Crosstalk Prediction Research Articles

Systematic characterization and prediction of post-translational modification cross-talk between proteins.

Protein post-translational modifications (PTMs) regulate a wide range of cellular protein functions. Many PTM sites from the same (intra) or different (inter) proteins often cooperate with each other to perform a function, which is defined as PTM cross-talk. PTM cross-talk within proteins attracted great attentions in the past a few years. However, the inter-protein PTM cross-talk is largely under studied due to its large protein pair space and lack of a gold standard dataset, even though the PTM interplay between proteins is a key element in cell signaling and regulatory networks. In this study, 199 inter-protein PTM cross-talk pairs in 82 pairs of human proteins were collected from literature, which to our knowledge is the first effort in compiling such dataset. By comparing with background PTM pairs from the same protein pairs, we found that inter-protein cross-talk PTM pairs have higher sequence co-evolution at both PTM residue and motif levels. Also, we found that cross-talk PTMs have higher co-modification across multiple species and 88 human tissues or conditions. Furthermore, we showed that these features are predictive for PTM cross-talk between proteins, and applied a random forest model to integrate these features with achieving an area under the receiver operating characteristic curve of 0.81 in 10-fold cross-validation, prevailing over using any single feature alone. Therefore, this method would be a valuable tool to identify inter-protein PTM cross-talk at proteome-wide scale. A web server for prioritization of both intra- and inter-protein PTM cross-talk candidates is at http://bioinfo.bjmu.edu.cn/ptm-x/. Python code for local computer is also freely available at https://github.com/huangyh09/PTM-X. Supplementary data are available at Bioinformatics online.

Core, Mode, and Spectrum Assignment Based on Machine Learning in Space Division Multiplexing Elastic Optical Networks

Recently, network traffic has been growing exponentially and almost reached the physical capacity limit of single mode fibers. Space division multiplexing (SDM) is a promising technology to overcome the looming fiber capacity crunch. Especially, few-mode multi-core fibers (FM-MCFs) can aggregate multiple cores into one fiber and two or more modes can be transmitted in one core, which can greatly increase the capacity yet introduce crosstalk constraints including inter- and intra-core crosstalk. To our best knowledge, there is no accurate crosstalk calculation model study in SDM optical networks with FM-MCFs. To address this issue, we first introduce the machine learning into the crosstalk prediction phase and propose a novel crosstalk estimation model (CEM) exploiting the beam propagation method called CEM-beam propagation method (BPM)-machine learning (ML), which can be used to evaluate the crosstalk during the design for the resource allocation scheme. Then, a crosstalk aware core, mode, and spectrum assignment (CA-CMSA) strategy is presented. The simulation results for crosstalk estimation at the wavelength level indicate that the crosstalk at lower frequencies is less than that at higher frequencies. Thus, the lower frequencies are always the first choice in the spectrum resource assignment phase. In addition, for our specific training set, the Levenberg-Marquardt (LM) algorithm based on machine learning performs better on the training, including regression values measurement and time consumption. The simulation results of the proposed CA-CMSA scheme also show that the resource allocation algorithm based on LM can improve resource utilization without increasing total connection set-up time. Thus, it will be the best choice for the resource assignment in SDM networks with FM-MCFs.

Perceptual Crosstalk Prediction on Autostereoscopic 3D Display

Perceptual crosstalk prediction for autostereoscopic 3D displays is of fundamental importance in determining the level of quality perceived by humans in terms of the display performance and the 3D viewing experience. However, no robust framework exists to quantify perceptual crosstalk while taking into account the hardware structure of a display as well as its content characteristics via content analysis. In this paper, we present a 3D perceptual crosstalk predictor (3D-PCP) that can be used to predict crosstalk in a unique way when viewing autostereoscopic 3D displays. 3D-PCP captures hardware features using an optical Fourier transform-light measurement device and content features through content analysis based on information theory. By deriving the disparity, luminance, color, and texture maps, this approach defines the visual entropy, mutual information, and relative entropy in order to investigate the influences of the 3D scene characteristics on perceptual crosstalk. The experimental results demonstrate that the 3D-PCP output is highly correlated with subjective scores.

Quality Assessment of Perceptual Crosstalk on Two-View Auto-Stereoscopic Displays.

Crosstalk is one of the most severe factors affecting the perceived quality of stereoscopic 3D images. It arises from a leakage of light intensity between multiple views, as in auto-stereoscopic displays. Well-known determinants of crosstalk include the co-location contrast and disparity of the left and right images, which have been dealt with in prior studies. However, when a natural stereo image that contains complex naturalistic spatial characteristics is viewed on an auto-stereoscopic display, other factors may also play an important role in the perception of crosstalk. Here, we describe a new way of predicting the perceived severity of crosstalk, which we call the Binocular Perceptual Crosstalk Predictor (BPCP). BPCP uses measurements of three complementary 3D image properties (texture, structural duplication, and binocular summation) in combination with two well-known factors (co-location contrast and disparity) to make predictions of crosstalk on two-view auto-stereoscopic displays. The new BPCP model includes two masking algorithms and a binocular pooling method. We explore a new masking phenomenon that we call duplicated structure masking, which arises from structural correlations between the original and distorted objects. We also utilize an advanced binocular summation model to develop a binocular pooling algorithm. Our experimental results indicate that BPCP achieves high correlations against subjective test results, improving upon those delivered by previous crosstalk prediction models.

Announcing the best transactions paper for the year 2015: "field-to-wire coupling model for the common mode in random bundles of twisted-wire pairs"

In the extraordinary scientific production of the late Prof. Clayton Paul - a giant in our discipline - understanding and prediction of crosstalk in twisted-wire pairs (TWPs) undoubtedly represents a milestone of his research work. He provided fundamental contributions to circuit interpretation of crosstalk, and thoroughly unveiled crosstalk sensitivity to TWP geometrical and electrical parameters. While this is actually well known to everybody in the EMC community, what is likely less evident is that his profound and sharp reflections on the outcomes of the numerical simulations he performed (some of them based on the so called “click model” [PAUL_REP1], others resorting to the Method of Moments) also contain fundamental hints for understanding and predicting radiated immunity properties of TWPs.

Modeling, Prediction, and Reduction of 3D Crosstalk in Circular Polarized Stereoscopic LCDs.

Crosstalk, which is the incomplete separation between the left and right views in 3D displays, induces ghosting and causes difficulty of the eyes to fuse the stereo image for depth perception. Circularly polarized (CP) liquid crystal display (LCD) is one of the main-stream consumer 3D displays with the prospering of 3D movies and gamings. The polarizing system including the patterned retarder is one of the major causes of crosstalk in CP LCD. The contributions of this paper are the modeling of the polarizing system of CP LCD, and a crosstalk reduction method that efficiently cancels crosstalk and preserves image contrast. For the modeling, the practical orientation of the polarized glasses (PG) is considered. In addition, this paper calculates the rotation of the light-propagation coordinate for the Stokes vector as light propagates from LCD to PG, and this calculation is missing in the previous works when applying Mueller calculus. The proposed crosstalk reduction method is formulated as a linear programming problem, which can be easily solved. In addition, we propose excluding the highly textured areas in the input images to further preserve image contrast in crosstalk reduction.

Oral administration of Lactobacillus plantarum 299v modulates gene expression in the ileum of pigs: prediction of crosstalk between intestinal immune cells and sub-mucosal adipocytes.

To study host–probiotic interactions in parts of the intestine only accessible in humans by surgery (jejunum, ileum and colon), pigs were used as model for humans. Groups of eight 6-week-old pigs were repeatedly orally administered with 5 × 1012 CFU Lactobacillus plantarum 299v (L. plantarum 299v) or PBS, starting with a single dose followed by three consecutive daily dosings 10 days later. Gene expression was assessed with pooled RNA samples isolated from jejunum, ileum and colon scrapings of the eight pigs per group using Affymetrix porcine microarrays. Comparison of gene expression profiles recorded from L. plantarum 299v-treated pigs with PBS-treated pigs indicated that L. plantarum 299v affected metabolic and immunological processes, particularly in the ileum. A higher expression level of several B cell-specific transcription factors/regulators was observed, suggesting that an influx of B cells from the periphery to the ileum and/or the proliferation of progenitor B cells to IgA-committed plasma cells in the Peyer’s patches of the ileum was stimulated. Genes coding for enzymes that metabolize leukotriene B4, 1,25-dihydroxyvitamin D3 and steroids were regulated in the ileum. Bioinformatics analysis predicted that these metabolites may play a role in the crosstalk between intestinal immune cells and sub-mucosal adipocytes. Together with regulation of genes that repress NFKB- and PPARG-mediated transcription, this crosstalk may contribute to tempering of inflammatory reactions. Furthermore, the enzyme adenosine deaminase, responsible for the breakdown of the anti-inflammatory mediator adenosine, was strongly down-regulated in response to L. plantarum 299v. This suggested that L. plantarum 299v-regulated production of adenosine by immune cells like regulatory T cells may also be a mechanism that tempers inflammation in the ileum, and perhaps also in other parts of the pig’s body.Electronic supplementary materialThe online version of this article (doi:10.1007/s12263-015-0461-7) contains supplementary material, which is available to authorized users.

Systematic Characterization and Prediction of Post-Translational Modification Cross-Talk *

Post-translational modification (PTM)(1) plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM cross-talk. Identification of PTM cross-talks is an emerging theme in proteomics and has elicited great interest, but their properties remain to be systematically characterized. To this end, we collected 193 PTM cross-talk pairs in 77 human proteins from the literature and then tested location preference and co-evolution at the residue and modification levels. We found that cross-talk events preferentially occurred among nearby PTM sites, especially in disordered protein regions, and cross-talk pairs tended to co-evolve. Given the properties of PTM cross-talk pairs, a naïve Bayes classifier integrating different features was built to predict cross-talks for pairwise combination of PTM sites. By using a 10-fold cross-validation, the integrated prediction model showed an area under the receiver operating characteristic (ROC) curve of 0.833, superior to using any individual feature alone. The prediction performance was also demonstrated to be robust to the biases in the collected PTM cross-talk pairs. The integrated approach has the potential for large-scale prioritization of PTM cross-talk candidates for functional validation and was implemented as a web server available at http://bioinfo.bjmu.edu.cn/ptm-x/.

The Model of Estimating MTL Crosstalk in Inhomogeneous Medium

Based on the transmission line theory, this paper applies the mode theory to predict the MTL(multi-conductor transmission line) crosstalk by selecting voltage as the research object, thus establish the model of estimating MTL crosstalk in inhomogeneous medium. Then make numerical calculation in MATLAB for the estimate model established in this paper, and also compare the calculated values with the simulated values in EMC studio. The compared results show that the calculated results of this model is highly consistent with the practical simulated values, verifying the correctness and feasibility of mode theory in MTL crosstalk prediction.

Predictive Application of PIDF and PPC for Interconnects' Crosstalk, TSV, and LER Issues in UDSM ICs and Nano-Systems

In this brief, a novel methodology for the prediction of three phenomena related to the interconnects in VLSI circuits will be presented. First, the power (including crosstalk-induced power) prediction for ultradeep submicron ICs and nano systems is proposed. The novelty of the method for crosstalk prediction is deduced by employing a polynomial progressive calibration. Second, as a part of this methodology, we present a new solution for power prediction of through-silicon-vias.

APPLICATION OF THE "EQUIVALENT CABLE BUNDLE METHOD" FOR MODELING CROSSTALK OF COMPLEX CABLE BUNDLES WITHIN UNIFORM STRUCTURE WITH ARBITRARY CROSS-SECTION

In this paper, the equivalent cable bundle method (ECBM), an e-cient simplifled modeling method of the complex cable bundles, is modifled for crosstalk prediction of complex cable bundles within uniform structure with arbitrary cross section. The foremost attributes of the modifled method are a) the cable bundle within uniform structure with arbitrary cross section can be mapped to equivalent cable bundle above an inflnite perfect electric conductor ground plane during the equivalence procedure, b) the culprit and victim conductors are divided into two groups separately during the grouping process, denoted as the culprit group and victim one, which do not participate in the equivalence procedure compared with the original ECBM for crosstalk problem, c) an efiective eight- phase procedure is established to deflne the electrical and geometrical characteristics of the reduced cable bundle model. Numerical simulations performed on a selected cable bundle surrounded by a rectangular cavity illustrate the e-ciency and the advantages of the method. This method is considered as a key step for the ECBM to flnd wide applications in real systems.

SIMPLIFICATION METHOD FOR MODELING CROSSTALK OF MULTICOAXIAL CABLE BUNDLES

In this work, a new efficient simplification method is proposed for crosstalk prediction of multicoaxial cable bundles (MCCB). The purpose of the new simplification method is to reduce the simulation time by reducing the complexity of the complete cable bundle model. A modified five-step procedure is established to define the electrical and geometrical characteristics of the reduced cable bundle by making the outer and inner conductor of the coaxial cable participate in the equivalence procedure respectively. After a short presentation of the MCCB coupling problem, the theory fundamentals of the new simplification method and numerical simulations performed on a simple MCCB are presented to demonstrate the efficiency and the advantages of the new simplification method.

A New Simplification Scheme for Crosstalk Prediction of Complex Cable Bundles Within a Cylindrical Cavity

In this letter, a new simplification scheme is proposed to extend the “equivalent cable bundle method” (ECBM) for modeling electromagnetic crosstalk of complex cable bundles within a cylindrical cavity. Anew six-step procedure is established to define the electrical and geometric characteristics of the reduced cable bundle model in the cylindrical cavity which is considered as the ground return. Numerical simulations performed on a simple cable bundle illustrate the efficiency and the advantages of the method. This study is a further step of the original ECBM and can find wide applications in a realistic environment.

A serious problem in using the Jarvis model for the prediction of crosstalk

The coupled transmission-line equations for a three-conductor, lossless transmission line are solved in symbolic form for its crosstalk voltages using various approximations [1, 2]. The most frequently-used approximate model for predicting crosstalk is referred to as the Jarvis model after its original publisher in 1963 [3]. The Jarvis model uses three approximations that simplify the result. One of the approximations requires that all four line terminations be matched which is unrealistic for virtually all crosstalk problems.

Analytical Prediction of Crosstalk Among Vias in Multilayer Printed Circuit Boards

Crosstalk among vias is a significant problem in high-speed multilayer printed circuit boards (PCBs), deteriorating signal quality and increasing jitter, especially when circuit density is high. In this paper, a two-step via crosstalk evaluation procedure is proposed. A fast approach for crosstalk estimation is developed for net screening as the first step. Then, more accurate but more time-consuming modeling can be performed for critical nets or the problematic nets identified in the screening. The main contribution of this study includes the analytical prediction of crosstalk among vias based on an infinite parallel-plane assumption. Its effectiveness and efficiency to predict the trends in the crosstalk among vias in practical PCB designs are demonstrated.

Bioinformatic Analysis and Post-Translational Modification Crosstalk Prediction of Lysine Acetylation

Recent proteomics studies suggest high abundance and a much wider role for lysine acetylation (K-Ac) in cellular functions. Nevertheless, cross influence between K-Ac and other post-translational modifications (PTMs) has not been carefully examined. Here, we used a variety of bioinformatics tools to analyze several available K-Ac datasets. Using gene ontology databases, we demonstrate that K-Ac sites are found in all cellular compartments. KEGG analysis indicates that the K-Ac sites are found on proteins responsible for a diverse and wide array of vital cellular functions. Domain structure prediction shows that K-Ac sites are found throughout a wide variety of protein domains, including those in heat shock proteins and those involved in cell cycle functions and DNA repair. Secondary structure prediction proves that K-Ac sites are preferentially found in ordered structures such as alpha helices and beta sheets. Finally, by mutating K-Ac sites in silico and predicting the effect on nearby phosphorylation sites, we demonstrate that the majority of lysine acetylation sites have the potential to impact protein phosphorylation, methylation, and ubiquitination status. Our work validates earlier smaller-scale studies on the acetylome and demonstrates the importance of PTM crosstalk for regulation of cellular function.

Single event crosstalk prediction in nanometer technologies

As CMOS technology continues to scale down, circuits become increasingly more sensitive to transient pulses caused by single event (SE) particles. On the other hand, coupling effects among interconnects can cause single event transients to contaminate electronically unrelated circuit paths which may increase the SE susceptibility of CMOS circuits. The coupling effects among interconnects need to be considered in single event hardening, modeling and analysis of CMOS logic gates due to technology scaling effects that increase both SE vulnerability and crosstalk effects. This work, for the first time, proposes an SE crosstalk noise estimation method for use in design automation tools. The proposed method uses an accurate 4-? model for interconnect and correctly models the effect of non-switching aggressors as well as aggressor tree branches noting the resistive shielding effect. The SE crosstalk noise expressions derived show very good results in comparison to HSPICE results. Results show that average error for noise peak is about 5.2% while allowing for very fast analysis in comparison to HSPICE.

Efficient Estimation of Crosstalk Statistics in Random Wire Bundles With Lacing Cords

This paper deals with crosstalk estimation in a set of individually insulated wires laced together to form a bundle, and running above a ground plane. A simplified and numerically efficient multiconductor transmission line model is developed, involving a single reference cross section with pseudocircular shape and staircase approximation for the wire trajectories. The presence of lacing cords along the bundle is modeled as a sinusoidal modulation of the reference cross-section dimension. It is shown that crosstalk in wire bundles is mainly affected by the relative positions of the generator and receptor wires, whose paths are to be accurately represented as smooth curved trajectories, whereas it results to be substantially insensitive to rough modeling of the paths of the remaining wires. The weak random nonuniformity of the generator and receptor wires proves to be the fundamental property to be reproduced in order to obtain physically sound crosstalk predictions. This is enforced by deducing the staircase approximation of the generator and receptor wires from a preliminary representation of only that wire pair in terms of splines with a very small number of nodes. Differently, the staircase trajectories of the remaining wires are obtained by direct mapping onto the reference cross section. Model performance is assessed by comparing crosstalk predictions versus measurement data and theoretical results available in the technical literature. Predictions compare appreciably well with measurements, also in the most critical case of high-impedance loads. The coupling distribution shows nonsymmetrical structure and a long tail to the right, as several other crosstalk analyses have shown.

Lock-in thermo-electric detector arrays: thermal cross-talk prediction by non-linear model

A non-linear numerical finite element method model of a thermo-electric focal plane array detector is presented here. Laser induced thermo-voltage profiles tend to spread out for small lock-in frequencies as the thermal diffusion length is inversely proportional to the square-root of the lock-in frequency. This leads to a frequency and spatial dependent thermal cross-talk level. In this paper we investigate the thermal cross-talk level quantitatively as a function of spatial coordinates and lock-in frequency. Experimental data are provided at an optical power level of 1 W. The impact of non-linear thermal parameters as the temperature dependence of the absorption coefficient, the thermal conductivity, the heat transfer coefficient and the Seebeck coefficient on the thermal profile and cross-talk level generated inside the detector material is studied in detail. Heat losses that are included in the model are conduction and laminar free convection. The relative importance of the above-mentioned non-linear thermal parameters in terms of thermal cross-talk for steady-state solutions is discussed as well.

Crosstalk Prediction for Three Conductors Nonuniform Transmission Lines: Theoretical Approach & Numerical Simulation

In this paper the crosstalk between nonuniform transmission lines is examined. Firstly, methods for prediction of crosstalk between microstrip transmission lines are reviewed. Classical coupled transmission line theory is used for uniform lines and cannot be used for nonuniform transmission lines. Secondly, equations are derived which can be solved to obtain formulas for the near-end and far-end crosstalk for nonuniform transmission lines. Finally, an example is worked which illustrates the crosstalk between three conductor nonuniform transmission lines. Obtained theoretical results were compared with simulations data. Comparison results shown that theoretical and simulation results are approximately the same.