scholarly journals Systematic analysis of noise reduction properties of coupled and isolated feed-forward loops

2021 ◽  
Vol 17 (12) ◽  
pp. e1009622
Author(s):  
Suchana Chakravarty ◽  
Attila Csikász-Nagy
Keyword(s):  
Noise Reduction ◽  
Signaling Pathways ◽  
Complex Function ◽  
Coupled Systems ◽  
Inactivation Kinetics ◽  
Noise Filtering ◽  
Noisy Environment ◽  
Biological Noise ◽  
Systematic Analysis ◽  
Feed Forward

Cells can maintain their homeostasis in a noisy environment since their signaling pathways can filter out noise somehow. Several network motifs have been proposed for biological noise filtering and, among these, feed-forward loops have received special attention. Specific feed-forward loops show noise reducing capabilities, but we notice that this feature comes together with a reduced signal transducing performance. In posttranslational signaling pathways feed-forward loops do not function in isolation, rather they are coupled with other motifs to serve a more complex function. Feed-forward loops are often coupled to other feed-forward loops, which could affect their noise-reducing capabilities. Here we systematically study all feed-forward loop motifs and all their pairwise coupled systems with activation-inactivation kinetics to identify which networks are capable of good noise reduction, while keeping their signal transducing performance. Our analysis shows that coupled feed-forward loops can provide better noise reduction and, at the same time, can increase the signal transduction of the system. The coupling of two coherent 1 or one coherent 1 and one incoherent 4 feed-forward loops can give the best performance in both of these measures.

Optical amplifier noise reduction in mm-wave links by signal-ASE noise filtering

1999 ◽  
Vol 35 (2) ◽  
pp. 159 ◽  
Author(s):  
R.A. Griffin ◽  
P.M. Lane ◽  
J.J. O'Reilly
Keyword(s):  
Noise Reduction ◽  
Optical Amplifier ◽  
Noise Filtering ◽  
Amplifier Noise

Abstract 489: Differential Phosphoproteomic Analysis of Platelet Activation by Specific Oxidized Phospholipids and Thrombin Reveals Mechanisms of Platelet Activation in Hyperlipidemia

2013 ◽  
Vol 33 (suppl_1) ◽  
Author(s):  
Alejandro Zimman ◽  
Bjoern Titz ◽  
Evangelia Komisopoulou ◽  
Thomas G Graeber ◽  
Eugene A Podrez
Keyword(s):  
Signaling Pathways ◽  
Signaling Pathway ◽  
Platelet Activation ◽  
Scavenger Receptor ◽  
Human Platelets ◽  
Oxidized Phospholipids ◽  
Systematic Analysis ◽  
Bioinformatic Tools ◽  
Induced Changes

We previously showed that specific oxidized phospholipids (oxPC CD36 ) activate platelets via the scavenger receptor CD36 and promote platelet hyper-reactivity in hyperlipidemia, however the signaling pathway(s) induced in platelets by oxPC CD36 are not defined. We employed mass spectrometry-based phosphoproteomics for the unbiased analysis of changes in protein phosphorylation induced by oxPC CD36 and thrombin, a strong platelet agonist, in human platelets. oxPC CD36 induced changes in phosphorylation of 148 unique phosphorylation sites (116 proteins) while thrombin induced changes of 297 unique sites (181 proteins). Most of the changes in phosphorylation induced by oxPC CD36 and thrombin identified in our study have never been reported before in platelets and include high- and low-abundant proteins with diverse molecular functions located in the plasma membrane, cytosol, or cytoskeleton. Analysis using multiple bioinformatic tools identified protein interaction networks, signaling pathways, activated kinases, and enriched phosphorylation motifs. Comparison between platelet agonists revealed multiple differences including the specific activation of a signaling pathway involving Src-family kinases (SFK), SYK kinase, and PLCγ2 by oxPC CD36 . Subsequent biochemical studies in human platelets demonstrated that this pathway is critical for platelet activation by oxPC CD36 and is downstream of CD36. In conclusion, systematic analysis of platelet activation pathways provided novel insights into the mechanism of platelet activation and specific signaling pathways induced by oxidized phospholipids that modulate platelet function in vivo in hyperlipidemia.

New Pathways in Lipopolysaccharide-Induced Toll-Like Receptor 4-to-Nuclear Factor-κB Signaling Through the Coupled Uniform Sequential Reaction Systems Model

2020 ◽  
Vol 12 (10) ◽  
pp. 1246-1256
Author(s):  
Bonawentura Kochel
Keyword(s):  
Signaling Pathways ◽  
Temporal Pattern ◽  
Coupled System ◽  
Direct Consequence ◽  
Nuclear Factor Κb ◽  
Coupled Systems ◽  
Toll Like Receptor 4 ◽  
Sequential Reaction ◽  
Reaction Systems ◽  
Systems Model

The coupled uniform sequential reaction systems (CUSERS) model, which allows for determining the structure of signaling pathways with incomplete information from the temporal patterns of their components, was applied to the experimental records of activities of TLR4 downstream species IKK and NF-κB in LPS-stimulated wild-type (WT), MyD88-deficient and TRIF-deficient macrophages. New signaling pathways targeting IKK were revealed in MyD88-deficient and TRIF-deficient macrophages, and shown to be described by the coupled systems formed by 3- and 5-component or 5- and 10-component pathways, respectively. By comparing the temporal pattern of IKK in WT macrophages with those in MyD88-deficient and TRIF-deficient macrophages, two new signaling pathways, which were absent in the above defective macrophages, were found and described by a system formed by coupling 9- and 10-component pathways. As a direct consequence of the above findings, a coupled system composed of six different 3-, 5-, 5-, 9-, 10- and 10-component pathways targeting IKK and describing its temporal pattern, IKK(f), in WT macrophages was constructed. This system significantly modifies the canonical NF-κB signaling by introducing novel pathways of IKK activation. The expression of nuclear NF-κB in WT macrophages was found to depend on two different signaling pathways and to be modelled by a coupled system composed of 1- and 4-component or 2- and 8-component pathways, in dependence on sampling frequencies used in different experiments. From the three-modal NF-κB(t) temporal pattern in LPS-stimulated WT fibroblasts, three 1-, 12- and 17-component signaling pathways targeting nuclear NF-κB were determined.

scholarly journals Ligand–Receptor Interactions Elucidate Sex-Specific Pathways in the Trajectory From Primordial Germ Cells to Gonia During Human Development

2021 ◽  
Vol 9 ◽  
Author(s):  
Arend W. Overeem ◽  
Yolanda W. Chang ◽  
Jeroen Spruit ◽  
Celine M. Roelse ◽  
Susana M. Chuva De Sousa Lopes
Keyword(s):  
Germ Cell ◽  
Signaling Pathways ◽  
Germ Cells ◽  
Tyrosine Kinases ◽  
Intracellular Localization ◽  
Primordial Germ Cells ◽  
Cell Lineage ◽  
Systematic Analysis ◽  
Receptor Interactions

The human germ cell lineage originates from primordial germ cells (PGCs), which are specified at approximately the third week of development. Our understanding of the signaling pathways that control this event has significantly increased in recent years and that has enabled the generation of PGC-like cells (PGCLCs) from pluripotent stem cells in vitro. However, the signaling pathways that drive the transition of PGCs into gonia (prospermatogonia in males or premeiotic oogonia in females) remain unclear, and we are presently unable to mimic this step in vitro in the absence of gonadal tissue. Therefore, we have analyzed single-cell transcriptomics data of human fetal gonads to map the molecular interactions during the sex-specific transition from PGCs to gonia. The CellPhoneDB algorithm was used to identify significant ligand–receptor interactions between germ cells and their sex-specific neighboring gonadal somatic cells, focusing on four major signaling pathways WNT, NOTCH, TGFβ/BMP, and receptor tyrosine kinases (RTK). Subsequently, the expression and intracellular localization of key effectors for these pathways were validated in human fetal gonads by immunostaining. This approach provided a systematic analysis of the signaling environment in developing human gonads and revealed sex-specific signaling pathways during human premeiotic germ cell development. This work serves as a foundation to understand the transition from PGCs to premeiotic oogonia or prospermatogonia and identifies sex-specific signaling pathways that are of interest in the step-by-step reconstitution of human gametogenesis in vitro.

Noise Reduction in Voice Controlled Logistic Systems

2013 ◽  
Vol 309 ◽  
pp. 260-267
Author(s):  
Laszlo Czap ◽  
Judit Pinter
Keyword(s):  
Noise Reduction ◽  
Speech Processing ◽  
Spectral Representation ◽  
Recognition System ◽  
Noise Signal ◽  
Noisy Environment ◽  
Human Communication ◽  
Driven System ◽  
Machine Interface ◽  
The Voice

The most comfortable way of human communication is speech, which is a possible channel of human-machine interface as well. Moreover, a voice driven system can be controlled with busy hands. Performance of a speech recognition system is highly decayed by presence of noise. Logistic systems typically work in noisy environment, so noise reduction is crucial in industrial speech processing systems. Traditional noise reduction procedures (e.g. Wiener and Kalman filters) are effective on stationary or Gaussian noise. The noise of a real workplace can be captured by an additional microphone: The voice microphone takes both speech and noise, while the noise mike takes only the noise signal. Because of the phase shift of the two signals, simple subtraction in time domain is ineffective. In this paper, we discuss a spectral representation modeling the noise and voice signals. A frequency spectrum based noise cancellation method is proposed and verified in real industrial environment.

Improvement of the Noise Filtering and Image Registration Methods for PSP Experiments

2003 ◽  
Author(s):  
Nobuyoshi Fujimatsu ◽  
Kozo Fujii ◽  
Yoshiaki Tamura
Keyword(s):  
Image Processing ◽  
Wavelet Transform ◽  
Image Registration ◽  
Noise Reduction ◽  
Shot Noise ◽  
Ccd Camera ◽  
Noise Filtering ◽  
Model Surface ◽  
Processing Procedure

Image processing procedure for noise reduction and image registration in the PSP experiments is investigated. A few kinds of filter are examined for the shot noise reduction caused by the CCD camera. The algorithm to detect a marker cell located on the model surface is proposed and an appropriate number size is shown. The algorithm using the wavelet transform is investigated to sharpen the edge around the model. The results indicate that the method developed in this paper effectively removes the shot noise and corrects the displacement of the model during wind-on.

scholarly journals Cell-Free Characterization of Coherent Feed-Forward Loop-Based Synthetic Genetic Circuits

2021 ◽  
Author(s):  
Pascal A. Pieters ◽  
Bryan L. Nathalia ◽  
Ardjan J. van der Linden ◽  
Peng Yin ◽  
Jongmin Kim ◽  
...  
Keyword(s):  
Fold Change ◽  
Translation System ◽  
Noise Filtering ◽  
Genetic Circuits ◽  
Flow Reactors ◽  
Feed Forward ◽  
Regulatory Pathways ◽  
Feed Forward Loop ◽  
Reference Circuit ◽  
Circuit Components

AbstractRegulatory pathways inside living cells employ feed-forward architectures to fulfill essential signal processing functions that aide in the interpretation of various types of inputs through noise-filtering, fold-change detection and adaptation. Although it has been demonstrated computationally that a coherent feed-forward loop (CFFL) can function as noise filter, a property essential to decoding complex temporal signals, this motif has not been extensively characterized experimentally or integrated into larger networks. Here we use post-transcriptional regulation to implement and characterize a synthetic CFFL in an Escherichia coli cell-free transcription-translation system and build larger composite feed-forward architectures. We employ microfluidic flow reactors to probe the response of the CFFL circuit using both persistent and short, noise-like inputs and analyze the influence of different circuit components on the steady-state and dynamics of the output. We demonstrate that our synthetic CFFL implementation can reliably repress background activity compared to a reference circuit, but displays low potential as a temporal filter, and validate these findings using a computational model. Our results offer practical insight into the putative noise-filtering behavior of CFFLs and show that this motif can be used to mitigate leakage and increase the fold-change of the output of synthetic genetic circuits.

Impulse Noise Filtering

2016 ◽  
pp. 102-115
Author(s):  
Abhijit Chandra ◽  
Srideep Maity
Keyword(s):  
Noise Reduction ◽  
Impulse Noise ◽  
Digital Images ◽  
State Of The Art ◽  
Noise Filtering ◽  
Two Dimensional ◽  
Design And Development ◽  
Image Details ◽  
Filtering Techniques

Digital images are often corrupted by various types of noises amongst which impulse noise is most prevalent. Impulse noise appears during transmission and/or acquisition of images. Intrusion of impulse noise degrades the quality of the image and causes the loss of fine image details. Reducing the effect of impulse noise from corrupted images is therefore considered as an essential task to be performed before letting the image for further processing. However, the process of noise reduction from an image should also take proper care towards the preservation of edges and fine details of an image. A number of efficient noise reduction algorithms have already been proposed in the literature over the last few decades which have nurtured this issue with utmost importance. Design and development of new two dimensional (2D) filters has grown sufficient interest amongst the researchers. This chapter attempts to throw enough light on the advancement in this field by illustratively describing existing state-of-the-art filtering techniques along with their capability of denoising impulse noises.

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