scholarly journals Scaffold modelling captures the structure-function-dynamics relationship in brain microcircuits

2021 ◽  
Author(s):  
Robin Gilbert De Schepper ◽  
Alice Geminiani ◽  
Stefano Masoli ◽  
Martina Francesca Rizza ◽  
Alberto Antonietti ◽  
...  
Keyword(s):  
Ground Truth ◽  
Signal Propagation ◽  
Neuron Models ◽  
Modeling Framework ◽  
Multiple Strategies ◽  
Spatio Temporal ◽  
Cell Placement ◽  
Flexible Management ◽  
The Impact

Modelling brain networks with complex configuration and cellular properties requires a set of neuroinformatic tools and an organized staged workflow. We have therefore developed the Brain Scaffold Builder (BSB), a new modeling framework embedding multiple strategies for cell placement and connectivity and a flexible management of cellular and network mechanisms. With BSB, for the first time, the mouse cerebellar cortex was reconstructed and simulated at cellular resolution, using morphologically realistic multi-compartmental single-neuron models. Embedded connection rules allowed BSB to generate the cerebellar connectome, unifying a collection of scattered experimental data into a coherent construct. Naturalistic background and sensory-burst stimulation were used for functional validation against recordings in vivo, monitoring the impact of subcellular mechanisms on signal propagation and spatio-temporal processing and providing a new ground-truth about circuit organization for the prediction of neural dynamics.

scholarly journals Model Simulations Unveil The Structure-Function-Dynamics Relationship of The Cerebellar Cortical Microcircuit

2021 ◽  
Author(s):  
Robin De Schepper ◽  
Alice Geminiani ◽  
Stefano Masoli ◽  
Martina Francesca Rizza ◽  
Alberto Antonietti ◽  
...  
Keyword(s):  
Structure Function ◽  
Molecular Layer ◽  
Mossy Fibers ◽  
Ground Truth ◽  
Signal Propagation ◽  
Neuron Models ◽  
Cellular Mechanisms ◽  
Modeling Framework ◽  
The Impact

Abstract The cerebellar network is renowned for its regular architecture that has inspired foundational computational theories. However, the relationship between circuit structure, function and dynamics remained elusive. To tackle the issue, we have developed an advanced computational modeling framework that allowed us to reconstruct and simulate the structure and function of the mouse cerebellar cortex using morphologically realistic multi-compartmental neuron models. The cerebellar connectome was generated through appropriate connection rules, unifying a collection of scattered experimental data into a coherent construct and providing a new model-based ground-truth about circuit organization. Naturalistic background and sensory-burst stimulation were then used for functional validation against recordings in vivo, monitoring the impact of cellular mechanisms on signal propagation and spatio-temporal processing. Our simulations show, for the first time, how mossy fibers entrain the local neuronal microcircuit boosting the formation of columns of activity travelling from the granular to the molecular layer providing a new resource for the investigation of cerebellar computation.

scholarly journals STIMULUS: Noninvasive Dynamic Patterns of Neurostimulation using Spatio-Temporal Interference

2017 ◽  
Author(s):  
Jiaming Cao ◽  
Pulkit Grover
Keyword(s):  
Computational Model ◽  
Electrode Pair ◽  
Modeling Framework ◽  
Model Based ◽  
Spatio Temporal ◽  
Spatial Interference ◽  
The Brain ◽  
Over Time ◽  
Do So

AbstractUsing a systematic computational and modeling framework, we provide a novel Spatio-Temporal Interference-based stiMULation focUsing Strategy (STIMULUS) for high spatial precision noninvasive neurostimulation deep inside the brain. To do so, we first replicate the results of the recently proposed temporal interference (TI) stimulation (which was only tested in-vivo) in a computational model based on a Hodgkin-Huxley model for neurons and a model of current dispersion in the head. Using this computational model, we obtain a nontrivial extension of the 2-electrode-pair TI proposed originally to multielectrode TI (> 2 electrode pairs) that yields significantly higher spatial precision. To further improve precision, we develop STIMULUS techniques for generating spatial interference patterns in conjunction with temporal interference, and demonstrate strict and significant improvements over multielectrode TI. Finally, we utilize the adaptivity that is inherent in STIMULUS to create multisite neurostimulation patterns that can be dynamically steered over time.

scholarly journals Group characterization of impact-induced, in vivo human brain kinematics

2021 ◽  
Vol 18 (179) ◽  
pp. 20210251
Author(s):  
Arnold D. Gomez ◽  
Philip V. Bayly ◽  
John A. Butman ◽  
Dzung L. Pham ◽  
Jerry L. Prince ◽  
...  
Keyword(s):  
Brain Size ◽  
Strain Tensor ◽  
Fluid Motion ◽  
Brain Response ◽  
Maximum Shear Strain ◽  
Neck Extension ◽  
Spatio Temporal ◽  
The Individual ◽  
The Impact

Brain movement during an impact can elicit a traumatic brain injury, but tissue kinematics vary from person to person and knowledge regarding this variability is limited. This study examines spatio-temporal brain–skull displacement and brain tissue deformation across groups of subjects during a mild impact in vivo . The heads of two groups of participants were imaged while subjected to a mild (less than 350 rad s −2 ) impact during neck extension (NE, n = 10) and neck rotation (NR, n = 9). A kinematic atlas of displacement and strain fields averaged across all participants was constructed and compared against individual participant data. The atlas-derived mean displacement magnitude was 0.26 ± 0.13 mm for NE and 0.40 ± 0.26 mm for NR, which is comparable to the displacement magnitudes from individual participants. The strain tensor from the atlas displacement field exhibited maximum shear strain (MSS) of 0.011 ± 0.006 for NE and 0.017 ± 0.009 for NR and was lower than the individual MSS averaged across participants. The atlas illustrates common patterns, containing some blurring but visible relationships between anatomy and kinematics. Conversely, the direction of the impact, brain size, and fluid motion appear to underlie kinematic variability. These findings demonstrate the biomechanical roles of key anatomical features and illustrate common features of brain response for model evaluation.

scholarly journals Effect of Neuritic Cables on Conductance Estimates for Remote Electrical Synapses

2003 ◽  
Vol 89 (4) ◽  
pp. 2215-2224 ◽  
Author(s):  
Astrid A. Prinz ◽  
Peter Fromherz
Keyword(s):  
Signal Propagation ◽  
Synaptic Conductance ◽  
Electrical Synapse ◽  
Protein Patterns ◽  
Electrical Synapses ◽  
Snail Neurons ◽  
Cable Properties ◽  
The Impact ◽  
Synaptic Conductances

The conductance of electrical synapses is usually estimated from voltage recordings at the neuronal somata under the assumption that each cell is isopotential. This approach neglects effects of intervening neurites. For a cell pair with unbranched neurites and an electrical synapse at their ends, we used cable theory to derive an analytical expression that relates the synaptic conductance to voltage recordings at the cell bodies and to the neurite properties. The equation implies that the conventional method significantly underestimates the actual synapse conductance if the neurite length is comparable to the electrotonic length constant and if the synaptic conductance is similar to the serial neurite conductance. For an experimental test, we cultured pairs of snail neurons on protein patterns, resulting in a geometry that matched the theoretical model. Using the isopotential theory, we estimated the synapse conductances and found them to be rather weak. To obtain the cable properties, we recorded spatiotemporal maps of signal propagation in the neurites using a voltage-sensitive dye. Fits of these maps to a passive cable model showed that the snail neurons are electrotonically rather compact. Given these features of our experimental system, the synaptic conductances derived with the nonisopotential model deviated from the estimates of the isopotential theory by about 13%. This discrepancy, although small, shows that even in electrotonically compact neurons coupled by weak synapses the impact of the neuritic cables on conductance estimates cannot be neglected. When applied to less compact and more strongly coupled cell pairs in vivo, our approach can supply the realistic estimates of synaptic conductances that are necessary for a better understanding of the role of electrical coupling in neural systems.

scholarly journals MEArec: A Fast and Customizable Testbench Simulator for Ground-truth Extracellular Spiking Activity

2020 ◽  
Vol 19 (1) ◽  
pp. 185-204 ◽  
Author(s):  
Alessio Paolo Buccino ◽  
Gaute Tomas Einevoll
Keyword(s):  
Ground Truth ◽  
Spike Sorting ◽  
Ground Truth Data ◽  
Extracellular Signals ◽  
Software Packages ◽  
Processing Step ◽  
Important Processing ◽  
Spatio Temporal

AbstractWhen recording neural activity from extracellular electrodes, both in vivo and in vitro, spike sorting is a required and very important processing step that allows for identification of single neurons’ activity. Spike sorting is a complex algorithmic procedure, and in recent years many groups have attempted to tackle this problem, resulting in numerous methods and software packages. However, validation of spike sorting techniques is complicated. It is an inherently unsupervised problem and it is hard to find universal metrics to evaluate performance. Simultaneous recordings that combine extracellular and patch-clamp or juxtacellular techniques can provide ground-truth data to evaluate spike sorting methods. However, their utility is limited by the fact that only a few cells can be measured at the same time. Simulated ground-truth recordings can provide a powerful alternative mean to rank the performance of spike sorters. We present here , a Python-based software which permits flexible and fast simulation of extracellular recordings. allows users to generate extracellular signals on various customizable electrode designs and can replicate various problematic aspects for spike sorting, such as bursting, spatio-temporal overlapping events, and drifts. We expect will provide a common testbench for spike sorting development and evaluation, in which spike sorting developers can rapidly generate and evaluate the performance of their algorithms.

scholarly journals MEArec: a fast and customizable testbench simulator for ground-truth extracellular spiking activity

2019 ◽  
Author(s):  
Alessio P. Buccino ◽  
Gaute T. Einevoll
Keyword(s):  
Ground Truth ◽  
Spike Sorting ◽  
Ground Truth Data ◽  
Extracellular Signals ◽  
Software Packages ◽  
Processing Step ◽  
Important Processing ◽  
Spatio Temporal

AbstractWhen recording neural activity from extracellular electrodes, both in vivo and in vitro, spike sorting is a required and very important processing step that allows for identification of single neurons’ activity. Spike sorting is a complex algorithmic procedure, and in recent years many groups have attempted to tackle this problem, resulting in numerous methods and software packages. However, validation of spike sorting techniques is complicated. It is an inherently unsupervised problem and it is hard to find universal metrics to evaluate performance. Simultaneous recordings that combine extracellular and patch-clamp or juxtacellular techniques can provide ground-truth data to evaluate spike sorting methods. However, their utility is limited by the fact that only a few cells can be measured at the same time. Simulated ground-truth recordings can provide a powerful alternative mean to rank the performance of spike sorters. We present here MEArec, a Python-based software which permits flexible and fast simulation of extracellular recordings. MEArec allows users to generate extracellular signals on various customizable electrode designs and can replicate various problematic aspects for spike sorting, such as bursting, spatio-temporal overlapping events, and drifts. We expect MEArec will provide a common testbench for spike sorting development and evaluation, in which spike sorting developers can rapidly generate and evaluate the performance of their algorithms.

Experimental Study of the Impact of Alisma plantago-aquatica Secretions on Pathogenic Bacteria

2014 ◽  
Vol 1 (3) ◽  
pp. 3-7
Author(s):  
O. Zhukorskyy ◽  
O. Hulay
Keyword(s):  
Pathogenic Bacteria ◽  
Initial Density ◽  
Biologically Active ◽  
Erysipelothrix Rhusiopathiae ◽  
Natural Focus ◽  
Test Species ◽  
Popula Tions ◽  
And Control ◽  
The Impact

Aim. To estimate the impact of in vivo secretions of water plantain (Alisma plantago-aquatica) on the popula- tions of pathogenic bacteria Erysipelothrix rhusiopathiae. Methods. The plants were isolated from their natural conditions, the roots were washed from the substrate residues and cultivated in laboratory conditions for 10 days to heal the damage. Then the water was changed; seven days later the selected samples were sterilized using fi lters with 0.2 μm pore diameter. The dilution of water plantain root diffusates in the experimental samples was 1:10–1:10,000. The initial density of E. rhusiopathiae bacteria populations was the same for both experimental and control samples. The estimation of the results was conducted 48 hours later. Results. When the dilution of root diffusates was 1:10, the density of erysipelothrixes in the experimental samples was 11.26 times higher than that of the control, on average, the dilution of 1:100 − 6.16 times higher, 1:1000 – 3.22 times higher, 1:10,000 – 1.81 times higher, respectively. Conclusions. The plants of A. plantago-aquatica species are capable of affecting the populations of E. rhusiopathiae pathogenic bacteria via the secretion of biologically active substances into the environment. The consequences of this interaction are positive for the abovementioned bacteria, which is demon- strated by the increase in the density of their populations in the experiment compared to the control. The intensity of the stimulating effect on the populations of E. rhusiopathiae in the root diffusates of A. plantago-aquatica is re- ciprocally dependent on the degree of their dilution. The investigated impact of water plantain on erysipelothrixes should be related to the topical type of biocenotic connections, the formation of which between the test species in the ecosystems might promote maintaining the potential of natural focus of rabies. Keywords: Alisma plantago-aquatica, in vivo secretions, Erysipelothrix rhusiopathiae, population density, topical type of connections.

The efficiency of application of virtual cross-sections method and hypotheses MELS in problems of wave signal propagation in elastic waveguides with rough surfaces

2016 ◽  
pp. 3564-3575 ◽  
Author(s):  
Ara Sergey Avetisyan
Keyword(s):  
Half Space ◽  
Cross Sections ◽  
Classical Method ◽  
Signal Propagation ◽  
Elastic Half Space ◽  
Layered Systems ◽  
Surface Layers ◽  
Inhomogeneous Surface ◽  
Wave Signal ◽  
The Impact

The efficiency of virtual cross sections method and MELS (Magneto Elastic Layered Systems) hypotheses application is shown on model problem about distribution of wave field in thin surface layers of waveguide when plane wave signal is propagating in it. The impact of surface non-smoothness on characteristics of propagation of high-frequency horizontally polarized wave signal in isotropic elastic half-space is studied. It is shown that the non-smoothness leads to strong distortion of the wave signal over the waveguide thickness and along wave signal propagation direction as well.  Numerical comparative analysis of change in amplitude and phase characteristics of obtained wave fields against roughness of weakly inhomogeneous surface of homogeneous elastic half-space surface is done by classical method and by proposed approach for different kind of non-smoothness.

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