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  • 1
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    HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-21
    Description: Motivation: Cancer cells are often characterized by epigenetic changes, which include aberrant histone modifications. In particular, local or regional epigenetic silencing is a common mechanism in cancer for silencing expression of tumor suppressor genes. Though several tools have been created to enable detection of histone marks in ChIP-seq data from normal samples, it is unclear whether these tools can be efficiently applied to ChIP-seq data generated from cancer samples. Indeed, cancer genomes are often characterized by frequent copy number alterations: gains and losses of large regions of chromosomal material. Copy number alterations may create a substantial statistical bias in the evaluation of histone mark signal enrichment and result in underdetection of the signal in the regions of loss and overdetection of the signal in the regions of gain. Results: We present HMCan (Histone modifications in cancer), a tool specially designed to analyze histone modification ChIP-seq data produced from cancer genomes. HMCan corrects for the GC-content and copy number bias and then applies Hidden Markov Models to detect the signal from the corrected data. On simulated data, HMCan outperformed several commonly used tools developed to analyze histone modification data produced from genomes without copy number alterations. HMCan also showed superior results on a ChIP-seq dataset generated for the repressive histone mark H3K27me3 in a bladder cancer cell line. HMCan predictions matched well with experimental data (qPCR validated regions) and included, for example, the previously detected H3K27me3 mark in the promoter of the DLEC1 gene, missed by other tools we tested. Availability: Source code and binaries can be downloaded at http://www.cbrc.kaust.edu.sa/hmcan/ , implemented in C++. Contact: haitham.ashoor@kaust.edu.sa Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    MAGFLOW: a physics-based model for the dynamics of lava-flow emplacement (2015)
    Geological Society (of London)
    Details
    Publication Date: 2015-08-01
    Description: The MAGFLOW model for lava-flow simulations is based on the cellular automaton (CA) approach, and uses a physical model for the thermal and rheological evolution of the flowing lava. We discuss the potential of MAGFLOW to improve our understanding of the dynamics of lava-flow emplacement and our ability to assess lava-flow hazards. Sensitivity analysis of the input parameters controlling the evolution function of the automaton demonstrates that water content and solidus temperatures are the parameters to which MAGFLOW is most sensitive. Additional tests also indicate that temporal changes in effusion rate strongly influence the accuracy of the predictive modelling of lava-flow paths. The parallel implementation of MAGFLOW on graphic processing units (GPUs) can achieve speed-ups of two orders of magnitude relative to the corresponding serial implementation, providing a lava-flow simulation spanning several days of eruption in just a few minutes. We describe and demonstrate the operation of MAGFLOW using two case studies from Mt Etna: one is a reconstruction of the detailed chronology of the lava-flow emplacement during the 2006 flank eruption; and the other is the production of the lava-flow hazard map of the persistent eruptive activity at the summit craters.
    Print ISSN: 0305-8719
    Electronic ISSN: 2041-4927
    Topics: Geosciences
    Published by Geological Society (of London)
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  • 3
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    GPUSPH: a Smoothed Particle Hydrodynamics model for the thermal and rheological evolution of lava flows (2015)
    Geological Society (of London)
    Details
    Publication Date: 2015-11-11
    Description: GPUSPH is a fully three-dimensional model for the simulation of the thermal and rheological evolution of lava flows that relies on the Smoothed Particle Hydrodynamics (SPH) numerical method. Thanks to the Lagrangian, meshless nature of SPH, the model incorporates a more complete physical description of the emplacement process and rheology of lava that considers the free surface, the irregular boundaries represented by the topography, the solidification fronts and the non-Newtonian rheology with temperature-dependent parameters. GPUSPH follows the very general Herschel–Bulkley rheological model, which encompasses Newtonian, power-law and Bingham flow behaviours, with both constant and temperature-dependent parameters, and can thus be used to explore in detail the impact of rheology on the behaviour of lava flows and on their emplacement. To illustrate this possibility, we present some preliminary applications of the model for studying the rheology of lava flows with different constitutive relationships and thermal regimes using the real topography of the Mt Etna volcano.
    Print ISSN: 0305-8719
    Electronic ISSN: 2041-4927
    Topics: Geosciences
    Published by Geological Society (of London)
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  • 4
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    HOTSAT: a multiplatform system for the thermal monitoring of volcanic activity using satellite data (2015)
    Geological Society (of London)
    Details
    Publication Date: 2015-10-31
    Description: The HOTSAT multiplatform system for the analysis of infrared data from satellites provides a framework that allows the detection of volcanic hotspots and an output of their associated radiative power. This multiplatform system can operate on both Moderate Resolution Imaging Spectroradiometer and Spinning Enhanced Visible and Infrared Imager data. The new version of the system is now implemented on graphics processing units and its interface is available on the internet under restricted access conditions. Combining the estimation of time-varying discharge rates using HOTSAT with the MAGFLOW physics-based model to simulate lava flow paths resulted in the first operational system in which satellite observations drive the modelling of lava flow emplacement. This allows the timely definition of the parameters and maps essential for hazard assessment, including the propagation time of lava flows and the maximum run-out distance. The system was first used in an operational context during the paroxysmal episode at Mt Etna on 12–13 January 2011, when we produced real-time predictions of the areas likely to be inundated by lava flows while the eruption was still ongoing. This allowed key at-risk areas to be rapidly and appropriately identified.
    Print ISSN: 0305-8719
    Electronic ISSN: 2041-4927
    Topics: Geosciences
    Published by Geological Society (of London)
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  • 5
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    HOTSAT: a multiplatform system for the thermal monitoring of volcanic activity using satellite data (2015)
    Geological Society of London
    Details
    Publication Date: 2015-10-29
    Print ISSN: 0305-8719
    Electronic ISSN: 2041-4927
    Topics: Geosciences
    Published by Geological Society of London
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  • 6
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    SPH on GPU with CUDA (2011)
    Details
    Publication Date: 2021-02-17
    Description: A Smoothed Particle Hydrodynamics (SPH) method for free surface flows has been implemented on a graphical processing unit (GPU) using the Compute Unified Device Architecture (CUDA) developed by Nvidia, resulting in tremendous speed-ups. The entire SPH code, with its three main components: neighbor list construction, force computation, and integration of the equation of motion, is computed on the GPU, fully exploiting its computational power. The simulation speed achieved is one to two orders of magnitude faster than the equivalent CPU code. Example applications are shown for paddle-generated waves in a basin and a dam-break wave impact on a structure. GPU implementation of SPH permits high resolution SPH modeling in hours and days rather than weeks and months on inexpensive and readily available hardware.
    Description: Published
    Description: 74-79
    Description: 2.1. TTC - Laboratorio per le reti informatiche, GRID e calcolo avanzato
    Description: JCR Journal
    Description: reserved
    Keywords: CUDA, fluid simulation, GPGPU, GPU, particle methods, smoothed particle hydrodynamics ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 7
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    Forecasting Lava Flow Hazard during the 2006 Etna Eruption: Using the Magflow Cellular Automata Model (2008)
    Elsevier
    Details
    Publication Date: 2020-11-16
    Description: The MAGFLOW cellular automata model was able to fairly accurately reproduce the time of the lava flow advance during the 2006 Etna eruption leading to very plausible flow predictions. MAGFLOW is intended for use in emergency response situations during an eruption to quickly forecast the lava flow path over some time interval from the immediate future to a long-time forecast. Major discrepancies between the observed and simulated paths occurred in the early phase of the 2006 eruption due to an underestimation of the initial flow rate, and at the time of the overlapping with the 2004-2005 lava flow. Very good representations of the areas likely to be inundated by lava flows were obtained when we adopt a time-varying effusion rate and include the 2004-2005 lava flow field in the Digital Elevation Model (DEM) of topography.
    Description: Published
    Description: 1050-1060
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
    Description: open
    Keywords: Lava Flow ; Etna volcano ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk ; 05. General::05.01. Computational geophysics::05.01.02. Cellular automata, fuzzy logic, genetic alghoritms, neural networks ; 05. General::05.01. Computational geophysics::05.01.05. Algorithms and implementation
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    SPH modeling of dynamic impact of tsunami bore on bridge piers (2016)
    Elsevier Science Limited
    Details
    Publication Date: 2021-02-17
    Description: The Smoothed Particle Hydrodynamics (SPH) method is applied to investigate the impact of a tsunami bore on simplified bridge piers in this study. This work was motivated by observations of bridge damage during several recent tsunami events, and its aim is to further the understanding of the dynamic interaction between a tsunami bore and a bridge pier. This study is carried out by simulating a well-conducted physical experiment on a tsunami bore impingement on vertical columns with an SPH model, GPUSPH. The influences of bridge pier shape and orientation on free surface evolution and hydrodynamic loading are carefully examined. Furthermore, the unsteady flow field that is around and in the wake of the bridge pier is analyzed. Finally, GPUSPH is applied to explore the hydrodynamic force caused by the bridge pier blockage, the wave impact on structures, and the bed shear stress around a bridge pier due to a strong tsunami bore.
    Description: Published
    Description: 26-42
    Description: 3IT. Calcolo scientifico e sistemi informatici
    Description: JCR Journal
    Description: restricted
    Keywords: Tsunami bore; Bridge piers; Wave–structure interaction; Hydrodynamic force; GPUSPH; Smoothed Particle Hydrodynamics ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    Modeling of the 2001 lava flow at Etna volcano by a Cellular Automata approach (2007)
    Elsevier
    Details
    Publication Date: 2017-04-04
    Description: The 2D Cellular Automata model, MAGFLOW, simulates lava flows and an algorithm based on the Monte Carlo approach solves the anisotropic flow direction problem. The model was applied to reproduce a lava flow formed during the 2001 Etna eruption. This eruption provided the opportunity to verify the ability of MAGFLOW to simulate the path of lava flows which was made possible due to the availability of the necessary data for both modeling and subsequent validation. MAGFLOW reproduced quite accurately the spread of flow. A good agreement was highlighted between the simulated and observed length on steep slopes, whereas the area covered by the lava flow tends to be overestimated. The major inconsistencies found in the comparison between simulated and observed lava flow due to neglecting the effects of ephemeral vent formation.
    Description: Published
    Description: 3.6. Fisica del vulcanismo
    Description: 4.3. TTC - Scenari di pericolosità vulcanica
    Description: JCR Journal
    Description: open
    Keywords: Lava flow ; Etna volcano ; Numerical simulation ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk ; 05. General::05.01. Computational geophysics::05.01.02. Cellular automata, fuzzy logic, genetic alghoritms, neural networks
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    Simulations of the 2004 lava flow at etna volcano by the magflow cellular automata model (2007)
    Details
    Publication Date: 2017-04-04
    Description: Lava flows represent a challenge for physically based modeling, since the mechanical properties of lava change over time. This change is ruled by a temperature field, which needs to be modeled. MAGFLOW Cellular Automata (CA) model was developed for physically based simulations of lava flows in near real-time. We introduced an algorithm based on the Monte Carlo approach to solve the anisotropic problem. As transition rule of CA, a steady state solution of Navier-Stokes equations was adopted in the case of isothermal laminar pressure-driven Bingham fluid. For the cooling mechanism, we consider the radiative heat loss only from the surface of the flow, and the change of the temperature due to mixture of lavas between cells with different temperatures. The model was applied to reproduce a real lava flow occurred during the 2004-2005 Etna eruption. The simulations were computed using three different empirical relationships between viscosity and temperature.
    Description: Submitted
    Description: JCR Journal
    Description: open
    Keywords: Mount Etna, ; lava flow, ; simulation, ; Cellular Automata ; 04. Solid Earth::04.08. Volcanology::04.08.08. Volcanic risk ; 05. General::05.01. Computational geophysics::05.01.02. Cellular automata, fuzzy logic, genetic alghoritms, neural networks
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: manuscript
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