scholarly journals Reproducible model development in the Cardiac Electrophysiology Web Lab

2018 ◽  
Author(s):  
Aidan C. Daly ◽  
Michael Clerx ◽  
Kylie A. Beattie ◽  
Jonathan Cooper ◽  
David J. Gavaghan ◽  
...  
Keyword(s):  
Experimental Data ◽  
Cardiac Electrophysiology ◽  
Model Building ◽  
Research Effort ◽  
Model Development ◽  
Cardiac Cells ◽  
Cardiac Cell ◽  
Cell Models ◽  
Experimental Protocol ◽  
Wide Range

AbstractThe modelling of the electrophysiology of cardiac cells is one of the most mature areas of systems biology. This extended concentration of research effort brings with it new challenges, foremost among which is that of choosing which of these models is most suitable for addressing a particular scientific question. In a previous paper, we presented our initial work in developing an online resource for the characterisation and comparison of electrophysiological cell models in a wide range of experimental scenarios. In that work, we described how we had developed a novel protocol language that allowed us to separate the details of the mathematical model (the majority of cardiac cell models take the form of ordinary differential equations) from the experimental protocol being simulated. We developed a fully-open online repository (which we termed the Cardiac Electrophysiology Web Lab) which allows users to store and compare the results of applying the same experimental protocol to competing models. In the current paper we describe the most recent and planned extensions of this work, focused on supporting the process of model building from experimental data. We outline the necessary work to develop a machine-readable language to describe the process of inferring parameters from wet lab datasets, and illustrate our approach through a detailed example of fitting a model of the hERG channel using experimental data. We conclude by discussing the future challenges in making further progress in this domain towards our goal of facilitating a fully reproducible approach to the development of cardiac cell models.

Computational Modelling of Optogenetics in Cardiac Cells

2012 ◽  
Author(s):  
Jonathan Wong ◽  
Oscar Abilez ◽  
Ellen Kuhl
Keyword(s):  
Finite Element ◽  
Ion Channel ◽  
Single Cell ◽  
Cardiac Myocytes ◽  
Cardiac Tissue ◽  
Channel Model ◽  
Computational Modelling ◽  
Cardiac Cells ◽  
Cardiac Cell ◽  
Cell Models

Channelrhodopsin-2 (ChR2) is a light-activated ion channel that can allow scientists to electrically activate cells via optical stimulation. Using a combination of existing computational electrophysiological and mechanical cardiac cell models with a novel ChR2 ion channel model, we created a model for ChR2-transduced cardiac myocytes. We implemented this model into a commonly available finite element platform and simulated both the single cell and the tissue electromechanical response. Our simulations show that it is possible to stimulate cardiac tissue optically with ChR2-transduced cells.

scholarly journals A deep learning algorithm to translate and classify cardiac electrophysiology: From iPSC-CMs to adult cardiac cells

2020 ◽  
Author(s):  
Parya Aghasafari ◽  
Pei-Chi Yang ◽  
Divya C. Kernik ◽  
Kauho Sakamoto ◽  
Yasunari Kanda ◽  
...  
Keyword(s):  
Experimental Data ◽  
Deep Learning ◽  
Action Potential ◽  
Cardiac Electrophysiology ◽  
Cardiac Cells ◽  
Cardiac Response ◽  
Patient Specific ◽  
Mature Adult ◽  
The Impact

AbstractExciting developments in both in vitro and in silico technologies have led to new ways to identify patient specific cardiac mechanisms. The development of induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) has been a critical in vitro advance in the study of patient-specific physiology, pathophysiology and response to drugs. However, the iPSC-CM methodology is limited by the low throughput and high variability of resulting electrophysiological measurements. Moreover, the iPSC-CMs generate immature action potentials, and it is not clear if observations in the iPSC-CM model system can be confidently interpreted to reflect impact in human adults. There has been no demonstrated method to allow reliable translation of results from the iPSC-CM to a mature adult cardiac response. Here, we demonstrate a new computational approach intended to address the current shortcomings of the iPSC-CM platform by developing and deploying a multitask network that was trained and tested using simulated data and then applied to experimental data. We showed that a deep learning network can be applied to classify cells into the drugged and drug free categories and can be used to predict the impact of electrophysiological perturbation across the continuum of aging from the immature iPSC-CM action potential to the adult ventricular myocyte action potential. We validated the output of the model with experimental data. The method can be applied broadly across a spectrum of aging, but also to translate data between species.

LIQUIDUS THERMO-BAROMETER FOR THE MODELING OF MAGNETITE — MELT EQUILIBRIUM

2018 ◽  
pp. 71-80
Author(s):  
N. S. Aryaeva ◽  
E. V. Koptev-Dvornikov ◽  
D. A. Bychkov
Keyword(s):  
Experimental Data ◽  
Liquidus Temperature ◽  
Vertical Structure ◽  
Maximum Error ◽  
Silicate Melt ◽  
System Of Equations ◽  
Wide Range ◽  
Basaltic Melts ◽  
Multidimensional Statistics

A system of equations of thermobarometer for magnetite-silicate melt equilibrium was obtained by method of multidimensional statistics of 93 experimental data of a magnetite solubility in basaltic melts. Equations reproduce experimental data in a wide range of basalt compositions, temperatures and pressures with small errors. Verification of thermobarometers showed the maximum error in liquidus temperature reproducing does not exceed ±7 °C. The level of cumulative magnetite appearance in the vertical structure of Tsypringa, Kivakka, Burakovsky intrusions predicted with errors from ±10 to ±50 m.

scholarly journals Experimental analysis and ANN prediction on performances of finned oval-tube heat exchanger under different air inlet angles with limited experimental data

Open Physics ◽  
2020 ◽  
Vol 18 (1) ◽  
pp. 968-980
Author(s):  
Xueping Du ◽  
Zhijie Chen ◽  
Qi Meng ◽  
Yang Song
Keyword(s):  
Heat Transfer ◽  
Experimental Data ◽  
Heat Exchanger ◽  
Correlation Equation ◽  
Tube Heat Exchanger ◽  
Flow Friction ◽  
Air Inlet ◽  
Comparison Results ◽  
Wide Range ◽  
Oval Tube

Abstract A high accuracy of experimental correlations on the heat transfer and flow friction is always expected to calculate the unknown cases according to the limited experimental data from a heat exchanger experiment. However, certain errors will occur during the data processing by the traditional methods to obtain the experimental correlations for the heat transfer and friction. A dimensionless experimental correlation equation including angles is proposed to make the correlation have a wide range of applicability. Then, the artificial neural networks (ANNs) are used to predict the heat transfer and flow friction performances of a finned oval-tube heat exchanger under four different air inlet angles with limited experimental data. The comparison results of ANN prediction with experimental correlations show that the errors from the ANN prediction are smaller than those from the classical correlations. The data of the four air inlet angles fitted separately have higher precisions than those fitted together. It is demonstrated that the ANN approach is more useful than experimental correlations to predict the heat transfer and flow resistance characteristics for unknown cases of heat exchangers. The results can provide theoretical support for the application of the ANN used in the finned oval-tube heat exchanger performance prediction.

scholarly journals Modelling the Inflation and Elastic Instabilities of Rubber-Like Spherical and Cylindrical Shells Using a New Generalised Neo-Hookean Strain Energy Function

2021 ◽  
Author(s):  
Afshin Anssari-Benam ◽  
Andrea Bucchi ◽  
Giuseppe Saccomandi
Keyword(s):  
Experimental Data ◽  
Energy Function ◽  
Limit Point ◽  
Strain Energy ◽  
Cylindrical Shells ◽  
Strain Energy Function ◽  
Model Parameters ◽  
Wide Range ◽  
Cylindrical Tubes ◽  
Gent Model

AbstractThe application of a newly proposed generalised neo-Hookean strain energy function to the inflation of incompressible rubber-like spherical and cylindrical shells is demonstrated in this paper. The pressure ($P$ P ) – inflation ($\lambda $ λ or $v$ v ) relationships are derived and presented for four shells: thin- and thick-walled spherical balloons, and thin- and thick-walled cylindrical tubes. Characteristics of the inflation curves predicted by the model for the four considered shells are analysed and the critical values of the model parameters for exhibiting the limit-point instability are established. The application of the model to extant experimental datasets procured from studies across 19th to 21st century will be demonstrated, showing favourable agreement between the model and the experimental data. The capability of the model to capture the two characteristic instability phenomena in the inflation of rubber-like materials, namely the limit-point and inflation-jump instabilities, will be made evident from both the theoretical analysis and curve-fitting approaches presented in this study. A comparison with the predictions of the Gent model for the considered data is also demonstrated and is shown that our presented model provides improved fits. Given the simplicity of the model, its ability to fit a wide range of experimental data and capture both limit-point and inflation-jump instabilities, we propose the application of our model to the inflation of rubber-like materials.

scholarly journals Application of Artificial Intelligence (AI) for Sustainable Highway and Road System

Symmetry ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 60
Author(s):  
Md Arifuzzaman ◽  
Muhammad Aniq Gul ◽  
Kaffayatullah Khan ◽  
S. M. Zakir Hossain
Keyword(s):  
Experimental Data ◽  
High Performance ◽  
Adhesion Force ◽  
Model Development ◽  
Real Life ◽  
Bayesian Optimization ◽  
Support Vector ◽  
Adhesive Properties ◽  
Bayesian Optimization Algorithm ◽  
The Mean

There are several environmental factors such as temperature differential, moisture, oxidation, etc. that affect the extended life of the modified asphalt influencing its desired adhesive properties. Knowledge of the properties of asphalt adhesives can help to provide a more resilient and durable asphalt surface. In this study, a hybrid of Bayesian optimization algorithm and support vector regression approach is recommended to predict the adhesion force of asphalt. The effects of three important variables viz., conditions (fresh, wet and aged), binder types (base, 4% SB, 5% SB, 4% SBS and 5% SBS), and Carbon Nano Tube doses (0.5%, 1.0% and 1.5%) on adhesive force are taken into consideration. Real-life experimental data (405 specimens) are considered for model development. Using atomic force microscopy, the adhesive strength of nanoscales of test specimens is determined according to functional groups on the asphalt. It is found that the model predictions overlap with the experimental data with a high R2 of 90.5% and relative deviation are scattered around zero line. Besides, the mean, median and standard deviations of experimental and the predicted values are very close. In addition, the mean absolute Error, root mean square error and fractional bias values were found to be low, indicating the high performance of the developed model.

scholarly journals Modeling Building Stock Development

2021 ◽  
Vol 13 (2) ◽  
pp. 723
Author(s):  
Antti Kurvinen ◽  
Arto Saari ◽  
Juhani Heljo ◽  
Eero Nippala
Keyword(s):  
Model Development ◽  
Housing Demand ◽  
Quality Data ◽  
Building Stock ◽  
Test Arena ◽  
Climate Targets ◽  
Wide Range ◽  
Key Variables ◽  
The Impact

It is widely agreed that dynamics of building stocks are relatively poorly known even if it is recognized to be an important research topic. Better understanding of building stock dynamics and future development is crucial, e.g., for sustainable management of the built environment as various analyses require long-term projections of building stock development. Recognizing the uncertainty in relation to long-term modeling, we propose a transparent calculation-based QuantiSTOCK model for modeling building stock development. Our approach not only provides a tangible tool for understanding development when selected assumptions are valid but also, most importantly, allows for studying the sensitivity of results to alternative developments of the key variables. Therefore, this relatively simple modeling approach provides fruitful grounds for understanding the impact of different key variables, which is needed to facilitate meaningful debate on different housing, land use, and environment-related policies. The QuantiSTOCK model may be extended in numerous ways and lays the groundwork for modeling the future developments of building stocks. The presented model may be used in a wide range of analyses ranging from assessing housing demand at the regional level to providing input for defining sustainable pathways towards climate targets. Due to the availability of high-quality data, the Finnish building stock provided a great test arena for the model development.

Investigations on the Mechanical Properties and Formability of Friction Stir Welded Tailored Blanks

2007 ◽  
Vol 344 ◽  
pp. 143-150 ◽  
Author(s):  
Gianluca Buffa ◽  
Livan Fratini ◽  
Marion Merklein ◽  
Detlev Staud
Keyword(s):  
Mechanical Properties ◽  
Stress Condition ◽  
Research Effort ◽  
High Strength Steels ◽  
High Strength ◽  
Tensile Tests ◽  
Friction Stir ◽  
Tailored Blanks ◽  
Sheet Stamping ◽  
Wide Range

Tight competition characterizing automotive industries in the last decades has determined a strong research effort aimed to improve utilized processes and materials in sheet stamping. As far as the latter are regarded light weight alloys, high strength steels and tailored blanks have been increasingly utilized with the aim to reduce parts weight and fuel consumptions. In the paper the mechanical properties and formability of tailored welded blanks made of a precipitation hardenable aluminum alloy but with different sheet thicknesses, have been investigated: both laser welding and friction stir welding have been developed to obtain the tailored blanks. For both welding operations a wide range of the thickness ratios has been considered. The formability of the obtained blanks has been characterized through tensile tests and cup deep drawing tests, in order to show the formability in dependency of the stress condition; what is more mechanical and metallurgical investigations have been made on the welded joints.

The Petrogenetic Model, an Extension of Bowen's Petrogenetic Grid

1962 ◽  
Vol 99 (6) ◽  
pp. 558-569 ◽  
Author(s):  
Peter J. Wyllie
Keyword(s):  
Experimental Data ◽  
Constant Pressure ◽  
Three Dimensional ◽  
Pore Fluid ◽  
Fluid Composition ◽  
Solid Reaction ◽  
Petrogenetic Model ◽  
Wide Range ◽  
Opposite Face ◽  
Reaction Surfaces

AbstractBowen's petrogenetic grid is a PT projection containing univariant curves for decarbonation, dehydration, and solid-solid reactions, with vapour pressure (Pf) equal to total pressure (Ps). Analysis of experimental data in the system MgO–CO2–H2O leads to an expansion of this grid. Three of the important variables in metamorphism when Pf = Ps are P, T, and variation of the pore fluid composition between H2O and CO2. These can be illustrated in a three-dimensional petrogenetic model; one face is a PT plane for reactions occurring with pure H2O, and the opposite face is a similar plane for reactions with pure CO2; these are separated by an axis for pore fluid composition varying between H2O and CO2. Superposition of the PT faces of the model provides the petrogenetic grid. The reactions within the model are represented by divariant surfaces, which may meet along univariant lines. For dissociation reactions, the surfaces curve towards lower temperatures as the proportion of non-reacting volatile increases, and solid-solid reaction surfaces are parallel to the vapour composition axis and perpendicular to the PT axes. The relative temperatures of reactions and the lines of intersections of the surfaces can be illustrated in isobaric sections. Isobaric sections are used to illustrate reactions proceeding at constant pressure with (1) pore fluid composition remaining constant during the reaction, with temperature increasing (2) pore fluid composition changing during the reaction, with temperature increasing, and (3) pore fluid changing composition at constant temperature. The petrogenetic model provides a convenient framework for a wide range of experimental data.

Fluorescence and differential light absorption recordings with calcium probes and potential-sensitive dyes in skinned cardiac cells

1982 ◽  
Vol 60 (4) ◽  
pp. 556-567 ◽  
Author(s):  
Alexandre Fabiato
Keyword(s):  
Cardiac Cells ◽  
Arsenazo Iii ◽  
Optical Methods ◽  
Cardiac Cell ◽  
Differential Absorption ◽  
Fluorescence Measurements ◽  
Merocyanine 540 ◽  
Inverted Microscope ◽  
Optimum Wavelength ◽  
Absorption Measurements

This report describes an optical system for microspectrophotometry in a single cardiac cell from which the sarcolemma has been removed by microdissection (skinned cardiac cell). This system is attached to the high power inverted microscope used for the microdissection and includes (a) a single variable wavelength microspectrophotometer used to define the spectrum of a given dye or Ca2+ probe; and (b) a dual wavelength, differential microspectrophotometer used to record differentially between the optimum wavelength and a wavelength separated by 25–30 nm. Results are presented using the following optical methods: (a) fluorescence measurements with chlorotetracycline to monitor the amount of Ca2+ bound to the inner face of the sarcoplasmic reticulum (SR) membrane; (b) differential absorption measurements with arsenazo III to measure changes of myoplasmic [Ca2+]free resulting from Ca2+ release from the SR; (c) fluorescence and (or) differential absorption measurements with the potential-sensitive dyes merocyanine 540, NK 2367, and di-S-C3(5) to monitor changes of charge distribution on the SR membrane during Ca2+ accumulation in the SR, as well as before and during Ca2+-induced release of Ca2+ from the SR. A small and rapid signal is observed which precedes the Ca2+-induced release of Ca2+ from the SR. It is detected as an increase of Ca2+ binding inside the SR with chlorotetracycline and as a "hyperpolarization" with potential-sensitive dyes, while no transient change of myoplasmic [Ca2+]free is detected with arsenazo III. This small and rapid signal preceding the Ca2+ release may be a first hint to an understanding of the mechanism whereby a small increase of [Ca2+]free outside the SR triggers Ca2+ release from the SR.

Sign in / Sign up

Export Citation Format

Share Document