The NEURON Book

Carnevale, Nicholas T.; Hines, Michael L.

doi:10.1017/cbo9780511541612

Cited by 1,322 publications

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“…60 Simulations were conducted in parallel using MPI for Python (mpi4py) on ARCUS-B (Advanced Research Computing, University of Oxford). Simulation of an islet with ~1000 β-cells for 200 sec took ~10 hours.…”

Section: Methodsmentioning

confidence: 99%

Beta-cell hubs maintain Ca²⁺ oscillations in human and mouse islet simulations

Lei

Kellard

Hara

et al. 2018

Islets

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Islet β-cells are responsible for secreting all circulating insulin in response to rising plasma glucose concentrations. These cells are a phenotypically diverse population that express great functional heterogeneity. In mice, certain β-cells (termed ‘hubs’) have been shown to be crucial for dictating the islet response to high glucose, with inhibition of these hub cells abolishing the coordinated Ca2+ oscillations necessary for driving insulin secretion. These β-cell hubs were found to be highly metabolic and susceptible to pro-inflammatory and glucolipotoxic insults. In this study, we explored the importance of hub cells in human by constructing mathematical models of Ca2+ activity in human islets. Our simulations revealed that hubs dictate the coordinated Ca2+ response in both mouse and human islets; silencing a small proportion of hubs abolished whole-islet Ca2+ activity. We also observed that if hubs are assumed to be preferentially gap junction coupled, then the simulations better adhere to the available experimental data. Our simulations of 16 size-matched mouse and human islet architectures revealed that there are species differences in the role of hubs; Ca2+ activity in human islets was more vulnerable to hub inhibition than mouse islets. These simulation results not only substantiate the existence of β-cell hubs, but also suggest that hubs may be favorably coupled in the electrical and metabolic network of the islet, and that targeted destruction of these cells would greatly impair human islet function.

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Section: Methodsmentioning

confidence: 99%

Beta-cell hubs maintain Ca²⁺ oscillations in human and mouse islet simulations

Lei

Kellard

Hara

et al. 2018

Islets

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“…GENESIS (102) (an acronym of GEneral NEural SImulation System) was one of the first systems developed for the simulation of biologically realistic models at different levels, ranging from subcellular components and biochemical reactions, to single neurons, large networks, and complete systems models. An analogous simulation environment is NEU-RON (108,119). Both provide ways to construct, test, and manage models, such that expertise in numerical methods or programming is not required for productive use.…”

Section: Simulation Toolsmentioning

confidence: 99%

Neuron tracing in perspective

2010

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The study of the structure and function of neuronal cells and networks is of crucial importance in the endeavor to understand how the brain works. A key component in this process is the extraction of neuronal morphology from microscopic imaging data. In the past four decades, many computational methods and tools have been developed for digital reconstruction of neurons from images, with limited success. As witnessed by the growing body of literature on the subject, as well as the organization of challenging competitions in the field, the quest for a robust and fully automated system of more general applicability still continues. The aim of this work, is to contribute by surveying recent developments in the field for anyone interested in taking up the challenge. Relevant aspects discussed in the article include proposed image segmentation methods, quantitative measures of neuronal morphology, currently available software tools for various related purposes, and morphology databases. ' 2010 International Society for Advancement of Cytometry

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“…The time dependence of Ca 2+ wave momenta is typically calculated with simulations using code such as NEURON [33], within multivariate differential equations describing interactions among quite a few neuronal elements and parameters. In this study, the resulting flow of Ca 2+ wave momenta will be further determined by its interactions in Π, the canonical momenta which includes A.…”

Section: A Ca 2+ Momentamentioning

confidence: 99%

Influence of Macrocolumnar EEG on Ca Waves

Ingber¹

2012

SSRN Journal

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Abstract-A "smoking gun" for explicit top-down neocortical mechanisms that directly drive bottom-up processes that describe memory, attention, etc. The top-down mechanism considered are macrocolumnar EEG firings in neocortex, as described by a statistical mechanics of neocortical interactions (SMNI), developed as a magnetic vector potential A. The bottom-up process considered are Ca 2+ waves prominent in synaptic and extracellar processes that are considered to greatly influence neuronal firings. Here, the complimentary effects are considered, i.e., the influence of A on Ca 2+ momentum, p. The canonical momentum of a charged particle in an electromagnetic field, Π = p + qA (SI units), is calculated, where the charge of Ca 2+ is q = 2e, e is the magnitude of the charge of an electron, valid in both classical and quantum mechanics. It is shown that A is large enough to influence p. This suggests that, instead of the common assumption that Ca 2+ waves contribute to neuronal activity, they may in fact at times be caused by the influence of A of larger-scale EEG.Index Terms-short-term memory, astrocytes, neocortical dynamics, vector potential I. SMOKING GUN FOR TOP-DOWN PROCESSESThere is a growing awareness of the importance of multiple scales in many physical and biological systems, including neuroscience [1], [2]. As yet, there does not seem to be any "smoking gun" for explicit top-down mechanisms that directly drive bottom-up processes that describe memory, attention, etc. Of course, there are many top-down type studies demonstrating that neuromodulator [3] and neuronal firing states, e.g., as defined by EEG frequencies, can modify the milieu or context of individual synaptic and neuronal activity, which is still consistent with ultimate bottom-up paradigms. However, there is a logical difference between top-down milieu as conditioned by some prior external or internal conditions, and some direct top-down processes that direct cause bottom-up interactions specific to STM. Here, the operative word is "cause". A. Magnetism Influences in Living SystemsThere is a body of evidence that suggests a specific topdown mechanism for neocortical STM processing.An example of a direct physical mechanism that affects neuronal processing not part of "standard" sensory influences is the strong possibility of magnetic influences in birds at quantum levels of interaction [4]- [6]. It should be noted that this is just a proposed mechanism [7].The strengths of magnetic fields in neocortex may be at a threshold to directly influence synaptic interactions with astrocytes, as proposed for long-term memory (LTM) [ rise to even stronger magnetic fields. Columnar excitatory and inhibitory processes largely take place in different neocortical laminae, providing possibilities for more specific mechanisms. II. SMNI CONTEXTSince 1981 about 30 papers on a statistical mechanics of neocortical interactions (SMNI) has been detailed properties of short-term memory, long-term memory, EEG analyses, and other properties of neocortex [11]-[16].This disc...

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The NEURON Book

Cited by 1,322 publications

References 0 publications

Beta-cell hubs maintain Ca²⁺ oscillations in human and mouse islet simulations

Beta-cell hubs maintain Ca²⁺ oscillations in human and mouse islet simulations

Neuron tracing in perspective

Influence of Macrocolumnar EEG on Ca Waves

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The NEURON Book

Cited by 1,322 publications

References 0 publications

Beta-cell hubs maintain Ca2+ oscillations in human and mouse islet simulations

Beta-cell hubs maintain Ca2+ oscillations in human and mouse islet simulations

Neuron tracing in perspective

Influence of Macrocolumnar EEG on Ca Waves

Contact Info

Product

Resources

About

Beta-cell hubs maintain Ca²⁺ oscillations in human and mouse islet simulations

Beta-cell hubs maintain Ca²⁺ oscillations in human and mouse islet simulations