scholarly journals Collective Oscillations in Coupled-Cell Systems

2021 ◽  
Vol 83 (6) ◽  
Author(s):  
Kuan-Wei Chen ◽  
Chih-Wen Shih
Keyword(s):  
Hopf Bifurcation ◽  
Single Cell ◽  
Single Cells ◽  
System Modeling ◽  
Average Frequency ◽  
Cell System ◽  
Coupled Systems ◽  
Cell Systems ◽  
Coupled Cell Systems ◽  
The One

AbstractWe investigate oscillations in coupled systems. The methodology is based on the Hopf bifurcation theorem and a condition extended from the Routh–Hurwitz criterion. Such a condition leads to locating the bifurcation values of the parameters. With such an approach, we analyze a single-cell system modeling the minimal genetic negative feedback loop and the coupled-cell system composed by these single-cell systems. We study the oscillatory properties for these systems and compare these properties between the model with Hill-type repression and the one with protein-sequestration-based repression. As the parameters move from the Hopf bifurcation value for single cells to the one for coupled cells, we compute the eigenvalues of the linearized systems to obtain the magnitude of the collective frequency when the periodic solution of the coupled-cell system is generated. Extending from this information on the parameter values, we further compute and compare the collective frequency for the coupled-cell system and the average frequency of the decoupled individual cells. To compare these scenarios with other biological oscillators, we perform parallel analysis and computations on a segmentation clock model.

SYNCHRONY-BREAKING HOPF BIFURCATION IN A MODEL OF ANTIGENIC VARIATION

2013 ◽  
Vol 23 (02) ◽  
pp. 1350021 ◽  
Author(s):  
BERNARD S. CHAN ◽  
PEI YU
Keyword(s):  
Plasmodium Falciparum ◽  
Hopf Bifurcation ◽  
Numerical Simulations ◽  
Antigenic Variation ◽  
Cross Reactivity ◽  
In Vivo Model ◽  
Main Attention ◽  
Cell Systems ◽  
Coupled Cell Systems

In this paper, we will analyze the bifurcation dynamics of an in vivo model of Plasmodium falciparum. The main attention of this model is focused on the dynamics of cross-reactivity from antigenic variation. We apply the techniques of coupled cell systems to study this model. It is shown that synchrony-breaking Hopf bifurcation occurs from a nontrivial synchronous equilibrium. In proving the existence of a Hopf bifurcation, we also discover the condition under which possible 2-color synchrony patterns arise from the bifurcation. The dynamics resulting from the bifurcation are qualitatively similar to known behavior of antigenic variation. These results are discussed and illustrated with specific examples and numerical simulations.

scholarly journals Single Cell Systems Analysis: Decision Geometry in Outliers

2019 ◽  
Author(s):  
Lianne Abrahams
Keyword(s):  
Decision Making ◽  
Graph Theory ◽  
Single Cell ◽  
Cancer Biology ◽  
Single Cells ◽  
Optimal Level ◽  
Clinical Relapse ◽  
Learning Approaches ◽  
Cell Systems ◽  
Substrate Variation

Anticer-therapeutics of the highest calibre currently focus on combinatorial targeting of specific oncoproteins and tumour suppressors. Clinical relapse depends upon intratumoral heterogeneity which serves as substrate variation during evolution of resistance to therapeutic regimens. The present review advocates single cell systems biology as the optimal level of analysis for remediation of clinical relapse. Graph theory approaches to understanding decision-making in single cells may be abstracted one level further, to the geometry of decision-making in outlier cells, in order to define evolution-resistant cancer biomarkers. Systems biologists currently working with omics data are invited to consider phase portrait analysis as a mediator between graph theory and deep learning approaches. Perhaps counter-intuitively, the tangible clinical needs of cancer patients may depend upon the adoption of higher level mathematical abstractions of cancer biology.

scholarly journals Characterization of fundamental networks

2019 ◽  
Vol 150 (1) ◽  
pp. 453-474
Author(s):  
Manuela A. D. Aguiar ◽  
Ana P. S. Dias ◽  
Pedro Soares
Keyword(s):  
Network Architecture ◽  
Cell System ◽  
Hidden Symmetries ◽  
Network Construction ◽  
Cell Systems ◽  
Cell Network ◽  
A Cell ◽  
Network Synchrony ◽  
Coupled Cell Systems

AbstractIn the framework of coupled cell systems, a coupled cell network describes graphically the dynamical dependencies between individual dynamical systems, the cells. The fundamental network of a network reveals the hidden symmetries of that network. Subspaces defined by equalities of coordinates which are flow-invariant for any coupled cell system consistent with a network structure are called the network synchrony subspaces. Moreover, for every synchrony subspace, each network admissible system restricted to that subspace is a dynamical system consistent with a smaller network called a quotient network. We characterize networks such that: the network is a subnetwork of its fundamental network, and the network is a fundamental network. Moreover, we prove that the fundamental network construction preserves the quotient relation and it transforms the subnetwork relation into the quotient relation. The size of cycles in a network and the distance of a cell to a cycle are two important properties concerning the description of the network architecture. In this paper, we relate these two architectural properties in a network and its fundamental network.

scholarly journals Single Cell Systems Analysis: Decision Geometry In Outliers

2020 ◽  
Author(s):  
Lianne Abrahams
Keyword(s):  
Decision Making ◽  
Graph Theory ◽  
Single Cell ◽  
Cancer Biology ◽  
Single Cells ◽  
Cancer Therapeutics ◽  
Supplementary Information ◽  
Clinical Relapse ◽  
Learning Approaches ◽  
Cell Systems

Abstract Motivation Anti-cancer therapeutics of the highest calibre currently focus on combinatorial targeting of specific oncoproteins and tumour suppressors. Clinical relapse depends upon intratumoral heterogeneity which serves as substrate variation during evolution of resistance to therapeutic regimens. Results The present review advocates single cell systems biology as the optimal level of analysis for remediation of clinical relapse. Graph theory approaches to understanding decision-making in single cells may be abstracted one level further, to the geometry of decision-making in outlier cells, in order to define evolution-resistant cancer biomarkers. Systems biologists currently working with omics data are invited to consider phase portrait analysis as a mediator between graph theory and deep learning approaches. Perhaps counter-intuitively, the tangible clinical needs of cancer patients may depend upon the adoption of higher level mathematical abstractions of cancer biology. Supplementary Information supplementary data available at Bioinformatics online.

In-Situ Dual Beam (FIBSEM) Techniques for Probe Pad Deposition and Dielectric Integrity Inspection in 0.2 μm Technology DRAM Single Cells

1999 ◽  
Author(s):  
Gunnar Zimmermann ◽  
Richard Chapman
Keyword(s):  
Electron Beam ◽  
Single Cell ◽  
Single Cells ◽  
Ion Beam ◽  
Gate Oxide ◽  
Ion Milling ◽  
Dual Beam ◽  
Sem Imaging ◽  
Innovative Techniques

Abstract Dual beam FIBSEM systems invite the use of innovative techniques to localize IC fails both electrically and physically. For electrical localization, we present a quick and reliable in-situ FIBSEM technique to deposit probe pads with very low parasitic leakage (Ipara < 4E-11A at 3V). The probe pads were Pt, deposited with ion beam assistance, on top of highly insulating SiOx, deposited with electron beam assistance. The buried plate (n-Band), p-well, wordline and bitline of a failing and a good 0.2 μm technology DRAM single cell were contacted. Both cells shared the same wordline for direct comparison of cell characteristics. Through this technique we electrically isolated the fail to a single cell by detecting leakage between the polysilicon wordline gate and the cell diffusion. For physical localization, we present a completely in-situ FIBSEM technique that combines ion milling, XeF2 staining and SEM imaging. With this technique, the electrically isolated fail was found to be a hole in the gate oxide at the bad cell.

scholarly journals Visually precise, low-damage, single-cell spatial manipulation with single-pixel resolution

2021 ◽  
Vol 12 (11) ◽  
pp. 4111-4118
Author(s):  
Qi Zhang ◽  
Yunlong Shao ◽  
Boye Li ◽  
Yuanyuan Wu ◽  
Jingying Dong ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cells ◽  
Pixel Resolution ◽  
Single Pixel

We achieved the low-damage spatial puncture of single cells at specific visual points with an accuracy of <65 nm.

scholarly journals Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

scholarly journals SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells

2021 ◽  
Vol 7 (8) ◽  
pp. eabe3610
Author(s):  
Conor J. Kearney ◽  
Stephin J. Vervoort ◽  
Kelly M. Ramsbottom ◽  
Izabela Todorovski ◽  
Emily J. Lelliott ◽  
...  
Keyword(s):  
Single Cell ◽  
Posttranslational Modification ◽  
Cellular Differentiation ◽  
Single Cells ◽  
Simultaneous Detection ◽  
Surface Protein ◽  
Rna Seq ◽  
Cell Level ◽  
Simultaneous Integration ◽  
Unique Surface

Multimodal single-cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states but does not allow for simultaneous integration of critical posttranslational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq), a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes, and the transcriptome at the single-cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor-infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.

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