covariates-to-hiv-preexposure-prophylaxis
#6
Kumpal Madrasi, Ayyappa Chaturvedula, Jessica E Haberer, Mark Sale, Michael J Fossler, David Bangsberg, Jared M Baeten, Connie Celum, Craig W Hendrix
Adherence is a major factor in the effectiveness of preexposure prophylaxis (PrEP) for HIV prevention. Modeling patterns of adherence helps to identify influential covariates of different types of adherence as well as to enable clinical trial simulation so that appropriate interventions can be developed. We developed a Markov mixed-effects model to understand the covariates influencing adherence patterns to daily oral PrEP. Electronic adherence records (date and time of medication bottle cap opening) from the Partners PrEP ancillary adherence study with a total of 1147 subjects were used...
December 6, 2016: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/27922569/mode-of-information-delivery-does-not-effect-anesthesia-trainee-performance-during-simulated-perioperative-pediatric-critical-events-a-trial-of-paper-versus-electronic-cognitive-aids
#7
Scott C Watkins, Shilo Anders, Anna Clebone, Elisabeth Hughes, Vikram Patel, Laura Zeigler, Yaping Shi, Matthew S Shotwell, Matthew D McEvoy, Matthew B Weinger
INTRODUCTION: Cognitive aids (CAs), including emergency manuals and checklists, have been recommended as a means to address the failure of healthcare providers to adhere to evidence-based standards of treatment during crisis situations. Unfortunately, users of CAs still commit errors, omit critical steps, fail to achieve perfect adherence to guidelines, and frequently choose to not use CA during both simulated and real crisis events. We sought to evaluate whether the mode in which a CA presents information (ie, paper vs...
December 2016: Simulation in Healthcare: Journal of the Society for Simulation in Healthcare
https://www.readbyqxmd.com/read/27922533/a-propensity-score-based-fine-stratification-approach-for-confounding-adjustment-when-exposure-is-infrequent
#8
Rishi J Desai, Kenneth J Rothman, Brian T Bateman, Sonia Hernandez-Diaz, Krista F Huybrechts
BACKGROUND: When exposure is infrequent, propensity score matching results in reduced precision because it discards a large proportion of unexposed patients. To our knowledge, the relative performance of propensity score stratification in these circumstances has not been examined. METHODS: Using an empirical example of the association of first-trimester statin exposure (prevalence=0.04%) with risk of congenital malformations and 1,000 simulated cohorts (n=20,000) with eight combinations of exposure prevalence (0...
November 29, 2016: Epidemiology
https://www.readbyqxmd.com/read/27921372/a-fuzzy-neural-network-sliding-mode-controller-for-vibration-suppression-in-robotically-assisted-minimally-invasive-surgery
#9
Hongqiang Sang, Chenghao Yang, Fen Liu, Jintian Yun, Guoguang Jin
BACKGROUND: It is very important for robotically assisted minimally invasive surgery to achieve a high-precision and smooth motion control. However, the surgical instrument tip will exhibit vibration caused by nonlinear friction and unmodeled dynamics, especially when the surgical robot system is attempting low-speed, fine motion. METHODS: A fuzzy neural network sliding mode controller (FNNSMC) is proposed to suppress vibration of the surgical robotic system. Nonlinear friction and modeling uncertainties are compensated by a Stribeck model, a radial basis function (RBF) neural network and a fuzzy system, respectively...
December 2016: International Journal of Medical Robotics + Computer Assisted Surgery: MRCAS
https://www.readbyqxmd.com/read/27921352/posttraumatic-stress-disorder-associated-with-unexpected-death-of-a-loved-one-cross-national-findings-from-the-world-mental-health-surveys
#10
Lukoye Atwoli, Dan J Stein, Andrew King, Maria Petukhova, Sergio Aguilar-Gaxiola, Jordi Alonso, Evelyn J Bromet, Giovanni de Girolamo, Koen Demyttenaere, Silvia Florescu, Josep Maria Haro, Elie G Karam, Norito Kawakami, Sing Lee, Jean-Pierre Lepine, Fernando Navarro-Mateu, Siobhan O'Neill, Beth-Ellen Pennell, Marina Piazza, Jose Posada-Villa, Nancy A Sampson, Margreet Ten Have, Alan M Zaslavsky, Ronald C Kessler
BACKGROUND: Unexpected death of a loved one (UD) is the most commonly reported traumatic experience in cross-national surveys. However, much remains to be learned about posttraumatic stress disorder (PTSD) after this experience. The WHO World Mental Health (WMH) survey initiative provides a unique opportunity to address these issues. METHODS: Data from 19 WMH surveys (n = 78,023; 70.1% weighted response rate) were collated. Potential predictors of PTSD (respondent sociodemographics, characteristics of the death, history of prior trauma exposure, history of prior mental disorders) after a representative sample of UDs were examined using logistic regression...
December 6, 2016: Depression and Anxiety
https://www.readbyqxmd.com/read/27921189/homogenized-constrained-mixture-models-for-anisotropic-volumetric-growth-and-remodeling
#11
F A Braeu, A Seitz, R C Aydin, C J Cyron
Constrained mixture models for soft tissue growth and remodeling have attracted increasing attention over the last decade. They can capture the effects of the simultaneous presence of multiple constituents that are continuously deposited and degraded at in general different rates, which is important to understand essential features of living soft tissues that cannot be captured by simple kinematic growth models. Recently the novel concept of homogenized constrained mixture models was introduced. It was shown that these models produce results which are very similar (and in certain limit cases even identical) to the ones of constrained mixture models based on multi-network theory...
December 5, 2016: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/27921169/drying-kinetics-of-deformable-and-cracking-nano-porous-gels
#12
J Thiery, E Keita, S Rodts, D Courtier Murias, T Kodger, A Pegoraro, P Coussot
The desiccation of porous materials encompasses a wide range of technological and industrial processes and is acutely sensitive to the hierarchical structure of the porous materials resulting in complex dynamics which are challenging to unravel. Macroscopic observations of the surface and geometry of model colloidal gels during desiccation under controlled air flow highlight the role of crack formation in drying. The density of cracks and their rate of appearance depend on the initial solid fraction of the gels and their adherence to the substrate...
December 2016: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/27921106/quantum-and-classical-inter-cage-hopping-of-hydrogen-molecules-in-clathrate-hydrate-temperature-and-cage-occupation-effects
#13
Christian J Burnham, Zdenek Futera, Niall J English
Building on our previous work (J. Phys. Chem. C, 2016, 120, 16561), using an empirical model we run both classical and path-integral molecular dynamics simulations for a type II clathrate hydrate containing different amounts of guest H2 molecules from 1 to 5 molecules per large cage, with results presented at temperatures of 50, 100 K and 200 K. We present results for the density isosurfaces of the guest molecules at all different occupations and temperatures, showing how the density approaches the perfect tetrahedral structure which has been found for the n = 4 case in which each molecule sits on the vertex of a tetrahedron about the centre of each large cage...
December 6, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27921074/initial-performance-studies-of-a-wearable-brain-positron-emission-tomography-camera-based-on-autonomous-thin-film-digital-geiger-avalanche-photodiode-arrays
#14
Charles R Schmidtlein, James N Turner, Michael O Thompson, Krishna C Mandal, Ida Häggström, Jiahan Zhang, John L Humm, David H Feiglin, Andrzej Krol
Using analytical and Monte Carlo modeling, we explored performance of a lightweight wearable helmet-shaped brain positron emission tomography (PET), or BET camera, based on thin-film digital Geiger avalanche photodiode arrays with Lutetium-yttrium oxyorthosilicate (LYSO) or [Formula: see text] scintillators for imaging in vivo human brain function of freely moving and acting subjects. We investigated a spherical cap BET and cylindrical brain PET (CYL) geometries with 250-mm diameter. We also considered a clinical whole-body (WB) LYSO PET/CT scanner...
January 2017: Journal of Medical Imaging
https://www.readbyqxmd.com/read/27921010/structural-insights-into-substrate-recognition-by-clostridium-difficile-sortase
#15
Jui-Chieh Yin, Chun-Hsien Fei, Yen-Chen Lo, Yu-Yuan Hsiao, Jyun-Cyuan Chang, Jay C Nix, Yuan-Yu Chang, Lee-Wei Yang, I-Hsiu Huang, Shuying Wang
Sortases function as cysteine transpeptidases that catalyze the covalent attachment of virulence-associated surface proteins into the cell wall peptidoglycan in Gram-positive bacteria. The substrate proteins targeted by sortase enzymes have a cell wall sorting signal (CWSS) located at the C-terminus. Up to date, it is still not well understood how sortases with structural resemblance among different classes and diverse species of bacteria achieve substrate specificity. In this study, we focus on elucidating the molecular basis for specific recognition of peptide substrate PPKTG by Clostridium difficile sortase B (Cd-SrtB)...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27920956/grassland-productivity-in-response-to-nutrient-additions-and-herbivory-is-scale-dependent
#16
Erica A H Smithwick, Douglas C Baldwin, Kusum J Naithani
Vegetation response to nutrient addition can vary across space, yet studies that explicitly incorporate spatial pattern into experimental approaches are rare. To explore whether there are unique spatial scales (grains) at which grass response to nutrients and herbivory is best expressed, we imposed a large (∼3.75 ha) experiment in a South African coastal grassland ecosystem. In two of six 60 × 60 m grassland plots, we imposed a scaled sampling design in which fertilizer was added in replicated sub-plots (1 × 1 m, 2 × 2 m, and 4 × 4 m)...
2016: PeerJ
https://www.readbyqxmd.com/read/27920940/3d-printing-in-neurosurgery-a-systematic-review
#17
REVIEW
Michael Randazzo, Jared M Pisapia, Nickpreet Singh, Jayesh P Thawani
BACKGROUND: The recent expansion of three-dimensional (3D) printing technology into the field of neurosurgery has prompted a widespread investigation of its utility. In this article, we review the current body of literature describing rapid prototyping techniques with applications to the practice of neurosurgery. METHODS: An extensive and systematic search of the Compendex, Scopus, and PubMed medical databases was conducted using keywords relating to 3D printing and neurosurgery...
2016: Surgical Neurology International
https://www.readbyqxmd.com/read/27920466/joint-models-for-multiple-longitudinal-processes-and-time-to-event-outcome
#18
Lili Yang, Menggang Yu, Sujuan Gao
Joint models are statistical tools for estimating the association between time-to-event and longitudinal outcomes. One challenge to the application of joint models is its computational complexity. Common estimation methods for joint models include a two-stage method, Bayesian and maximum-likelihood methods. In this work, we consider joint models of a time-to-event outcome and multiple longitudinal processes and develop a maximum-likelihood estimation method using the expectation-maximization (EM) algorithm...
2016: Journal of Statistical Computation and Simulation
https://www.readbyqxmd.com/read/27920368/use-of-the-concordance-index-for-predictors-of-censored-survival-data
#19
Adam R Brentnall, Jack Cuzick
The concordance index is often used to measure how well a biomarker predicts the time to an event. Estimators of the concordance index for predictors of right-censored data are reviewed, including those based on censored pairs, inverse probability weighting and a proportional-hazards model. Predictive and prognostic biomarkers often lose strength with time, and in this case the aforementioned statistics depend on the length of follow up. A semi-parametric estimator of the concordance index is developed that accommodates converging hazards through a single parameter in a Pareto model...
December 5, 2016: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/27920331/3d-model-analysis-of-ankle-flexion-on-anatomic-reduction-of-a-syndesmotic-injury
#20
Jason M Schon, Jacob D Mikula, Jonathon D Backus, Melanie B Venderley, Grant J Dornan, Robert F LaPrade, Thomas O Clanton
BACKGROUND: The effect of ankle positioning during suture-button fixation for syndesmosis repair on range of motion (ROM) and anatomic reduction has yet to be investigated. The purpose of this cadaveric study was to compare the effects of 3 different ankle positions during suture-button repair on volumetric reduction of the syndesmosis, fibular displacement, and ROM of the ankle using 3-dimensional computed tomography (CT) analysis. The null hypothesis was that ankle position during fixation would not affect syndesmotic volume restoration, fibular displacement, or ROM...
December 5, 2016: Foot & Ankle International
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