Crosstalk Analysis Research Articles

Quantitative analysis of cross-talk in partly deuterated samples of nuclear spins hyperpolarized by dynamic nuclear polarization (DNP) in the thermal mixing regime.

Dynamical nuclear polarization (DNP) is a powerful method that allows one to polarize virtually any spin-bearing nucleus by transferring electron polarization by microwave irradiation of the electron Zeeman transitions. Under certain conditions, the DNP process can be described in thermodynamical terms using the thermal mixing (TM) model. Different nuclear species can exchange energy indirectly through their interactions with the electron spins and reach a common spin temperature. Such "cross-talk" effects can occur between proton (H) and deuterium (D) nuclei in de- and re-polarization experiments. In this work, we investigate such effects experimentally, using either protonated or deuterated TEMPOL radicals as polarizing agents. An analysis of these experiments based on Provotorov's equations allows one to extract the relevant kinetic parameters, such as the rates of energy transfer between the different reservoirs, and the heat capacity of the non-Zeeman (NZ) electron reservoir, while the heat capacities of the proton and deuterium reservoirs can be estimated based on their usual expressions. These parameters allow one to make predictions of the behaviour of heteronuclei such as carbon-13 or phosphorous-31, provided that their heat capacities are negligible. Finally, we present an experimental study of the dependence of Provotorov's kinetic parameters on the TEMPOL concentration and on the H/D ratio, thus providing insight into the nature of "hidden" spins that are not observable directly because of their proximity to the radicals.

Crosstalk Peak Overshoot Analysis of VLSI Interconnects

As technology extended from deep sub-micron technology to nanometer regimes, the conventional copper (Cu) wire will not be able to continue. Now a substitute approaches such as Carbon Nano Tube (CNT) interconnects have been suggested to ignore the problems associated with global interconnects. Hence in this work, crosstalk analysis of Complementary metal oxide semiconductor (CMOS) buffer-driven of different interconnects have been analyzed for peak overshoot and overshoot width of Cu and CNTs for 16nm technology. For analyzing peak overshoot, the interconnect lengths are varied from 100um to 500um in 16 technology node for Cu, single walled carbon nanotube (SWCNT) and multi-walled carbon nanotube (MWCNT). The values of the peak overshoot and overshoot width changes, as the interconnect length increases, the peak overshoot and width is going to be increases. As Compared to Cu, SWCNT and MWCNT, the peak overshoot and width for SWCNT is lesser than copper and MWCNT. The MWCNT interconnect is less than that of conventional Copper interconnects.

Image-based crosstalk analysis of cell–cell interactions during sprouting angiogenesis using blood-vessel-on-a-chip

BackgroundSprouting angiogenesis is an important mechanism for morphogenetic phenomena, including organ development, wound healing, and tissue regeneration. In regenerative medicine, therapeutic angiogenesis is a clinical solution for recovery from ischemic diseases. Mesenchymal stem cells (MSCs) have been clinically used given their pro-angiogenic effects. MSCs are reported to promote angiogenesis by differentiating into pericytes or other vascular cells or through cell–cell communication using multiple protein–protein interactions. However, how MSCs physically contact and move around ECs to keep the sprouting angiogenesis active remains unknown.MethodsWe proposed a novel framework of EC–MSC crosstalk analysis using human umbilical vein endothelial cells (HUVECs) and MSCs obtained from mice subcutaneous adipose tissue on a 3D in vitro model, microvessel-on-a-chip, which allows cell-to-tissue level study. The microvessels were fabricated and cultured for 10 days in a collagen matrix where MSCs were embedded.ResultsImmunofluorescence imaging using a confocal laser microscope showed that MSCs smoothed the surface of the microvessel and elongated the angiogenic sprouts by binding to the microvessel’s specific microstructures. Additionally, three-dimensional modeling of HUVEC–MSC intersections revealed that MSCs were selectively located around protrusions or roots of angiogenic sprouts, whose surface curvature was excessively low or high, respectively.ConclusionsThe combination of our microvessel-on-a-chip system for 3D co-culture and image-based crosstalk analysis demonstrated that MSCs are selectively localized to concave–convex surfaces on scaffold structures and that they are responsible for the activation and stabilization of capillary vessels.

Crosstalk Analysis of SLGNR-Based VLSI Interconnects

Crosstalk Analysis of SLGNR-Based VLSI Interconnects

Single-read tRNA-seq analysis reveals coordination of tRNA modification and aminoacylation and fragmentation.

Transfer RNA (tRNA) utilizes multiple properties of abundance, modification, and aminoacylation in translational regulation. These properties were typically studied one-by-one; however, recent advance in high throughput tRNA sequencing enables their simultaneous assessment in the same sequencing data. How these properties are coordinated at the transcriptome level is an open question. Here, we develop a single-read tRNA analysis pipeline that takes advantage of the pseudo single-molecule nature of tRNA sequencing in NGS libraries. tRNAs are short enough that a single NGS read can represent one tRNA molecule, and can simultaneously report on the status of multiple modifications, aminoacylation, and fragmentation of each molecule. We find correlations among modification-modification, modification-aminoacylationand modification-fragmentation. We identify interdependencies among one of the most common tRNA modifications, m1A58, as coordinators of tissue-specific gene expression. Our method, SingLe-read Analysis of Crosstalks (SLAC), reveals tRNAome-wide networks of modifications, aminoacylation, and fragmentation. We observe changes of these networks under different stresses, and assign a function for tRNA modification in translational regulation and fragment biogenesis. SLAC leverages the richness of the tRNA-seq data and provides new insights on the coordination of tRNA properties.

Comparative Ubiquitination Proteomics Revealed the Salt Tolerance Mechanism in Sugar Beet Monomeric Additional Line M14.

Post-translational modifications (PTMs) are important molecular processes that regulate organismal responses to different stresses. Ubiquitination modification is not only involved in human health but also plays crucial roles in plant growth, development, and responses to environmental stresses. In this study, we investigated the ubiquitination proteome changes in the salt-tolerant sugar beet monomeric additional line M14 under salt stress treatments. Based on the expression of the key genes of the ubiquitination system and the ubiquitination-modified proteins before and after salt stress, 30 min of 200 mM NaCl treatment and 6 h of 400 mM NaCl treatment were selected as time points. Through label-free proteomics, 4711 and 3607 proteins were identified in plants treated with 200 mM NaCl and 400 mM NaCl, respectively. Among them, 611 and 380 proteins were ubiquitinated, with 1085 and 625 ubiquitination sites, in the two salt stress conditions, respectively. A quantitative analysis revealed that 70 ubiquitinated proteins increased and 47 ubiquitinated proteins decreased. At the total protein level, 42 were induced and 20 were repressed with 200 mM NaCl, while 28 were induced and 27 were repressed with 400 mM NaCl. Gene ontology, KEGG pathway, protein interaction, and PTM crosstalk analyses were performed using the differentially ubiquitinated proteins. The differentially ubiquitinated proteins were mainly involved in cellular transcription and translation processes, signal transduction, metabolic pathways, and the ubiquitin/26S proteasome pathway. The uncovered ubiquitinated proteins constitute an important resource of the plant stress ubiquitinome, and they provide a theoretical basis for the marker-based molecular breeding of crops for enhanced stress tolerance.

Analysis of Crosstalk in GNR-Based Global Interconnects

Analysis of Crosstalk in GNR-Based Global Interconnects

Analysis of Crosstalk in Coupled On-Chip VLSI Interconnects

Analysis of Crosstalk in Coupled On-Chip VLSI Interconnects

Crosstalk-Aware Automatic Topology Customization and Optimization for Wavelength-Routed Optical NoCs

Optical network-on-chip (ONoC) is an emerging upgrade for electronic network-on-chip (ENoC). As a kind of ONoC, wavelength-routed ONoC (WRONoC) shows ultrahigh bandwidth and ultralow latency in data communication. Manually designed WRONoC topologies typically reserve all to all links. This causes the waste of resources. Topology customization for each individual communication network can save resources, but requires automation for efficient design. The state-of-the-art design automation method is not efficient and does not support crosstalk analysis and signal-to-noise ratio (SNR) optimization. Moreover, the state of the art does not consider the physical locations of the data sending/receiving ports, causing unavoidable detours and crossings in the physical layout. In this work, we present FAST+: an automatic topology customization and optimization method. Compared with the state of the art, FAST+ operates much more efficiently and proposes a concrete router-level crosstalk-analysis method and a novel SNR optimization algorithm. This work also provides solutions to avoid detours and crossings in the physical layout. When SNR optimization is not enabled, experimental results show that FAST+ runs thousands times faster than the state of the art on average while providing multiple better or equally good topologies regarding resource usage and the worst case insertion loss. When SNR optimization is enabled, FAST+ provides <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.75\times $ </tex-math></inline-formula> better worst case SNR on average after the optimization while not sacrificing resource usage and the worst case insertion loss.

Crosstalk Analysis of Printed Circuit Board Traces With Right-Angled Bent Corners via Time Domain Hybrid Method

Discontinuous impedance exists when bent corners are introduced into the traces of printed circuit board (PCB). By combining transmission line (TL) equations, higher order finite-difference time-domain (FDTD) method, state variable method, and Norton's theorem, an efficient time domain hybrid method is proposed to realize the fast crosstalk simulation of the traces with right-angled bent corners (RABCs) in this work. First, the whole structure of the traces is decomposed into a cascade network, which consists of multiple equal length parallel microstrip lines (EL-PMSLs) and the RABC structures. Then, the crosstalk responses on these EL-PMSLs can be quickly solved by applying TL equations combined with the higher order FDTD method. With the application of Norton's theorem, the equivalent circuit model of whole PCB traces is constructed. Finally, the equivalent circuits of the RABC structures are extracted, and the port voltages of these RABCs are calculated via state variable method and fed back to these EL-PMSLs as boundaries, thus the round-trip transmission of interference signals on the PCB traces is realized. Numerous crosstalk simulations of PCB traces with typical RABC structures, as well as extracted from a practical PCB, are presented and compared with the results of commercial software CST to verify the correctness and efficiency of the proposed method.

Deciphering the Genetic Crosstalk between Microglia and Oligodendrocyte Precursor Cells during Demyelination and Remyelination Using Transcriptomic Data

Demyelinating disorders show impaired remyelination due to failure in the differentiation of oligodendrocyte progenitor cells (OPCs) into mature myelin-forming oligodendrocytes, a process driven by microglia-OPC crosstalk. Through conducting a transcriptomic analysis of microarray studies on the demyelination-remyelination cuprizone model and using human samples of multiple sclerosis (MS), we identified molecules involved in this crosstalk. Differentially expressed genes (DEGs) of specific regions/cell types were detected in GEO transcriptomic raw data after cuprizone treatment and in MS samples, followed by functional analysis with GO terms and WikiPathways. Additionally, microglia-OPC crosstalk between microglia ligands, OPC receptors and target genes was examined with the NicheNet model. We identified 108 and 166 DEGs in the demyelinated corpus callosum (CC) at 2 and 4 weeks of cuprizone treatment; 427 and 355 DEGs in the remyelinated (4 weeks of cuprizone treatment + 14 days of normal diet) compared to 2- and 4-week demyelinated CC; 252 DEGs in MS samples and 2730 and 12 DEGs in OPC and microglia of 4-week demyelinated CC. At this time point, we found 95 common DEGs in the CC and OPCs, and one common DEG in microglia and OPCs, mostly associated with myelin and lipid metabolism. Crosstalk analysis identified 47 microglia ligands, 43 OPC receptors and 115 OPC target genes, all differentially expressed in cuprizone-treated samples and associated with myelination. Our differential expression pipeline identified demyelination/remyelination transcriptomic biomarkers in studies using diverse platforms and cell types/tissues. Cellular crosstalk analysis yielded novel markers of microglia ligands, OPC receptors and target genes.

Single-Cell RNA Profiling of Primary Myelofibrosis Reveals RUX Resistance Decreasing Mononuclear Phagocytes in Peripheral Blood

BACKGROUND: Primary myelofibrosis (PMF) is often but not always harbored JAK2, CALR, or MPL mutations. Mainly clinical features involve bone marrow reticulin/collagen fibrosis, hepatosplenomegaly, extramedullary hematopoiesis (EMH) and shortened survival. Ruxolitinib (RUX) is one of significantly current therapeutics for PMF by selective inhibiting of Janus kinase (JAK) 1 and 2. RUX-intolerant contribute to the deterioration of PMF. Hence, more therapeutic interventions require refined dissection during the development of RUX resistance at either cellular or transcriptional levels. AIMS: Our objective is to elucidate the cellular constitution and transcriptional alterations presenting in peripheral blood (PB) obtained from PMF patients with/without RUX resistance. METHODS: By analyzing the transcriptomes of 84,525 single cells and identifying major mononuclear cell types from peripheral blood of healthy donors (HD, n=2), PMF patients at baseline (BL, n=3) and PMF patients with ruxolitinib resistance (RUX-r, n=3) on the basis of their molecular signatures, the spatiotemporal interplay among cell types was characterized. RESULTS: We illustrated the dynamics of all major PB mononuclear cell (PBMC) types, including T cells, mononuclear phagocytes, neutrophils, hematopoietic stem cells，basophil，plasmacytoid dendritic cells, erythrocytes progenitors and macrophages, so as those of their subtypes ，respectively，among the progression of RUX resistance. RUX-r and BL presented a statistically significant decrease in T cell and B cell compared with HD, respectively. Meanwhile, compared to HD, neutrophils, HSCs and Erythroid progenitors were dramatically increased in both BL and RUX-r. Interestingly, numbers of MPs displayed a statistically significant reduction in RUX-r and significant increase in BL compared to HD, respectively. Further analysis showed a significantly higher proportion of CD+T cells naïve in RUX-r. Cellular crosstalk analysis uncovered stagewise utilization of PBMC during the procession of RUX resistance. Specifically, mononuclear phagocyte inactivation and subtype switching was considered as an essential event in patients with RUX resistance. CONCLUSIONS: Taken together, this study not only demonstrated dynamically changing cell type crosstalk during the progression of RUX resistance but also shed light on potential therapeutic strategies for RUX resistant primary myelofibrosis patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Characterization and analysis of electrical crosstalk in a linear array of CMOS image sensors.

In this paper, the influences of the depth and width of the oxide trench isolation between pixels, pixel epitaxial layer thickness for different impurity doping concentrations, and light exposure time on electrical crosstalk are characterized in an array of pinned photodiode CMOS image sensor pixels. The simulation results show that with a proper and simultaneous selection of epitaxial layer doping concentration and epitaxial layer thickness, the electrical crosstalk at long wavelengths can be reduced above 66%. The use of oxide trench isolation depth less than pixel p-well depth leads to an increase in electrical crosstalk of more than 12%. The effect of increasing light exposure time on increasing electrical crosstalk can be minimized by selecting proper epitaxial layer thicknesses.

Correction to: XPM induced crosstalk analysis in radio over fiber system with sub‑plank higher‑order dispersion parameters

Correction to: XPM induced crosstalk analysis in radio over fiber system with sub‑plank higher‑order dispersion parameters

Activating NO-sGC crosstalk in the mouse vascular niche promotes vascular integrity and mitigates acute lung injury.

Disruption of endothelial cell (ECs) and pericytes interactions results in vascular leakage in acute lung injury (ALI). However, molecular signals mediating EC-pericyte crosstalk have not been systemically investigated, and whether targeting such crosstalk could be adopted to combat ALI remains elusive. Using comparative genome-wide EC-pericyte crosstalk analysis of healthy and LPS-challenged lungs, we discovered that crosstalk between endothelial nitric oxide and pericyte soluble guanylate cyclase (NO-sGC) is impaired in ALI. Indeed, stimulating the NO-sGC pathway promotes vascular integrity and reduces lung edema and inflammation-induced lung injury, while pericyte-specific sGC knockout abolishes this protective effect. Mechanistically, sGC activation suppresses cytoskeleton rearrangement in pericytes through inhibiting VASP-dependent F-actin formation and MRTFA/SRF-dependent de novo synthesis of genes associated with cytoskeleton rearrangement, thereby leading to the stabilization of EC-pericyte interactions. Collectively, our data demonstrate that impaired NO-sGC crosstalk in the vascular niche results in elevated vascular permeability, and pharmacological activation of this crosstalk represents a promising translational therapy for ALI.

Evolutionary Signals in Coronaviral Structural Proteins Suggest Possible Complex Mechanisms of Post-Translational Regulation in SARS-CoV-2 Virus.

Post-translational regulation of proteins has emerged as a central topic of research in the field of functional proteomics. Post-translational modifications (PTMs) dynamically control the activities of proteins and are involved in a wide range of biological processes. Crosstalk between different types of PTMs represents a key mechanism of regulation and signaling. Due to the current pandemic of the novel and dangerous SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) virus, here we present an in silico analysis of different types of PTMs in structural proteins of coronaviruses. A dataset of PTM sites was studied at three levels: conservation analysis, mutational analysis and crosstalk analysis. We identified two sets of PTMs which could have important functional roles in the regulation of the structural proteins of coronaviruses. Additionally, we found seven interesting signals of potential crosstalk events. These results reveal a higher level of complexity in the mechanisms of post-translational regulation of coronaviral proteins and provide new insights into the adaptation process of the SARS-CoV-2 virus.

Liquid pressure sensing system based on distributed polarization crosstalk analysis in polarization maintaining fiber

Liquid pressure sensing system based on distributed polarization crosstalk analysis in polarization maintaining fiber

Integrated analysis of potential gene crosstalk between non-alcoholic fatty liver disease and diabetic nephropathy.

Growing evidence indicates that non-alcoholic fatty liver disease (NAFLD) is related to the occurrence and development of diabetic nephropathy (DN). This bioinformatics study aimed to explore optimal crosstalk genes and related pathways between NAFLD and DN. Gene expression profiles were downloaded from Gene Expression Omnibus. CIBERSORT algorithm was employed to analyze the similarity of infiltrating immunocytes between the two diseases. Protein-protein interaction (PPI) co-expression network and functional enrichment analysis were conducted based on the identification of common differentially expressed genes (DEGs). Least absolute shrinkage and selection operator (LASSO) regression and Boruta algorithm were implemented to initially screen crosstalk genes. Machine learning models, including support vector machine, random forest model, and generalized linear model, were utilized to further identify the optimal crosstalk genes between DN and NAFLD. An integrated network containing crosstalk genes, transcription factors, and associated pathways was developed. Four gene expression datasets, including GSE66676 and GSE48452 for NAFLD and GSE30122 and GSE1009 for DN, were involved in this study. There were 80 common DEGs between the two diseases in total. The PPI network built with the 80 common genes included 77 nodes and 83 edges. Ten optimal crosstalk genes were selected by LASSO regression and Boruta algorithm, including CD36, WIPI1, CBX7, FCN1, SLC35D2, CP, ZDHHC3, PTPN3, LPL, and SPP1. Among these genes, LPL and SPP1 were the most significant according to NAFLD-transcription factor network. Five hundred twenty-nine nodes and 1,113 edges comprised the PPI network of activated pathway-gene. In addition, 14 common pathways of these two diseases were recognized using Gene Ontology (GO) analysis; among them, regulation of the lipid metabolic process is closely related to both two diseases. This study offers hints that NAFLD and DN have a common pathogenesis, and LPL and SPP1 are the most relevant crosstalk genes. Based on the common pathways and optimal crosstalk genes, our proposal carried out further research to disclose the etiology and pathology between the two diseases.

Accurate Crosstalk Noise Modeling and Analysis of Non-Identical Lossy Interconnections Using Convex Optimization Method

Recent studies on integrated circuits interconnections are mainly concentrated on the analysis of crosstalk and delay, by taking the trade-off between accuracy, speed, and complexity into consideration. The new idea of this paper is to apply the convex optimization method to analyze crosstalk and delay of the lossy coupled interconnections in identical and non-identical forms. For this purpose, a simple and comprehensive model is proposed to cover the functional and dynamic crosstalk in a computationally-effective way. More specifically, various case studies are determined to analyze the transient response of the coupled transmission lines with arbitrary excitation sources in the presence of both capacitive and inductive coupling characteristics. To validate the model, the numerical and Advanced Design System (ADS) simulation results are compared to indicate the desired accuracy. The calculated crosstalk percentage error of the proposed model with respect to ADS and HSPICE are less than 1.03% and 1.19%, respectively. In addition, the computational speed of the proposed method is about twice higher than ADS and HSPICE. The proposed model is extendible to handle <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${N}$ </tex-math></inline-formula> coupled lines, making it appropriate to model complex integrated circuit interconnections.

Transmission Line Modeling and Crosstalk Analysis of Multibraided Shielded TWP/Twinax Cables

In this article, the transmission line model of multibraided shielded cables is improved by including the proximity effect in the shield model. This is performed by deriving the analytical expressions of the transfer impedance and admittance of a shielded structure with nonuniform current distribution around the shield surfaces. After that, the formulations are generalized to be applicable for shielded twisted-wire pair (TWP) and twinax cables with line apertures and braided structure with nonuniform shield current. It is found that the nonuniform distribution of the currents in the outer and inner shield surfaces have high effects on the inner induced common-mode and differential-mode currents of braided shielded cables. In addition, the crosstalk between multishielded TWP and twinax cables is investigated in detail, indicating that the proximity effects between the shields have a critical impact on generating the crosstalk between the shielded cables. The proposed model is validated with the commercial software FEKO and excellent agreements are achieved.