scholarly journals Iliski, a software for robust calculation of transfer functions

2020 ◽  
Author(s):  
Ali-Kemal Aydin ◽  
William D. Haselden ◽  
Julie Dang ◽  
Patrick J. Drew ◽  
Serge Charpak ◽  
...  
Keyword(s):  
Blood Flow ◽  
Transfer Function ◽  
Open Source ◽  
Neuronal Activity ◽  
Operating Systems ◽  
Transfer Functions ◽  
A Priori ◽  
Deterministic Optimization ◽  
Pathophysiological Mechanisms ◽  
Pre Treatment

1.AbstractUnderstanding the relationships between biological events is paramount to unravel pathophysiological mechanisms. These relationships can be modeled with Transfer Functions (TFs), with no need of a priori hypotheses as to the shape of the transfer function. Here we present Iliski, a software dedicated to TFs computation between two signals. It includes different pre-treatment routines and TF computation processes: deconvolution, deterministic and non-deterministic optimization algorithms that are adapted to disparate datasets. We apply Iliski to data on neurovascular coupling, an ensemble of biological events that link neuronal activity to local changes of blood flow, highlighting the software benefits and caveats in the computation and evaluation of TFs. We also propose a workflow that will help users to choose the best computation according to the dataset. Iliski is available under the open-source license CC BY 4.0 on GitLab (https://gitlab.com/AliK_A/iliski) and can be used on the most common operating systems, either within the MATLAB environment, or as a standalone application.

scholarly journals Iliski, a software for robust calculation of transfer functions

2021 ◽  
Vol 17 (6) ◽  
pp. e1008614
Author(s):  
Ali-Kemal Aydin ◽  
William D. Haselden ◽  
Julie Dang ◽  
Patrick J. Drew ◽  
Serge Charpak ◽  
...  
Keyword(s):  
Blood Flow ◽  
Transfer Function ◽  
Open Source ◽  
Neuronal Activity ◽  
Operating Systems ◽  
Transfer Functions ◽  
A Priori ◽  
Biological Processes ◽  
Cellular Mechanisms ◽  
Pre Treatment

Understanding the relationships between biological processes is paramount to unravel pathophysiological mechanisms. These relationships can be modeled with Transfer Functions (TFs), with no need of a priori hypotheses as to the shape of the transfer function. Here we present Iliski, a software dedicated to TFs computation between two signals. It includes different pre-treatment routines and TF computation processes: deconvolution, deterministic and non-deterministic optimization algorithms that are adapted to disparate datasets. We apply Iliski to data on neurovascular coupling, an ensemble of cellular mechanisms that link neuronal activity to local changes of blood flow, highlighting the software benefits and caveats in the computation and evaluation of TFs. We also propose a workflow that will help users to choose the best computation according to the dataset. Iliski is available under the open-source license CC BY 4.0 on GitHub (https://github.com/alike-aydin/Iliski) and can be used on the most common operating systems, either within the MATLAB environment, or as a standalone application.

Predicting cerebral blood flow response to orthostatic stress from resting dynamics: effects of healthy aging

2001 ◽  
Vol 281 (3) ◽  
pp. R716-R722 ◽  
Author(s):  
K. Narayanan ◽  
James J. Collins ◽  
Jason Hamner ◽  
Seiji Mukai ◽  
Lewis A. Lipsitz
Keyword(s):  
Blood Flow ◽  
Cerebral Blood Flow ◽  
Transfer Function ◽  
Healthy Aging ◽  
Transfer Functions ◽  
Cerebral Blood Flow Velocity ◽  
Elderly Subjects ◽  
Elderly Age ◽  
Healthy Elderly ◽  
Posture Change

The transfer function relating arterial pressure (AP) to cerebral blood flow velocity (CBFV) during resting conditions has been used to predict the CBFV response to hypotension. We hypothesized that this approach could predict the CBFV response to posture change in elderly individuals if impaired autoregulation allowed changes in AP to be passively transferred to CBFV. AP (Finapres) and CBFV (middle cerebral artery transcranial Doppler) were measured in 10 healthy young (age 24 ± 1 yr) and 10 healthy elderly (age 72 ± 3 yr) subjects during 5 min of quiet sitting and 1 min of active standing while breathing was paced at 0.25 Hz. Transfer functions between AP and CBFV changes during sitting were estimated from each full waveform in both low-frequency (LF; 0.05–0.2 Hz) and heartbeat-frequency (HBF; 0.7–1.4 Hz) ranges. The impulse-response function was used to compute changes in CBFV during posture change. The LF transfer function did not predict orthostatic changes in CBFV in either group, suggesting normal cerebral autoregulation. In the HBF range, the prediction was high in elderly ( R = 0.65 ± 0.23) but not young subjects ( R = 0.19 ± 0.35; P < 0.003, young vs. elderly). Thus rapidly acting regulatory mechanisms that reduce the transmission of beat-to-beat changes in AP to CBFV may be engaged during posture change in young but not elderly subjects.

Frequency domain of renal autoregulation in the conscious dog

1995 ◽  
Vol 269 (3) ◽  
pp. F317-F322 ◽  
Author(s):  
U. Wittmann ◽  
B. Nafz ◽  
H. Ehmke ◽  
H. R. Kirchheim ◽  
P. B. Persson
Keyword(s):  
Blood Flow ◽  
Phase Shift ◽  
Transfer Function ◽  
Arterial Pressure ◽  
Dynamic Range ◽  
Transfer Functions ◽  
Driving Pressure ◽  
Acute Administration ◽  
Frequency Range ◽  
Renal Autoregulation

The dynamic range in which renal blood flow (RBF) autoregulation occurs was determined in eight conscious foxhounds chronically catheterized in the abdominal aorta and implanted with a transit-time flow probe over the renal artery. Sinusoidal driving pressures (amplitude of 10 mmHg) were forced on the renal arterial pressure at different frequencies by a servo-control device, and transfer functions were calculated. Only one frequency range was found below which the gain of the transfer function declined and in which the phase angle increased (n = 8). This indicates the presence of a potent mechanism for renal autoregulation in the examined frequency range between 0.0031 and 0.08 Hz, which buffers changes in blood flow < 0.02 Hz. After furosemide treatment, one indicator for autoregulation (phase shift of transfer function) was significantly blunted at low frequencies (n = 6). Furosemide, however, did not reduce the phase shift to zero, suggesting that some autoregulation still remained in the frequency range between 0.04 and 0.08 Hz. In conclusion, autoregulation of RBF during sinusoidal changes in driving pressure between 0.0031 and 0.02 Hz is mediated by a single mechanism, which can be blocked by the acute administration of furosemide. The residual phase shift between arterial pressure and RBF in the transfer function observed during sinusoidal changes in driving pressure between 0.04 and 0.08 Hz suggests the presence of a second mechanism for RBF autoregulation.

Effect of captopril on fluctuations of blood pressure and renal blood flow in rats

1993 ◽  
Vol 264 (1) ◽  
pp. F37-F44 ◽  
Author(s):  
J. He ◽  
D. J. Marsh
Keyword(s):  
Blood Pressure ◽  
Blood Flow ◽  
Transfer Function ◽  
Renal Blood Flow ◽  
Transfer Functions ◽  
Moving Average ◽  
Mean Value ◽  
Tubuloglomerular Feedback ◽  
Frequency Resolution ◽  
Arterial Blood

Arterial blood pressure and renal blood flow (RBF) fluctuations in rats were studied by autoregressive (AR) and autoregressive-moving average (ARMA) modeling. These estimation procedures provided greater sensitivity and frequency resolution than classic fast Fourier transform (FFT)-based methods and also require shorter observation periods. We estimated the transfer function of RBF autoregulation to test whether inhibition of angiotensin-converting enzyme impairs whole kidney dynamic autoregulation. The transfer function in control animals measured with the ARMA method was similar to transfer functions obtained previously, using FFT methods. Because of better frequency resolution, we also detected an oscillation in RBF at 50 mHz, the same frequency as an oscillation in tubular pressure and glomerular filtration rate that had been attributed to tubuloglomerular feedback (TGF), but that FFT methods had not previously found in whole kidney blood flow. Captopril increased the amplitude of RBF fluctuations and increased the gain of the transfer function at frequencies below 100 mHz, a frequency bandwidth previously associated with TGF. The increased gain indicates that TGF operates less effectively to mediate dynamic autoregulation when angiotensin conversion is inhibited. Gain at frequencies greater than 100 mHz, previously ascribed to the myogenic mechanism, was not affected by captopril. These results show that angiotensin, by modulating TGF, reduces fluctuations of RBF about the mean value.

Analytic integration of contrast transfer functions

1988 ◽  
Vol 46 ◽  
pp. 822-823
Author(s):  
Peter Rez
Keyword(s):  
Wave Function ◽  
Transfer Function ◽  
Transfer Functions ◽  
Spherical Aberration ◽  
Continuous Distribution ◽  
Objective Lens ◽  
Direction Parallel ◽  
Scattering Angle ◽  
Analytic Integration ◽  
Image Position

In high resolution microscopy the image amplitude is given by the convolution of the specimen exit surface wave function and the microscope objective lens transfer function. This is usually done by multiplying the wave function and the transfer function in reciprocal space and integrating over the effective aperture. For very thin specimens the scattering can be represented by a weak phase object and the amplitude observed in the image plane is1where fe (Θ) is the electron scattering factor, r is a postition variable, Θ a scattering angle and x(Θ) the lens transfer function. x(Θ) is given by2where Cs is the objective lens spherical aberration coefficient, the wavelength, and f the defocus.We shall consider one dimensional scattering that might arise from a cross sectional specimen containing disordered planes of a heavy element stacked in a regular sequence among planes of lighter elements. In a direction parallel to the disordered planes there will be a continuous distribution of scattering angle.

Trombone Transfer Functions: Comparison Between Frequency-Swept Sine Wave and Human Performer Input

2012 ◽  
Vol 37 (4) ◽  
pp. 447-454
Author(s):  
James W. Beauchamp
Keyword(s):  
Transfer Function ◽  
Transfer Functions ◽  
Cutoff Frequency ◽  
Sine Wave ◽  
Nonlinear Propagation ◽  
Linear Filter ◽  
Wave System ◽  
General Effect ◽  
Filter Characteristic ◽  
High Pass

Abstract Source/filter models have frequently been used to model sound production of the vocal apparatus and musical instruments. Beginning in 1968, in an effort to measure the transfer function (i.e., transmission response or filter characteristic) of a trombone while being played by expert musicians, sound pressure signals from the mouthpiece and the trombone bell output were recorded in an anechoic room and then subjected to harmonic spectrum analysis. Output/input ratios of the signals’ harmonic amplitudes plotted vs. harmonic frequency then became points on the trombone’s transfer function. The first such recordings were made on analog 1/4 inch stereo magnetic tape. In 2000 digital recordings of trombone mouthpiece and anechoic output signals were made that provide a more accurate measurement of the trombone filter characteristic. Results show that the filter is a high-pass type with a cutoff frequency around 1000 Hz. Whereas the characteristic below cutoff is quite stable, above cutoff it is extremely variable, depending on level. In addition, measurements made using a swept-sine-wave system in 1972 verified the high-pass behavior, but they also showed a series of resonances whose minima correspond to the harmonic frequencies which occur under performance conditions. For frequencies below cutoff the two types of measurements corresponded well, but above cutoff there was a considerable difference. The general effect is that output harmonics above cutoff are greater than would be expected from linear filter theory, and this effect becomes stronger as input pressure increases. In the 1990s and early 2000s this nonlinear effect was verified by theory and measurements which showed that nonlinear propagation takes place in the trombone, causing a wave steepening effect at high amplitudes, thus increasing the relative strengths of the upper harmonics.

BCL::Conf – Improved Open-Source Knowledge-Based Conformation Sampling using the Crystallographic Open Database

2020 ◽  
Author(s):  
Jeffrey Mendenhall ◽  
Benjamin Brown ◽  
Sandeepkumar Kothiwale ◽  
Jens Meiler
Keyword(s):  
Ligand Binding ◽  
Open Source ◽  
Operating Systems ◽  
Generation Algorithm ◽  
Rotamer Library ◽  
Conformer Generation ◽  
Knowledge Based

<div>This paper describes recent improvements made to the BCL::Conf rotamer generation algorithm and comparison of its performance against other freely available and commercial conformer generation software. We demonstrate that BCL::Conf, with the use of rotamers derived from the COD, more effectively recovers crystallographic ligand-binding conformations seen in the PDB than other commercial and freely available software. BCL::Conf is now distributed with the COD-derived rotamer library, free for academic use. The BCL can be downloaded at <a href="http://meilerlab.org/index.php/bclcommons/show/b_apps_id/1">http://meilerlab.org/ bclcommons</a> for Windows, Linux, or Apple operating systems.<br></div>

Structural-parametric model of an electroelastic actuator for nanomechanics

2020 ◽  
pp. 3-11
Author(s):  
S.M. Afonin
Keyword(s):  
Transfer Function ◽  
Piezoelectric Actuator ◽  
Transfer Functions ◽  
Piezoelectric Effect ◽  
Parametric Model ◽  
Elastic Compliance ◽  
Parametric Models ◽  
Piezo Actuator ◽  
Structural Scheme ◽  
Model Transfer

Structural-parametric models, structural schemes are constructed and the transfer functions of electro-elastic actuators for nanomechanics are determined. The transfer functions of the piezoelectric actuator with the generalized piezoelectric effect are obtained. The changes in the elastic compliance and rigidity of the piezoactuator are determined taking into account the type of control. Keywords electro-elastic actuator, piezo actuator, structural-parametric model, transfer function, parametric structural scheme

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

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