50 results on '"Bordas R"'
Search Results
2. Tensile Properties of Inconel 718 Produced by LMD-Wire
- Author
-
Cormier, J., Cabeza, S., Burlot, G., Bordas, R., Bordas-Czaplicki, M., Machado Alves da Fonseca, F., Polenz, S., Marquardt, F., Lopez, E., Villechaise, P., Ott, Eric A., editor, Andersson, Joel, editor, Sudbrack, Chantal, editor, Bi, Zhongnan, editor, Bockenstedt, Kevin, editor, Dempster, Ian, editor, Fahrmann, Michael, editor, Jablonski, Paul, editor, Kirka, Michael, editor, Liu, Xingbo, editor, Nagahama, Daisuke, editor, Smith, Tim, editor, Stockinger, Martin, editor, and Wessman, Andrew, editor
- Published
- 2023
- Full Text
- View/download PDF
3. A novel type of semi-active jet turbulence grid
- Author
-
Szaszák, N., Roloff, C., Bordás, R., Bencs, P., Szabó, S., and Thévenin, D.
- Published
- 2018
- Full Text
- View/download PDF
4. A BIDOMAIN MODEL OF THE VENTRICULAR SPECIALIZED CONDUCTION SYSTEM OF THE HEART
- Author
-
BORDAS, R. M., GILLOW, K., GAVAGHAN, D., RODRIGUEZ, B., and KAY, D.
- Published
- 2012
- Full Text
- View/download PDF
5. First Episode Psychosis and intensity of care after discharge : difference at two years between lost and maintained follow-up patients
- Author
-
Bordas, R., primary, Laffont, E., additional, Jourdan, C., additional, Pujol, M., additional, and Lamary, L., additional
- Published
- 2022
- Full Text
- View/download PDF
6. Rabbit-specific ventricular model of cardiac electrophysiological function including specialized conduction system
- Author
-
Bordas, R., Gillow, K., Lou, Q., Efimov, I.R., Gavaghan, D., Kohl, P., Grau, V., and Rodriguez, B.
- Published
- 2011
- Full Text
- View/download PDF
7. Epidemiology of Clostridioides difficile infection in hospitalized patients in Spain: An eight-year review (2012-2019)
- Author
-
Asensio A, Vallejo-Plaza A, Parra L, Orti-Bordas R, Salcedo I, Ramos A, and Cantero M
- Subjects
Clostridioides difficile infection ,Epidemiology ,Vaccination CDI risk factors ,Community-associated infection ,Healthcare-associated infection - Abstract
Background: Clostridioides difficile infection (CDI) is a disease that is potentially preventable by vaccination. A good knowledge of its epidemiology, which can change over time, is warranted for prevention purposes and to help decision-making on the use of vaccines in public health programs. The objective of the research was to determine the epidemiology of healthcare-associated CDI (HA-CDI) and community-associated CDI (CA-CDI) in hospitalized patients in Spain using point prevalence data. Methods: Point prevalence survey data on infections of hospitalized patients for years 2012-2019 were analyzed. HA-CDI and CA-CDI prevalence rates were calculated. Both HA-CDI and CA-CDI, as well as age group prevalence rates, were examined for trends. Patient comorbidities were tested for association to CDI. Results: The prevalence of CDI in Spanish hospitals has grown exponentially from 14.1% in 2012 to 35.9% in 2019 (cases/10.000 hospitalized patients). Almost two thirds of the cases are of nosocomial onset. This increase was observed for HA-CDI and CA-CDI at an annual rate of 1.11% (CI 95% 1.08-1.15) and 1.09% (CI 95% 1.04-1.13), respectively. Patients 50 years old or older represent 87% of the total number of cases. Patients suffering from neoplasm (OR 1.39), immunodeficiency (OR 3.26), neutropenia (OR 3.70), cirrhosis (OR 1.92) and chronic renal failure (OR 1.91) have a significant increased risk of developing CDI, after adjusting for age. Conclusion: In Spain, the prevalence rate of both HA-CDI and CA-CDI have been increasing. Burden of CDI as well as clinical and epidemiological characteristics of CDI patients will help to support public health decision-making. (C) 2021 Sociedad Espanola de Enfermedades Infecciosas y Microbiologia Clinica. Published by Elsevier Espana, S.L.U. All rights reserved.
- Published
- 2022
8. Implication of substance use in suicidal or violent behaviours in a first episode psychosis spectrum disorder population : A 45 patients retrospective study
- Author
-
Bordas, R., primary, Jourdan, C., additional, Basso, C., additional, Laffont, E., additional, Pujol, M., additional, and Lamary, L., additional
- Published
- 2021
- Full Text
- View/download PDF
9. Chaste: Cancer, Heart and Soft Tissue Environment
- Author
-
Cooper, F, Baker, R, Bernabeu, M, Bordas, R, Bowler, L, Bueno-Orovio, A, Byrne, H, Carapella, V, Cardone-Noott, L, Cooper, J, Dutta, S, Evans, B, Fletcher, A, Grogan, J, Guo, W, Harvey, D, Hendrix, M, Kay, D, Kursawe, J, Maini, P, McMillan, B, Mirams, G, Osborne, J, Pathmanathan, P, Pitt-Francis, J, Robinson, M, Rodriguez, B, Spiteri, R, Gavaghan, D, Cooper, F, Baker, R, Bernabeu, M, Bordas, R, Bowler, L, Bueno-Orovio, A, Byrne, H, Carapella, V, Cardone-Noott, L, Cooper, J, Dutta, S, Evans, B, Fletcher, A, Grogan, J, Guo, W, Harvey, D, Hendrix, M, Kay, D, Kursawe, J, Maini, P, McMillan, B, Mirams, G, Osborne, J, Pathmanathan, P, Pitt-Francis, J, Robinson, M, Rodriguez, B, Spiteri, R, and Gavaghan, D
- Abstract
Chaste (Cancer, Heart And Soft Tissue Environment) is an open source simulation package for the numerical solution of mathematical models arising in physiology and biology. To date, Chaste development has been driven primarily by applications that include continuum modelling of cardiac electrophysiology ('Cardiac Chaste'), discrete cell-based modelling of soft tissues ('Cell-based Chaste'), and modelling of ventilation in lungs ('Lung Chaste'). Cardiac Chaste addresses the need for a high-performance, generic, and verified simulation framework for cardiac electrophysiology that is freely available to the scientific community. Cardiac chaste provides a software package capable of realistic heart simulations that is efficient, rigorously tested, and runs on HPC platforms. Cell-based Chaste addresses the need for efficient and verified implementations of cell-based modelling frameworks, providing a set of extensible tools for simulating biological tissues. Computational modelling, along with live imaging techniques, plays an important role in understanding the processes of tissue growth and repair. A wide range of cell-based modelling frameworks have been developed that have each been successfully applied in a range of biological applications. Cell-based Chaste includes implementations of the cellular automaton model, the cellular Potts model, cell-centre models with cell representations as overlapping spheres or Voronoi tessellations, and the vertex model. Lung Chaste addresses the need for a novel, generic and efficient lung modelling software package that is both tested and verified. It aims to couple biophysically-detailed models of airway mechanics with organ-scale ventilation models in a package that is freely available to the scientific community. Chaste is designed to be modular and extensible, providing libraries for common scientific computing infrastructure such as linear algebra operations, finite element meshes, and ordinary and partial differential equati
- Published
- 2020
10. A Bayesian Optimisation Workflow for Field Development Planning Under Geological Uncertainty
- Author
-
Bordas, R., primary, Heritage, J.R., additional, Javed, M.A., additional, Peacock, G., additional, Taha, T., additional, Ward, P., additional, Vernon, I., additional, and Hammersley, R.P., additional
- Published
- 2020
- Full Text
- View/download PDF
11. Caractéristiques cliniques et parcours de soins après un premier épisode psychotique : une étude rétrospective
- Author
-
Bordas, R., primary, Lamary, L., additional, Jourdan, C., additional, Basso, C., additional, Laffont, E., additional, and Pujol, M., additional
- Published
- 2019
- Full Text
- View/download PDF
12. 2SPD-005 Mapping the use of reserve group antibiotics in hospitals
- Author
-
Bordas, R, primary, Matuz, M, additional, Viola, R, additional, Csatordai, M, additional, Soos, G, additional, and Benko, R, additional
- Published
- 2018
- Full Text
- View/download PDF
13. Chaste: a test-driven approach to software development for physiological modelling
- Author
-
Pitt-Francis, J, Pathmanathan, P, Bernabeu, M, Bordas, R, Cooper, J, Fletcher, A, Mirams, G, Murray, P, Osbourne, J, Walter, A, Chapman, S, Garny, A, van Leeuwen, I, Maini, P, Rodriguez, B, Whiteley, J, Byrne, H, and Gavaghan, D
- Abstract
Chaste is a software library and set of test suites for modelling phenomena in the domain of computational biology. Specifically these the modelling problems arise in the fields of cancer modelling, cardiac simulation and soft-tissue engineering (Chaste stands for ‘Cancer, heart and soft-tissue environment’). It is released under the LGPL 2.1 licence. Chaste has been developed using agile programming methods. The project began 5 years when it was reasoned that the modelling of a variety of physio-logical phenomena requires both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project was formed as part of the larger Integrative Biology e-Science (IB) Project ([14]), an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a focus on cardiac and cancer modelling.
- Published
- 2016
14. Integrated approach for the study of anatomical variability in the cardiac Purkinje system: From high resolution MRI to electrophysiology simulation
- Author
-
Bordas, R, Grau, V, Burton, R, Hales, P, Schneider, J, Gavaghan, D, Kohl, P, and Rodriguez, B
- Subjects
medicine.diagnostic_test ,Computer science ,Purkinje fibers ,High resolution ,Magnetic resonance imaging ,Image processing ,Magnetic Resonance Imaging ,Electrophysiology ,Purkinje Fibers ,medicine.anatomical_structure ,medicine ,Gross anatomy ,Animals ,Rabbits ,Biomedical engineering - Abstract
The ordered electrical stimulation of the ven- tricles is achieved by a specialized network of fibres known as the Purkinje system. The gross anatomy and basic functional role of the Purkinje system is well understood. However, very little is known about the detailed anatomy of the Purkinje system, its inter-individual variability and the implications of the variability in ventricular function, in part due to limitations in experimental techniques. In this study, we aim to provide new insight into the inter- individual variability of the free running Purkinje system anatomy and its impact on ventricular electrophysiological function. As a first step towards achieving this aim, high resolution magnetic resonance imaging (MRI) datasets of rat and the rabbit ventricles are obtained and analysed using a novel semi-automatic image processing algorithm for segmentation of the free-running Purkinje system. Segmented geometry from the MRI datasets is used to construct a computational model of the Purkinje system, which is incorporated in to an anatomically-based ventric- ular geometry to simulate ventricular electrophysiological activity.
- Published
- 2016
15. numerical guide to the solution of the bidomain equations of cardiac electrophysiology
- Author
-
Pathmanathan, P, Bernabeu, M, Bordas, R, Cooper, J, Garny, A, Pitt−Francis, J, Whiteley, J, and Gavaghan, D
- Abstract
Simulation of cardiac electrical activity using the bidomain equations can be a massively computationally demanding problem. This study provides a comprehensive guide to numerical bidomain modelling. Each component of bidomain simulations-discretisation, ODE-solution, linear system solution, and parallelisation-is discussed, and previously-used methods are reviewed, new methods are proposed, and issues which cause particular difficulty are highlighted. Particular attention is paid t
- Published
- 2016
16. Ten Simple Rules for a Successful Cross-Disciplinary Collaboration
- Author
-
Knapp, B, Bardenet, R, Bernabeu, MO, Bordas, R, Bruna, M, Calderhead, B, Cooper, J, Fletcher, AG, Groen, D, Kuijper, B, Lewis, J, McInerny, G, Minssen, T, Osborne, J, Paulitschke, V, Pitt-Francis, J, Todoric, J, Yates, CA, Gavaghan, D, Deane, CM, Knapp, B, Bardenet, R, Bernabeu, MO, Bordas, R, Bruna, M, Calderhead, B, Cooper, J, Fletcher, AG, Groen, D, Kuijper, B, Lewis, J, McInerny, G, Minssen, T, Osborne, J, Paulitschke, V, Pitt-Francis, J, Todoric, J, Yates, CA, Gavaghan, D, and Deane, CM
- Published
- 2015
17. Chaste: An Open Source C plus plus Library for Computational Physiology and Biology
- Author
-
Prlic, A, Mirams, GR, Arthurs, CJ, Bernabeu, MO, Bordas, R, Cooper, J, Corrias, A, Davit, Y, Dunn, S-J, Fletcher, AG, Harvey, DG, Marsh, ME, Osborne, JM, Pathmanathan, P, Pitt-Francis, J, Southern, J, Zemzemi, N, Gavaghan, DJ, Prlic, A, Mirams, GR, Arthurs, CJ, Bernabeu, MO, Bordas, R, Cooper, J, Corrias, A, Davit, Y, Dunn, S-J, Fletcher, AG, Harvey, DG, Marsh, ME, Osborne, JM, Pathmanathan, P, Pitt-Francis, J, Southern, J, Zemzemi, N, and Gavaghan, DJ
- Abstract
Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.
- Published
- 2013
18. Integrated approach for the study of anatomical variability in the cardiac Purkinje system: From high resolution MRI to electrophysiology simulation
- Author
-
Bordas, R, primary, Grau, V, additional, Burton, R A B, additional, Hales, P, additional, Schneider, J E, additional, Gavaghan, D, additional, Kohl, P, additional, and Rodriguez, B, additional
- Published
- 2010
- Full Text
- View/download PDF
19. P02-04 - Characteristics of Secluded, Restrained and Aggressive Patients in a Locked Short Term Psychiatric Unit
- Author
-
Bordas, R., primary, Very, E., additional, Bui, E., additional, Paux, J., additional, Courtey, C., additional, Lecoules, N., additional, and Schmitt, L., additional
- Published
- 2010
- Full Text
- View/download PDF
20. Score de violence, agitation et niveau de traitement : peut-on corréler ?
- Author
-
Bordas, R., primary, Bui, E., additional, Lecoules, N., additional, Courtet, C., additional, Azema, O., additional, Lauque, D., additional, and Schmitt, L., additional
- Published
- 2009
- Full Text
- View/download PDF
21. P53 ONCOPROTEIN EXPRESSION AND p53 GENE MUTATIONS IN CD30+ CUTANEOUS T-CELL LYMPHOID PROLIFERATIONS.
- Author
-
Pujol, R M., primary, Estivill, C., additional, Lopez, O., additional, Bordas, R., additional, and Nomdedeu, J., additional
- Published
- 1998
- Full Text
- View/download PDF
22. Strategies to stimulate low responder patients with endometriosis
- Author
-
Perelló, J., Saiz, M.J., Parés, P., Bordás, R., Viscasillas, P., and Calaf, J.
- Published
- 2010
- Full Text
- View/download PDF
23. 2SPD-005 Mapping the use of reserve group antibiotics in hospitals
- Author
-
Bordas, R, Matuz, M, Viola, R, Csatordai, M, Soos, G, and Benko, R
- Abstract
BackgroundAll antibiotics were categorised into access, watch and reserve groups in the latest List of Essential Medicines by the WHO.1Antibiotics belonging to the reserve group should be protected and kept as a last resort when all others fail to give therapeutic effect.PurposeTo map the consumption of reserve class antibiotics during the past 5 years.Material and methodsThe study was done on reserve group antibiotics which were selected based on the WHO definition. National data, regarding distribution to hospitals, were collected from wholesales statistics for the period between 2012 and 2016. Additionally, regional consumption data for 2016 were collected. Antibiotic use was analysed according to the Anatomical Therapeutic Chemical – Defined Daily Dose method (version 2017) and expressed in DDD per 100 patient-days.ResultsDuring the study period an increase in the national use of reserve antibiotics from 0.13 to 0.26 DDD per 100 patient-days could be observed. This corresponds to a relative increase from 0.57% to 1.13% in the total use of antibiotics in the hospital. A noticeable increase in the use of colistine (from 0.09 to 0.19 DDD per 100 patient-days) and tigecycline (from 0.01 to 0.03 DDD per 100 patient-days) accounts for a great part of this upward trend. A huge variation in the regional use of reserve group antibiotics were also detected (mean: 0.26; min: 0.02; max: 1.08 DDD per 100 patient-days). Three out of four counties providing tertiary care were among the top consumers of these antibiotics.ConclusionThough the collected data is a crude measure, it shows a trend in the increase (roughly doubled) in the absolute and relative use of reserve antibiotics nationally. This trend could be explained by several factors, as an increase in antibiotic resistance and increased access of these drugs. The detected large regional variations require further research. Since these antibiotics belong to the last-line treatment options, tight monitoring is essential, to maintain their therapeutic value.Reference and/or Acknowledgements1. WHO Model List of Essential Medicines, 20th List, World Health Organisation, 2017.No conflict of interest
- Published
- 2018
- Full Text
- View/download PDF
24. Simulating bronchoconstriction in a patient specific model of the major airways.
- Author
-
Bordas, R. M., Brook, B., Kay, D., and Burrowes, K.
- Subjects
- *
FLUID dynamics , *VENTILATION , *AIRWAY (Anatomy) - Abstract
The use of computational fluid dynamics (CFD) to simulate ventilation in the major airways of the lung has been shown to demonstrate greater specificity in assessing lung function over spirometry measures and visual analysis of computed tomography (CT) images. Currently, CFD is limited to simulating ventilation in a static airway geometry derived directly from CT. It cannot be used to assess the change in ventilation as a result of acute bronchoconstriction or long term remodelling of the airway wall. We have developed a multiscale biomechanical model of bronchoconstriction in the major airways. The model integrates an active tension produced by airway smooth muscle (ASM) and the passive mechanical properties of airway walls and lung parenchyma to simulate constriction and allow assessment of changes in ventilation. Initially, a finite element model (FEM) of the mechanics of a single airway embedded in a layer of parenchyma was developed. The model was used to parameterise material laws governing the airway wall mechanics in generations 1-10 and to validate the mechanical behaviour of the model in comparison to experimental data. ASM is embedded circumferentially in the model acting at a given angle to the airway cross section. The model is used to assess the reduction in airflow in response to ASM contraction in both normal and remodelled airway wall cases and the distribution of mechanical stress in the airway wall. To extend the methodology to a patient specific setting, a CT scan of a healthy adult was segmented to obtain a surface mesh of the airway wall. A volumetric mesh encompassing the airway walls was subsequently generated for use with the FEM model. Wall thickness in the mesh is varied to represent airway wall remodelling. The single airway model was used to investigate changes in airway resistance in response to remodelling. For example, a 19.5x increase in resistance between a normal and a remodelled generation 3 airway in response to a ASM activation (15 degree fibre angle at 8 cmH2O pleural pressure) was shown. The patient specific model was used to demonstrate the change in airflow and material stress around a number of bifurcations for several prescribed ASM tensions, again demonstrating the change in flow in response to ASM constriction and airway wall thickening. We have developed a methodology for simulating bronchoconstriction on patient specific geometries. The single airway model is well validated and validation of the patient specific model against clinical data is ongoing. The method reveals the importance of the structure of airway bifurcations in governing total airflow in the major airways. The results suggest that simulating bronchoconstriction on patient specific geometries can provide insight into the reduction in ventilation due to acute ASM contraction and chronic airway wall remodelling. [ABSTRACT FROM AUTHOR]
- Published
- 2013
25. Impact of tissue microstructure on a model of cardiac electromechanics based on MRI data
- Author
-
Carapella, V, Grau, V, Burrage, K, Bordas, R, and Pathmanathan, P
- Subjects
Biology and other natural sciences (mathematics) ,Mathematical biology ,Life Sciences ,Biomedical engineering - Abstract
Cardiac motion is a highly complex and integrated process of vital importance as it sustains the primary function of the heart, that is pumping blood. For this reason cardiac motion abnormalities are often associated with severe pathologies. Clinical non-invasive techniques can assess this fundamental connection between motion aberrant behaviour and pathology only to a certain extent. Computational models of cardiac motion would thus be of great help in linking local to global motion abnormalities and to pathology. No current model of the heart though is able yet to realistically simulate motion patterns in the healthy or diseased heart and therefore prediction of clinically relevant parameters such as ejection fraction, stroke volume, wall thickening and wall motion are not yet totally reliable. It is well known that cardiac tissue microstructure, that is cardiac cells organisation into fibres and sheets, has an important role in cardiac motion, as suggested by experimental and computational research, but current models of cardiac function, although already embedding structural information in the models equations, are not yet able to correctly link structure to function and therefore predict realistic cardiac motion. The hypothesis underlying this project is that a more realistic representation of tissue structure within an electromechanical model of the heart, with fibre and sheet orientation extracted from data rather than mathematically defined, together with a more careful definition of tissue material properties, would better take into account the high heterogeneity of tissue structure, thus improving the predictive power of the model. The aim of the project is to investigate how different settings of tissue structural arrangement affect the motion prediction of an electromechanical model applied to murine left ventricular geometries obtained from magnetic resonance imaging. The project relies on the integration of cardiac imaging data and mathematical modelling in the belief that realistic models of cardiac function need to reach the best compromise between the level of modelling detail and the amount and quality of information that can be actually obtained from data and used either to instruct or validate such models.
- Published
- 2011
26. Epidemiology of Clostridioides difficile infection in hospitalized patients in Spain: An eight-year review (2012-2019).
- Author
-
Asensio Á, Vallejo-Plaza A, Parra LM, Orti-Bordas R, Salcedo I, Ramos A, and Cantero M
- Abstract
Background: Clostridioides difficile infection (CDI) is a disease that is potentially preventable by vaccination. A good knowledge of its epidemiology, which can change over time, is warranted for prevention purposes and to help decision-making on the use of vaccines in public health programs. The objective of the research was to determine the epidemiology of healthcare-associated CDI (HA-CDI) and community-associated CDI (CA-CDI) in hospitalized patients in Spain using point prevalence data., Methods: Point prevalence survey data on infections of hospitalized patients for years 2012-2019 were analyzed. HA-CDI and CA-CDI prevalence rates were calculated. Both HA-CDI and CA-CDI, as well as age group prevalence rates, were examined for trends. Patient comorbidities were tested for association to CDI., Results: The prevalence of CDI in Spanish hospitals has grown exponentially from 14.1% in 2012 to 35.9% in 2019 (cases/10.000 hospitalized patients). Almost two thirds of the cases are of nosocomial onset. This increase was observed for HA-CDI and CA-CDI at an annual rate of 1.11% (CI 95% 1.08-1.15) and 1.09% (CI 95% 1.04-1.13), respectively. Patients 50 years old or older represent 87% of the total number of cases. Patients suffering from neoplasm (OR 1.39), immunodeficiency (OR 3.26), neutropenia (OR 3.70), cirrhosis (OR 1.92) and chronic renal failure (OR 1.91) have a significant increased risk of developing CDI, after adjusting for age., Conclusion: In Spain, the prevalence rate of both HA-CDI and CA-CDI have been increasing. Burden of CDI as well as clinical and epidemiological characteristics of CDI patients will help to support public health decision-making., (Copyright © 2021 Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. Publicado por Elsevier España, S.L.U. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
27. Chaste: Cancer, Heart and Soft Tissue Environment.
- Author
-
Cooper FR, Baker RE, Bernabeu MO, Bordas R, Bowler L, Bueno-Orovio A, Byrne HM, Carapella V, Cardone-Noott L, Jonatha C, Dutta S, Evans BD, Fletcher AG, Grogan JA, Guo W, Harvey DG, Hendrix M, Kay D, Kursawe J, Maini PK, McMillan B, Mirams GR, Osborne JM, Pathmanathan P, Pitt-Francis JM, Robinson M, Rodriguez B, Spiteri RJ, and Gavaghan DJ
- Abstract
Chaste (Cancer, Heart And Soft Tissue Environment) is an open source simulation package for the numerical solution of mathematical models arising in physiology and biology. To date, Chaste development has been driven primarily by applications that include continuum modelling of cardiac electrophysiology ('Cardiac Chaste'), discrete cell-based modelling of soft tissues ('Cell-based Chaste'), and modelling of ventilation in lungs ('Lung Chaste'). Cardiac Chaste addresses the need for a high-performance, generic, and verified simulation framework for cardiac electrophysiology that is freely available to the scientific community. Cardiac chaste provides a software package capable of realistic heart simulations that is efficient, rigorously tested, and runs on HPC platforms. Cell-based Chaste addresses the need for efficient and verified implementations of cell-based modelling frameworks, providing a set of extensible tools for simulating biological tissues. Computational modelling, along with live imaging techniques, plays an important role in understanding the processes of tissue growth and repair. A wide range of cell-based modelling frameworks have been developed that have each been successfully applied in a range of biological applications. Cell-based Chaste includes implementations of the cellular automaton model, the cellular Potts model, cell-centre models with cell representations as overlapping spheres or Voronoi tessellations, and the vertex model. Lung Chaste addresses the need for a novel, generic and efficient lung modelling software package that is both tested and verified. It aims to couple biophysically-detailed models of airway mechanics with organ-scale ventilation models in a package that is freely available to the scientific community. Chaste is designed to be modular and extensible, providing libraries for common scientific computing infrastructure such as linear algebra operations, finite element meshes, and ordinary and partial differential equation solvers. This infrastructure is used by libraries for specific applications, such as continuum mechanics, cardiac models, and cell-based models. The software engineering techniques used to develop Chaste are intended to ensure code quality, re-usability and reliability. Primary applications of the software include cardiac and respiratory physiology, cancer and developmental biology.
- Published
- 2020
- Full Text
- View/download PDF
28. Treatment of Cystitis by Hungarian General Practitioners: A Prospective Observational Study.
- Author
-
Benko R, Matuz M, Juhasz Z, Bognar J, Bordas R, Soos G, Hajdu E, and Peto Z
- Abstract
Background: Lower urinary tract infections (LUTIs) are amongst the most common community acquired infections with frequent antibiotic prescribing. Objectives: To assess empiric antibiotic choice in different types of lower urinary tract infections. We also aimed to identify determinants of fluoroquinolone prescribing, as well as to determine the rate of short antibiotic courses. The frequencies of executing laboratory tests and recommending analgesics/anti-inflammatory drugs were also assessed. Methods: A prospective observational study was performed in 19 different Hungarian primary care practices. Participating general practitioners (GPs) filled out data sheets for each patient with a suspected urinary tract infection. Details of drug use were evaluated. Comparison of different LUTI groups were made by descriptive statistics and univariate analysis. Possible determinants of fluoroquinolone prescribing were assessed by logistic regression. Results: Data sheets of 372 patients were analyzed. The majority of patients (68.82%) had acute uncomplicated cystitis. While antibiotics were prescribed for almost every patient (uncomplicated cases: 92.58%, complicated cases: 94.83%), analgesics/anti-inflammatory drugs were recommended at a rate of 7.81% in uncomplicated, and 13.79% in complicated cystitis cases. Ciprofloxacin was the most commonly prescribed antibacterial agent in both types of cystitis. Short-term antibiotic therapy was prescribed in one third of relevant cases. Logistic regression found a weak association between fluoroquinolone use and patient's age and presence of complicating factors. Conclusions: Many aspects of suboptimal cystitis management were identified (e.g. unnecessarily broad spectra agents, too long antibiotic courses). In this study, patient characteristics has weakly influenced fluoroquinolone prescribing. Based on these results there is considerable room for improvement in primary care antibiotic therapy of cystitis in Hungary., (Copyright © 2019 Benko, Matuz, Juhasz, Bognar, Bordas, Soos, Hajdu and Peto.)
- Published
- 2019
- Full Text
- View/download PDF
29. Lung Computational Models and the Role of the Small Airways in Asthma.
- Author
-
Foy BH, Soares M, Bordas R, Richardson M, Bell A, Singapuri A, Hargadon B, Brightling C, Burrowes K, Kay D, Owers-Bradley J, and Siddiqui S
- Subjects
- Adult, Aged, Female, Forced Expiratory Volume, Humans, Male, Middle Aged, Models, Anatomic, Respiratory Function Tests methods, Spirometry methods, Airway Remodeling physiology, Asthma diagnosis, Asthma physiopathology, Asthma therapy, Pulmonary Disease, Chronic Obstructive diagnosis, Pulmonary Disease, Chronic Obstructive physiopathology, Pulmonary Disease, Chronic Obstructive therapy
- Abstract
Rationale: Asthma is characterized by disease within the small airways. Several studies have suggested that forced oscillation technique-derived resistance at 5 Hz (R5) - resistance at 20 Hz (R20) is a measure of small airway disease; however, there has been limited validation of this measurement to date. Objectives: To validate the use of forced oscillation R5 - R20 as a measure of small airway narrowing in asthma, and to investigate the role that small airway narrowing plays in asthma. Methods: Patient-based complete conducting airway models were generated from computed tomography scans to simulate the impact of different degrees of airway narrowing at different levels of the airway tree on forced oscillation R5 - R20 ( n = 31). The computational models were coupled with regression models in an asthmatic cohort ( n = 177) to simulate the impact of small airway narrowing on asthma control and quality of life. The computational models were used to predict the impact on small airway narrowing of type-2 targeting biologics using pooled data from two similarly design randomized, placebo-controlled biologic trials ( n = 137). Measurements and Main Results: Simulations demonstrated that narrowing of the small airways had a greater impact on R5 - R20 than narrowing of the larger airways and was associated (above a threshold of approximately 40% narrowing) with marked deterioration in both asthma control and asthma quality of life, above the minimal clinical important difference. The observed treatment effect on R5 - R20 in the pooled trials equated to a predicted small airway narrowing reversal of approximately 40%. Conclusions: We have demonstrated, using computational modeling, that forced oscillation R5 - R20 is a direct measure of anatomical narrowing in the small airways and that small airway narrowing has a marked impact on both asthma control and quality of life and may be modified by biologics.
- Published
- 2019
- Full Text
- View/download PDF
30. Cross-national comparison of paediatric antibiotic use in Norway, Portugal and Hungary.
- Author
-
Benko R, Matuz M, Silva A, Ferreira J, Machado MC, Furtado C, Fungie Galistiani G, Bordas R, and Blix HS
- Subjects
- Adolescent, Child, Drug Prescriptions, Drug Utilization, Female, Humans, Hungary epidemiology, Macrolides therapeutic use, Male, Norway epidemiology, Penicillins therapeutic use, Portugal epidemiology, Retrospective Studies, Tetracyclines, Ambulatory Care statistics & numerical data, Anti-Bacterial Agents therapeutic use
- Abstract
A cross-national comparison was performed on paediatric (0-19 years) antibiotic use in Hungary, Norway and Portugal to explore and compare the scale and pattern of paediatric antibiotic use in these three European countries. Ambulatory care systemic antibiotic use (ATC: J01) was retrieved from national databases for year 2014. The main outcome measure was number of antibacterial packages per child inhabitant per year (packages/child/year) and was further stratified by age groups. Paediatric antibiotic use peaked in Hungary with 1.3 packages/child/year, followed by Portugal (0.8) and Norway (0.3). This ranking was retained and was most prominent in the 5- to 9-year and 10- to 14-year age groups. The pattern of antibiotic use in different paediatric age groups varied also substantially between countries. Narrow-spectrum penicillins were much commonly used in Norway in all paediatric age subgroups in comparison with Hungary and Portugal. Newer, broad-spectrum cephalosporins and macrolides were widely prescribed for Hungarian and Portuguese children in all paediatric subgroups in contrast to Norway, while tetracyclines were commonly prescribed for Norwegian adolescents. The scale and pattern of paediatric antibiotic use in Hungary and Portugal were very different compared with Norway. The high antibiotic exposure and the high consumption of broad-spectrum penicillins begin in childhood in Hungary and Portugal which underpins the responsibility of paediatric GPs., (© 2018 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).)
- Published
- 2019
- Full Text
- View/download PDF
31. The prediction of viscous losses and pressure drop in models of the human airways.
- Author
-
Wells AK, Jones IP, Hamill IS, and Bordas R
- Subjects
- Bronchi physiology, Exhalation, Humans, Pressure, Models, Biological
- Abstract
This paper examines the viscous flow resistance in branching tubes as applied to simplified models of the lungs and compares the results of computational fluid dynamics simulations for a range of conditions with measurement data. The results are in good agreement with the available measurement data for both inspiration and expiration. A detailed sensitivity analysis of the dissipation and viscous resistance in a branch then examines the ratio of the viscous resistance to that for a fully developed Poiseuille flow, Z. As other researchers have noted, the calculated resistances give lower values than those from the standard correlation of Pedley et al. The results demonstrate that the resistance is sensitive to the velocity profile upstream of the bifurcations and explain from fluid dynamical considerations the apparent sensitivity of the resistance to the generation number of the branch. The paper also suggests a revised value for the calibration constant in the expression for Z. Finally, a limited set of results are presented for junction losses, and for expiration., (Copyright © 2017 John Wiley & Sons, Ltd.)
- Published
- 2018
- Full Text
- View/download PDF
32. Weight decrease improves live birth rates in obese women undergoing IVF: a pilot study.
- Author
-
Espinós JJ, Polo A, Sánchez-Hernández J, Bordas R, Pares P, Martínez O, and Calaf J
- Subjects
- Adult, Embryo Transfer, Female, Follicle Stimulating Hormone administration & dosage, Humans, Life Style, Obesity complications, Obesity physiopathology, Pilot Projects, Pregnancy, Pregnancy Complications physiopathology, Pregnancy Rate, Prospective Studies, Birth Rate, Fertilization in Vitro, Live Birth, Obesity therapy, Pregnancy Complications therapy, Weight Loss
- Abstract
Obese women have lower pregnancy rates than normal-weight women undergoing assisted reproductive treatment. We conducted a pilot study to evaluate whether a 12-week diet and exercise intervention before an IVF cycle would influence pregnancy rates in obese women. Forty-one patients were enrolled in this study. They were randomly allocated to two groups: an intervention group (n = 21), who underwent an individualized diet and physical exercise programme supervised by a dietician, and a control group (n = 20), who started IVF with no previous intervention. The primary outcome was clinical pregnancy rate after a single treatment cycle. Mean weight loss in the study group after the intervention was 5.4 kg (range 1.1-14.6 kg). The study and control groups had similar total FSH consumption, number of oocytes and embryos obtained, and number and quality of embryos transferred. There was a non-significant trend towards a higher clinical pregnancy rate after fresh embryo transfer (66.7% versus 41.2%). The intervention group had a significantly higher cumulative live birth rate (61.9% versus 30%, P = 0.045) (odds ratio for intervention group, 3.8; 95% confidence interval, 1.03 to 13.9) The data suggest that weight loss resulted in a significantly increased cumulative live birth rate., (Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2017
- Full Text
- View/download PDF
33. A stabilized finite element method for finite-strain three-field poroelasticity.
- Author
-
Berger L, Bordas R, Kay D, and Tavener S
- Abstract
We construct a stabilized finite-element method to compute flow and finite-strain deformations in an incompressible poroelastic medium. We employ a three-field mixed formulation to calculate displacement, fluid flux and pressure directly and introduce a Lagrange multiplier to enforce flux boundary conditions. We use a low order approximation, namely, continuous piecewise-linear approximation for the displacements and fluid flux, and piecewise-constant approximation for the pressure. This results in a simple matrix structure with low bandwidth. The method is stable in both the limiting cases of small and large permeability. Moreover, the discontinuous pressure space enables efficient approximation of steep gradients such as those occurring due to rapidly changing material coefficients or boundary conditions, both of which are commonly seen in physical and biological applications., (© The Author(s) 2017.)
- Published
- 2017
- Full Text
- View/download PDF
34. Modelling responses of the inert-gas washout and MRI to bronchoconstriction.
- Author
-
Foy BH, Kay D, and Bordas R
- Subjects
- Computer Simulation, Humans, Lung Compliance physiology, Monte Carlo Method, Tomography, X-Ray Computed, Bronchoconstriction physiology, Lung diagnostic imaging, Lung metabolism, Magnetic Resonance Imaging, Models, Cardiovascular, Noble Gases metabolism
- Abstract
Many lung diseases lead to an increase in ventilation heterogeneity (VH). Two clinical practices for the measurement of patient VH are in vivo imaging, and the inert gas multiple breath washout (MBW). In this study computational modelling was used to compare the responses of MBW indices LCI and s
cond and MRI measured global and local ventilation indices, σr and σlocal , to constriction of airways in the conducting zone of the lungs. The simulations show that scond , LCI and σr behave quite similarly to each other, all being sensitive to increases in the severity of constriction, while exhibiting little sensitivity to the depth at which constriction occurs. In contrast, the local MRI index σlocal shows strong sensitivity to depth of constriction, but lowered sensitivity to constriction severity. We finish with an analysis of the sensitivity of MRI indices to grid sizes, showing that results should be interpreted with reference to the image resolution. Overall we conclude that the application of both local and global VH measures may help to classify different types of bronchoconstriction., (Copyright © 2016 Elsevier B.V. All rights reserved.)- Published
- 2017
- Full Text
- View/download PDF
35. A poroelastic model coupled to a fluid network with applications in lung modelling.
- Author
-
Berger L, Bordas R, Burrowes K, Grau V, Tavener S, and Kay D
- Subjects
- Animals, Computer Simulation, Elastic Modulus physiology, Humans, Porosity, Lung physiopathology, Lung Diseases physiopathology, Models, Biological, Pulmonary Gas Exchange, Pulmonary Ventilation, Rheology methods
- Abstract
We develop a lung ventilation model based on a continuum poroelastic representation of lung parenchyma that is strongly coupled to a pipe network representation of the airway tree. The continuous system of equations is discretized using a low-order stabilised finite element method. The framework is applied to a realistic lung anatomical model derived from computed tomography data and an artificially generated airway tree to model the conducting airway region. Numerical simulations produce physiologically realistic solutions and demonstrate the effect of airway constriction and reduced tissue elasticity on ventilation, tissue stress and alveolar pressure distribution. The key advantage of the model is the ability to provide insight into the mutual dependence between ventilation and deformation. This is essential when studying lung diseases, such as chronic obstructive pulmonary disease and pulmonary fibrosis. Thus the model can be used to form a better understanding of integrated lung mechanics in both the healthy and diseased states. Copyright © 2015 John Wiley & Sons, Ltd., (Copyright © 2015 John Wiley & Sons, Ltd.)
- Published
- 2016
- Full Text
- View/download PDF
36. Development and Analysis of Patient-Based Complete Conducting Airways Models.
- Author
-
Bordas R, Lefevre C, Veeckmans B, Pitt-Francis J, Fetita C, Brightling CE, Kay D, Siddiqui S, and Burrowes KS
- Subjects
- Aged, Airway Resistance, Female, Humans, Lung diagnostic imaging, Male, Middle Aged, Tomography, X-Ray Computed, Lung anatomy & histology, Lung physiology, Models, Anatomic
- Abstract
The analysis of high-resolution computed tomography (CT) images of the lung is dependent on inter-subject differences in airway geometry. The application of computational models in understanding the significance of these differences has previously been shown to be a useful tool in biomedical research. Studies using image-based geometries alone are limited to the analysis of the central airways, down to generation 6-10, as other airways are not visible on high-resolution CT. However, airways distal to this, often termed the small airways, are known to play a crucial role in common airway diseases such as asthma and chronic obstructive pulmonary disease (COPD). Other studies have incorporated an algorithmic approach to extrapolate CT segmented airways in order to obtain a complete conducting airway tree down to the level of the acinus. These models have typically been used for mechanistic studies, but also have the potential to be used in a patient-specific setting. In the current study, an image analysis and modelling pipeline was developed and applied to a number of healthy (n = 11) and asthmatic (n = 24) CT patient scans to produce complete patient-based airway models to the acinar level (mean terminal generation 15.8 ± 0.47). The resulting models are analysed in terms of morphometric properties and seen to be consistent with previous work. A number of global clinical lung function measures are compared to resistance predictions in the models to assess their suitability for use in a patient-specific setting. We show a significant difference (p < 0.01) in airways resistance at all tested flow rates in complete airway trees built using CT data from severe asthmatics (GINA 3-5) versus healthy subjects. Further, model predictions of airways resistance at all flow rates are shown to correlate with patient forced expiratory volume in one second (FEV1) (Spearman ρ = -0.65, p < 0.001) and, at low flow rates (0.00017 L/s), FEV1 over forced vital capacity (FEV1/FVC) (ρ = -0.58, p < 0.001). We conclude that the pipeline and anatomical models can be used directly in mechanistic modelling studies and can form the basis for future patient-based modelling studies.
- Published
- 2015
- Full Text
- View/download PDF
37. Dynamic flow characteristics in normal and asthmatic lungs.
- Author
-
Kim M, Bordas R, Vos W, Hartley RA, Brightling CE, Kay D, Grau V, and Burrowes KS
- Subjects
- Bronchoconstriction, Female, Humans, Inhalation, Middle Aged, Models, Biological, Pulmonary Ventilation, Asthma physiopathology, Lung physiopathology, Rheology
- Abstract
Complex flow patterns exist within the asymmetric branching airway network in the lungs. These flow patterns are known to become increasingly heterogeneous during disease as a result of various mechanisms such as bronchoconstriction or alterations in lung tissue compliance. Here, we present a coupled model of tissue deformation and network airflow enabling predictions of dynamic flow properties, including temporal flow rate, pressure distribution, and the occurrence of reverse flows. We created two patient-specific airway geometries, one for a healthy subject and one for a severe asthmatic subject, derived using a combination of high-resolution CT data and a volume-filling branching algorithm. In addition, we created virtually constricted airway geometry by reducing the airway radii of the healthy subject model. The flow model was applied to these three different geometries to solve the pressure and flow distribution over a breathing cycle. The differences in wave phase of the flows in parallel airways induced by asymmetric airway geometry and bidirectional interaction between intra-acinar and airway network pressures were small in central airways but were more evident in peripheral airways. The asthmatic model showed elevated ventilation heterogeneity and significant flow disturbance. The reverse flows in the asthmatic model not only altered the local flow characteristics but also affected total lung resistance. The clinical significance of temporal flow disturbance on lung ventilation in normal airway model is obscure. However, increased flow disturbance and ventilation heterogeneity observed in the asthmatic model suggests that reverse flow may be an important factor for asthmatic lung function., (Copyright © 2015 John Wiley & Sons, Ltd.)
- Published
- 2015
- Full Text
- View/download PDF
38. Ten simple rules for a successful cross-disciplinary collaboration.
- Author
-
Knapp B, Bardenet R, Bernabeu MO, Bordas R, Bruna M, Calderhead B, Cooper J, Fletcher AG, Groen D, Kuijper B, Lewis J, McInerny G, Minssen T, Osborne J, Paulitschke V, Pitt-Francis J, Todoric J, Yates CA, Gavaghan D, and Deane CM
- Subjects
- Algorithms, Organizational Objectives, Cooperative Behavior, Interdisciplinary Communication, Interdisciplinary Studies, Leadership, Models, Organizational, Science organization & administration
- Published
- 2015
- Full Text
- View/download PDF
39. Structure of human Bloom's syndrome helicase in complex with ADP and duplex DNA.
- Author
-
Swan MK, Legris V, Tanner A, Reaper PM, Vial S, Bordas R, Pollard JR, Charlton PA, Golec JM, and Bertrand JA
- Subjects
- Bloom Syndrome genetics, Catalytic Domain, Crystallography, X-Ray, Humans, Hydrolysis, Models, Molecular, Mutation, Nucleic Acid Heteroduplexes, Protein Conformation, RecQ Helicases genetics, Adenosine Diphosphate metabolism, RecQ Helicases chemistry, RecQ Helicases metabolism
- Abstract
Bloom's syndrome is an autosomal recessive genome-instability disorder associated with a predisposition to cancer, premature aging and developmental abnormalities. It is caused by mutations that inactivate the DNA helicase activity of the BLM protein or nullify protein expression. The BLM helicase has been implicated in the alternative lengthening of telomeres (ALT) pathway, which is essential for the limitless replication of some cancer cells. This pathway is used by 10-15% of cancers, where inhibitors of BLM are expected to facilitate telomere shortening, leading to apoptosis or senescence. Here, the crystal structure of the human BLM helicase in complex with ADP and a 3'-overhang DNA duplex is reported. In addition to the helicase core, the BLM construct used for crystallization (residues 640-1298) includes the RecQ C-terminal (RQC) and the helicase and ribonuclease D C-terminal (HRDC) domains. Analysis of the structure provides detailed information on the interactions of the protein with DNA and helps to explain the mechanism coupling ATP hydrolysis and DNA unwinding. In addition, mapping of the missense mutations onto the structure provides insights into the molecular basis of Bloom's syndrome.
- Published
- 2014
- Full Text
- View/download PDF
40. Quantitative study of the effect of tissue microstructure on contraction in a computational model of rat left ventricle.
- Author
-
Carapella V, Bordas R, Pathmanathan P, Lohezic M, Schneider JE, Kohl P, Burrage K, and Grau V
- Subjects
- Animals, Female, Male, Rats, Heart Ventricles, Models, Cardiovascular, Myocardial Contraction physiology, Ventricular Function physiology
- Abstract
Tissue microstructure, in particular the alignment of myocytes (fibre direction) and their lateral organisation into sheets, is fundamental to cardiac function. We studied the effect of microstructure on contraction in a computational model of rat left ventricular electromechanics. Different fibre models, globally rule-based or locally optimised to DT-MRI data, were compared, in order to understand whether a subject-specific fibre model would enhance the predictive power of our model with respect to the global ones. We also studied the impact of sheets on ventricular deformation by comparing: (a) a transversely isotropic versus an orthotropic material law and (b) a linear model with a bimodal model of sheet transmural variation. We estimated ejection fraction, wall thickening and base-to-apex shortening and compared them with measures from cine-MRI. We also evaluated Lagrangian strains as local metrics of cardiac deformation. Our results show that the subject-specific fibre model provides little improvement in the metric predictions with respect to global fibre models while material orthotropy allows closer agreement with measures than transverse isotropy. Nonetheless, the impact of sheets in our model is smaller than that of fibres. We conclude that further investigation of the modelling of sheet dynamics is necessary to fully understand the impact of tissue structure on cardiac deformation.
- Published
- 2014
- Full Text
- View/download PDF
41. A comparison of fully automated methods of data analysis and computer assisted heuristic methods in an electrode kinetic study of the pathologically variable [Fe(CN)6](3-/4-) process by AC voltammetry.
- Author
-
Morris GP, Simonov AN, Mashkina EA, Bordas R, Gillow K, Baker RE, Gavaghan DJ, and Bond AM
- Abstract
Fully automated and computer assisted heuristic data analysis approaches have been applied to a series of AC voltammetric experiments undertaken on the [Fe(CN)6](3-/4-) process at a glassy carbon electrode in 3 M KCl aqueous electrolyte. The recovered parameters in all forms of data analysis encompass E(0) (reversible potential), k(0) (heterogeneous charge transfer rate constant at E(0)), α (charge transfer coefficient), Ru (uncompensated resistance), and Cdl (double layer capacitance). The automated method of analysis employed time domain optimization and Bayesian statistics. This and all other methods assumed the Butler-Volmer model applies for electron transfer kinetics, planar diffusion for mass transport, Ohm's Law for Ru, and a potential-independent Cdl model. Heuristic approaches utilize combinations of Fourier Transform filtering, sensitivity analysis, and simplex-based forms of optimization applied to resolved AC harmonics and rely on experimenter experience to assist in experiment-theory comparisons. Remarkable consistency of parameter evaluation was achieved, although the fully automated time domain method provided consistently higher α values than those based on frequency domain data analysis. The origin of this difference is that the implemented fully automated method requires a perfect model for the double layer capacitance. In contrast, the importance of imperfections in the double layer model is minimized when analysis is performed in the frequency domain. Substantial variation in k(0) values was found by analysis of the 10 data sets for this highly surface-sensitive pathologically variable [Fe(CN)6](3-/4-) process, but remarkably, all fit the quasi-reversible model satisfactorily.
- Published
- 2013
- Full Text
- View/download PDF
42. Chaste: an open source C++ library for computational physiology and biology.
- Author
-
Mirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, Corrias A, Davit Y, Dunn SJ, Fletcher AG, Harvey DG, Marsh ME, Osborne JM, Pathmanathan P, Pitt-Francis J, Southern J, Zemzemi N, and Gavaghan DJ
- Subjects
- Computer Simulation, Humans, Models, Cardiovascular, Neoplasms, Computational Biology methods, Databases, Factual
- Abstract
Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to 're-invent the wheel' with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials.
- Published
- 2013
- Full Text
- View/download PDF
43. A numerical guide to the solution of the bi-domain equations of cardiac electrophysiology.
- Author
-
Pathmanathan P, Bernabeu MO, Bordas R, Cooper J, Garny A, Pitt-Francis JM, Whiteley JP, and Gavaghan DJ
- Subjects
- Animals, Computer Simulation, Algorithms, Heart physiology, Models, Cardiovascular
- Abstract
Simulation of cardiac electrical activity using the bi-domain equations can be a massively computationally demanding problem. This study provides a comprehensive guide to numerical bi-domain modelling. Each component of bi-domain simulations--discretization, ODE-solution, linear system solution, and parallelization--is discussed, and previously-used methods are reviewed, new methods are proposed, and issues which cause particular difficulty are highlighted. Particular attention is paid to the choice of stimulus currents, compatibility conditions for the equations, the solution of singular linear systems, and convergence of the numerical scheme., (2010 Elsevier Ltd. All rights reserved.)
- Published
- 2010
- Full Text
- View/download PDF
44. Integrated approach for the study of anatomical variability in the cardiac Purkinje system: from high resolution MRI to electrophysiology simulation.
- Author
-
Bordas R, Grau V, Burton RB, Hales P, Schneider JE, Gavaghan D, Kohl P, and Rodriguez B
- Subjects
- Animals, Rabbits, Electrophysiology methods, Magnetic Resonance Imaging methods, Purkinje Fibers physiology
- Abstract
The ordered electrical stimulation of the ventricles is achieved by a specialized network of fibres known as the Purkinje system. The gross anatomy and basic functional role of the Purkinje system is well understood. However, very little is known about the detailed anatomy of the Purkinje system, its inter-individual variability and the implications of the variability in ventricular function, in part due to limitations in experimental techniques. In this study, we aim to provide new insight into the inter-individual variability of the free running Purkinje system anatomy and its impact on ventricular electrophysiological function. As a first step towards achieving this aim, high resolution magnetic resonance imaging (MRI) datasets of rat and the rabbit ventricles are obtained and analysed using a novel semi-automatic image processing algorithm for segmentation of the free-running Purkinje system. Segmented geometry from the MRI datasets is used to construct a computational model of the Purkinje system, which is incorporated in to an anatomically-based ventricular geometry to simulate ventricular electrophysiological activity.
- Published
- 2010
- Full Text
- View/download PDF
45. CHASTE: incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open source library.
- Author
-
Bernabeu MO, Bordas R, Pathmanathan P, Pitt-Francis J, Cooper J, Garny A, Gavaghan DJ, Rodriguez B, Southern JA, and Whiteley JP
- Subjects
- Computer Graphics, User-Computer Interface, Algorithms, Computational Biology, Models, Biological
- Abstract
Recent work has described the software engineering and computational infrastructure that has been set up as part of the Cancer, Heart and Soft Tissue Environment (CHASTE) project. CHASTE is an open source software package that currently has heart and cancer modelling functionality. This software has been written using a programming paradigm imported from the commercial sector and has resulted in a code that has been subject to a far more rigorous testing procedure than that is usual in this field. In this paper, we explain how new functionality may be incorporated into CHASTE. Whiteley has developed a numerical algorithm for solving the bidomain equations that uses the multi-scale (MS) nature of the physiology modelled to enhance computational efficiency. Using a simple geometry in two dimensions and a purpose-built code, this algorithm was reported to give an increase in computational efficiency of more than two orders of magnitude. In this paper, we begin by reviewing numerical methods currently in use for solving the bidomain equations, explaining how these methods may be developed to use the MS algorithm discussed above. We then demonstrate the use of this algorithm within the CHASTE framework for solving the monodomain and bidomain equations in a three-dimensional realistic heart geometry. Finally, we discuss how CHASTE may be developed to include new physiological functionality--such as modelling a beating heart and fluid flow in the heart--and how new algorithms aimed at increasing the efficiency of the code may be incorporated.
- Published
- 2009
- Full Text
- View/download PDF
46. Simulation of cardiac electrophysiology on next-generation high-performance computers.
- Author
-
Bordas R, Carpentieri B, Fotia G, Maggio F, Nobes R, Pitt-Francis J, and Southern J
- Subjects
- Algorithms, Finite Element Analysis, Humans, Computers, Electrocardiography, Heart physiology
- Abstract
Models of cardiac electrophysiology consist of a system of partial differential equations (PDEs) coupled with a system of ordinary differential equations representing cell membrane dynamics. Current software to solve such models does not provide the required computational speed for practical applications. One reason for this is that little use is made of recent developments in adaptive numerical algorithms for solving systems of PDEs. Studies have suggested that a speedup of up to two orders of magnitude is possible by using adaptive methods. The challenge lies in the efficient implementation of adaptive algorithms on massively parallel computers. The finite-element (FE) method is often used in heart simulators as it can encapsulate the complex geometry and small-scale details of the human heart. An alternative is the spectral element (SE) method, a high-order technique that provides the flexibility and accuracy of FE, but with a reduced number of degrees of freedom. The feasibility of implementing a parallel SE algorithm based on fully unstructured all-hexahedra meshes is discussed. A major computational task is solution of the large algebraic system resulting from FE or SE discretization. Choice of linear solver and preconditioner has a substantial effect on efficiency. A fully parallel implementation based on dynamic partitioning that accounts for load balance, communication and data movement costs is required. Each of these methods must be implemented on next-generation supercomputers in order to realize the necessary speedup. The problems that this may cause, and some of the techniques that are beginning to be developed to overcome these issues, are described.
- Published
- 2009
- Full Text
- View/download PDF
47. Documentation of hazards and safety perceptions for mechanized logging operations in East Central Alabama.
- Author
-
Bordas RM, Davis GA, Hopkins BL, Thomas RE, and Rummer RB
- Subjects
- Accidents, Occupational psychology, Accidents, Occupational statistics & numerical data, Alabama epidemiology, Attitude to Health, Data Collection, Extraction and Processing Industry, Humans, Inservice Training, Risk-Taking, United States, United States Occupational Safety and Health Administration, Accidents, Occupational prevention & control, Equipment Safety, Forestry, Occupational Health legislation & jurisprudence
- Abstract
The logging industry remains one of the most hazardous in the nation. Despite more stringent safety regulations and improvements in equipment safety features, the rate of logging fatalities has decreased at a much lower rate than the decrease in the rate of illnesses and injuries in the same occupation. The objective of this research was to identify and assess the hazards associated with logging operations in the Southeast region of the U.S. and propose interventions, taking into consideration the fact that, currently, most operations in the region are fully mechanized. Five logging crews in East Central Alabama participated in the study and were observed repeatedly during their normal operations. Researchers observed loggers engaging in multiple unsafe behaviors, but none of those led to an injury. The incidence of unsafe behaviors may be due in part to a lack of awareness of the hazards. Results indicate that Occupational Safety and Health Administration (OSHA) regulations appear to have little influence on logging safety. Loggers believe that most safety training recommendations are difficult to implement and negatively impact productivity. Thus, there seem to be fundamental drawbacks in the logging industry regarding effective delivery of safety training to loggers. The present study was a joint venture by the Industrial and Systems Engineering and Psychology departments of Auburn University, with support from the United States Forest Service (USFS).
- Published
- 2001
- Full Text
- View/download PDF
48. Subcutaneous angiocentric T-cell lymphoma associated with fatal hemophagocytic syndrome.
- Author
-
Baselga E, Pujol RM, Costa I, Bordas R, and De Moragas JM
- Subjects
- Aged, Fatal Outcome, Female, Genotype, Histiocytosis, Non-Langerhans-Cell genetics, Histocytochemistry, Humans, Immunohistochemistry, Lymphoma, T-Cell, Cutaneous genetics, Skin Neoplasms genetics, Histiocytosis, Non-Langerhans-Cell complications, Histiocytosis, Non-Langerhans-Cell pathology, Lymphoma, T-Cell, Cutaneous complications, Lymphoma, T-Cell, Cutaneous pathology, Skin Neoplasms complications, Skin Neoplasms pathology
- Published
- 1997
- Full Text
- View/download PDF
49. [Domiciliary intervention].
- Author
-
Múñiz Bordas R, Domínguez Santamaría AE, and Prieto Gondell A
- Subjects
- Nursing Evaluation Research, Primary Nursing organization & administration, Primary Nursing statistics & numerical data, Spain, Home Care Services organization & administration, Home Care Services statistics & numerical data
- Published
- 1992
50. [Clinical study of a new oral hypoglycemic agent: glypentide (UR-661)].
- Author
-
Calvet JM, Matarrodona M, and Bordas R
- Subjects
- Administration, Oral, Adolescent, Adult, Aged, Benzamides administration & dosage, Benzamides therapeutic use, Child, Child, Preschool, Cyclopentanes administration & dosage, Cyclopentanes analogs & derivatives, Cyclopentanes therapeutic use, Drug Evaluation, Female, Humans, Hypoglycemic Agents therapeutic use, Infant, Male, Middle Aged, Sulfonylurea Compounds therapeutic use, Tablets, Diabetes Mellitus drug therapy, Hypoglycemic Agents administration & dosage, Sulfonylurea Compounds administration & dosage
- Published
- 1974
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.