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Computational model

Lucia Russo, Paola Russo, Constantinos I Siettos
Based on complex network theory, we propose a computational methodology which addresses the spatial distribution of fuel breaks for the inhibition of the spread of wildland fires on heterogeneous landscapes. This is a two-level approach where the dynamics of fire spread are modeled as a random Markov field process on a directed network whose edge weights are determined by a Cellular Automata model that integrates detailed GIS, landscape and meteorological data. Within this framework, the spatial distribution of fuel breaks is reduced to the problem of finding network nodes (small land patches) which favour fire propagation...
2016: PloS One
Todd C Rae, Paul Martin Johnson, Wataru Yano, Eishi Hirasaki
The semicircular canals of the inner ear constitute the organ of balance, tracking head rotation during movement and facilitating stabilisation of vision. Morphological characteristics of the canals are correlated with agility scores related to locomotion. To date, however, the relationship between canal morphology and specific locomotor behaviours, such as leaping, is unclear. Knowledge of such a relationship could strengthen the inferences of locomotion of extinct taxa. To test this, crania of two sets of closely related primate species (Presbytis melalophos and P...
October 26, 2016: Folia Primatologica; International Journal of Primatology
K Slooten
Several methods exist to compute the likelihood ratio LR(M, g) evaluating the possible contribution of a person of interest with genotype g to a mixed trace M. In this paper we generalize this LR to a likelihood ratio LR(M1, M2) involving two possibly mixed traces M1 and M2, where the question is whether there is a donor in common to both traces. In case one of the traces is in fact a single genotype, then this likelihood ratio reduces to the usual LR(M, g). We explain how our method conceptually is a logical consequence of the fact that LR calculations of the form LR(M, g) can be equivalently regarded as a probabilistic deconvolution of the mixture...
October 12, 2016: Forensic Science International. Genetics
J L Santiago, R Borge, F Martin, D de la Paz, A Martilli, J Lumbreras, B Sanchez
The distribution of pollutants is spatially heterogeneous within urban streets making difficult to build a realistic concentration map. In this paper, a methodology based on computational fluid dynamic modeling with Reynolds-averaged Navier-Stokes approach is used to compute maps of concentration for a period of several weeks. The methodology is evaluated by comparing simulation results against experimental data from two different campaigns where a large number of passive samplers deployed in an area with heavy vehicular traffic in Madrid (Spain)...
October 22, 2016: Science of the Total Environment
Irving E Wang, Thomas R Clandinin
The activity and maintenance of neurons requires substantial metabolic energy, resulting in selective pressure to decrease resource consumption by the nervous system. The wiring economy principle proposes that animals have evolved mechanisms that wire circuits efficiently by minimizing neurite length. Computational modeling of neuronal morphology, microcircuit organization, and neural networks reveals that wiring economy is a significant determinant of nervous system layout. The strategies for reducing wiring costs are shared across phyla and point to the possibility of generalizable rules that specify the development of efficient nervous systems...
October 24, 2016: Current Biology: CB
Federico Melaccio, María Del Carmen Marín, Alessio Valentini, Fabio Montisci, Silvia Rinaldi, Marco Cherubini, Xuchun Yang, Yoshitaka Kato, Michael Stenrup, Yoelvis Orozco-Gonzalez, Nicolas Ferré, Hoi Ling Luk, Hideki Kandori, Massimo Olivucci
We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side-chains and distributions of external counterions. Starting with such information a model formed by a fixed environment system, a flexible cavity system and a chromophore system is automatically generated...
October 25, 2016: Journal of Chemical Theory and Computation
Malachi W Gillick-Healy, Elizabeth V Jennings, Helge Muller-Bunz, Yannick Ortin, Kirill Nikitin, Declan G Gilheany
The energy barriers in our recently discovered Walden inversion of chlorophosphonium salts are similar to those in Cope rearrangements of caged cyclic hydrocarbons. We have therefore designed a molecular system integrating the two processes, thereby producing the first embodiment in a chemical species of two entirely different and independent stereomutation mechanisms at the same nominal asymmetric centre. Thus, the energy barrier to the rearrangement of 9-phenyl-9-phosphabarbaralane oxide, easily prepared by a new high-yielding synthesis, was found to be ca...
October 25, 2016: Chemistry: a European Journal
Carl Neuerburg, Theresa Loer, Lena Mittlmeier, Christina Polan, Zsuzsanna Farkas, Lesca Miriam Holdt, Sandra Utzschneider, Jens Schwiesau, Thomas M Grupp, Wolfgang Böcker, Attila Aszodi, Christian Wedemeyer, Christian Kammerlander
Aseptic loosening mediated by wear particle-induced osteolysis (PIO) remains the major cause of implant loosening in endoprosthetic surgery. The development of new vitamin E (α-tocopherol)-blended ultra-high molecular weight polyethylene (VE-UHMWPE) with increased oxidation resistance and improved mechanical properties has raised hopes. Furthermore, regenerative approaches may be opened, as vitamin E supplementation has shown neuroprotective characteristics mediated via calcitonin gene-related peptide (CGRP), which is known to affect bone remodeling in PIO...
October 18, 2016: International Journal of Molecular Medicine
Arne Liebau, Olivia Pogorzelski, Alec N Salt, Stefan K Plontke
OBJECTIVE: Controlled and uncontrolled studies with primary intratympanic or combined intratympanic and systemic application of glucocorticosteroids for idiopathic sudden hearing loss were analyzed by means of a meta-analysis in an attempt to establish optimal local drug delivery protocols. STUDY DESIGN: A total of 25 studies with 28 treatment groups between January 2000 and June 2014 were selected that adequately described drug delivery protocols. Cochlear drug levels were calculated by a validated computer model of drug dispersion in the inner ear fluids based on the concentration and volume of glucocorticoids applied, the time the drug remained in the middle ear, and the specific timing of injections...
October 21, 2016: Otology & Neurotology
Elizabeth A Belloli, Irina Degtiar, Xin Wang, Gregory A Yanik, Linda J Stuckey, Stijn E Verleden, Ella A Kazerooni, Brian D Ross, Susan Murray, Craig J Galbán, Vibha N Lama
RATIONALE: The predominant cause of chronic lung allograft failure is small airway obstruction arising from bronchiolitis obliterans. However, clinical methodologies for evaluating presence and degree of small airway disease are lacking. OBJECTIVES: To determine if Parametric Response Mapping (PRM), a novel computed tomography (CT) voxel-wise methodology, can offer insight into chronic allograft failure phenotypes and provide prognostic information following spirometric decline...
October 25, 2016: American Journal of Respiratory and Critical Care Medicine
Bethany G Caulkins, Robert P Young, Ryan A Kudla, Chen Yang, Thomas J Bittbauer, Baback Bastin, Eduardo Hilario, Li Fan, Michael J Marsella, Michael F Dunn, Leonard J Mueller
Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography - the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry - to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established...
October 25, 2016: Journal of the American Chemical Society
Lina Humbeck, Oliver Koch
The ever increasing bioactivity data that are produced nowadays allow exhaustive data mining and knowledge discovery approaches that change chemical biology research. A wealth of chemoinformatics tools, web services and applications therefore exists that supports a careful evaluation and analysis of experimental data to draw conclusions that can influence the further development of chemical probes and potential lead structures. This review focuses on open-source approaches that can be handled by scientists who are not familiar with computational methods having no expert knowledge in chemoinformatics and modeling...
October 25, 2016: ACS Chemical Biology
Fang Zheng, Harris Perlman, Patrick Matthys, Yurong Wen, Tony Lahoutte, Serge Muyldermans, Shemin Lu, Patrick De Baetselier, Steve Schoonooghe, Nick Devoogdt, Geert Raes
Single-photon emission computed tomography combined with micro-CT (SPECT/μCT) imaging using Nanobodies against complement receptor of the Ig superfamily (CRIg), found on tissue macrophages such as synovial macrophages, has promising potential to visualize joint inflammation in experimental arthritis. Here, we further addressed the specificity and assessed the potential for arthritis monitoring. Signals obtained with (99m)Tc-labelled NbV4m119 Nanobody were compared in joints of wild type (WT) versus CRIg(-/-) mice with collagen-induced arthritis (CIA) or K/BxN serum transfer-induced arthritis (STIA)...
October 25, 2016: Scientific Reports
Hui Shen, Desmond K P Chau, Jianpo Su, Ling-Li Zeng, Weixiong Jiang, Jufang He, Jintu Fan, Dewen Hu
Brain responses to facial attractiveness induced by facial proportions are investigated by using functional magnetic resonance imaging (fMRI), in 41 young adults (22 males and 19 females). The subjects underwent fMRI while they were presented with computer-generated, yet realistic face images, which had varying facial proportions, but the same neutral facial expression, baldhead and skin tone, as stimuli. Statistical parametric mapping with parametric modulation was used to explore the brain regions with the response modulated by facial attractiveness ratings (ARs)...
October 25, 2016: Scientific Reports
Hyo Jung Cho, Bohyun Kim, Jung-Dong Lee, Dae Ryong Kang, Jai Keun Kim, Jei Hee Lee, Sung Jae Shin, Kee Myung Lee, Byung Moo Yoo, Kwang Jae Lee, Soon Sun Kim, Jae Youn Cheong, Sung Won Cho
OBJECTIVES: This study was performed to evaluate long-term outcome of indeterminate nodules detected on cirrhotic liver and to develop risk prediction model for hepatocellular carcinoma (HCC) progression of indeterminate nodules on hepatitis B virus (HBV)-related cirrhotic liver. METHODS: Indeterminate nodules up to 2 cm with uncertain malignant potential detected on computed tomography of cirrhotic liver during HCC surveillance were analyzed retrospectively. HCC risk prediction model of indeterminate nodules in HBV-related cirrhotic liver was deduced based on result of Cox regression analysis...
October 25, 2016: American Journal of Gastroenterology
Juan Manuel Gomez, Lyubov Chumakova, Natalia A Bulgakova, Nicholas H Brown
Interphase microtubule organization is critical for cell function and tissue architecture. In general, physical mechanisms are sufficient to drive microtubule organization in single cells, whereas cells within tissues are thought to utilize signalling mechanisms. By improving the imaging and quantitation of microtubule alignment within developing Drosophila embryos, here we demonstrate that microtubule alignment underneath the apical surface of epithelial cells follows cell shape. During development, epidermal cell elongation and microtubule alignment occur simultaneously, but by perturbing cell shape, we discover that microtubule organization responds to cell shape, rather than the converse...
October 25, 2016: Nature Communications
Matti Stenroos
Boundary element methods (BEM) are used for forward computation of bioelectromagnetic fields in multi-compartment volume conductor models. Most BEM approaches assume that each compartment is in contact with at most one external compartment. In this work, I present a general surface integral equation and BEM discretization that remove this limitation and allow BEM modeling of general piecewise-homogeneous medium. The new integral equation allows positioning of field points at junctioned boundary of more than two compartments, enabling the use of linear collocation BEM in such a complex geometry...
November 21, 2016: Physics in Medicine and Biology
Shekhar S Chandra, Jason A Dowling, Peter B Greer, Jarad Martin, Chris Wratten, Peter Pichler, Jurgen Fripp, Stuart Crozier
Active shape models (ASMs) have proved successful in automatic segmentation by using shape and appearance priors in a number of areas such as prostate segmentation, where accurate contouring is important in treatment planning for prostate cancer. The ASM approach however, is heavily reliant on a good initialisation for achieving high segmentation quality. This initialisation often requires algorithms with high computational complexity, such as three dimensional (3D) image registration. In this work, we present a fast, self-initialised ASM approach that simultaneously fits multiple objects hierarchically controlled by spatially weighted shape learning...
November 21, 2016: Physics in Medicine and Biology
Youngwoo Kim, Sonu K Bae, Tianming Cheng, Cheng Tao, Yinghui Ge, Arlene B Chapman, Vincente E Torres, Alan S L Yu, Michal Mrug, William M Bennett, Michael F Flessner, Doug P Landsittel, Kyongtae T Bae
Liver and liver cyst volume measurements are important quantitative imaging biomarkers for assessment of disease progression in autosomal dominant polycystic kidney disease (ADPKD) and polycystic liver disease (PLD). To date, no study has presented automated segmentation and volumetric computation of liver and liver cysts in these populations. In this paper, we proposed an automated segmentation framework for liver and liver cysts from bounded abdominal MR images in patients with ADPKD. To model the shape and variations in ADPKD livers, the spatial prior probability map (SPPM) of liver location and the tissue prior probability maps (TPPMs) of liver parenchymal tissue intensity and cyst morphology were generated...
November 21, 2016: Physics in Medicine and Biology
Harriet Lea-Banks, Boon Teo, Eleanor Stride, Constantin C Coussios
A significant barrier to successful drug delivery is the limited penetration of nanoscale therapeutics beyond the vasculature. Building on recent in vivo findings in the context of cancer drug delivery, the current study investigates whether modification of nanoparticle drug-carriers to increase their density can be used to enhance their penetration into viscoelastic materials under ultrasound exposure. A computational model is first presented to predict the transport of identically sized nanoparticles of different densities in an ultrasonic field in the presence of an oscillating microbubble, by a combination of primary and secondary acoustic radiation forces, acoustic streaming and microstreaming...
November 21, 2016: Physics in Medicine and Biology
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