scholarly journals Dissecting whole-brain conduction delays through MRI microstructural measures

2021 ◽  
Author(s):  
Matteo Mancini ◽  
Qiyuan Tian ◽  
Qiuyun Fan ◽  
Mara Cercignani ◽  
Susie Y. Huang
Keyword(s):  
Conduction Velocity ◽  
Large Scale ◽  
Structural Connectivity ◽  
Network Models ◽  
Axonal Diameter ◽  
Main Determinants ◽  
Conduction Velocity Distributions ◽  
Connection Length ◽  
Different Characteristics ◽  
Large Scale Simulations

AbstractNetwork models based on structural connectivity have been increasingly used as the blueprint for large-scale simulations of the human brain. As the nodes of this network are distributed through the cortex and interconnected by white matter pathways with different characteristics, modeling the associated conduction delays becomes important. The goal of this study is to estimate and characterize these delays directly from the brain structure. To achieve this, we leveraged microstructural measures from a combination of advanced magnetic resonance imaging acquisitions and computed the main determinants of conduction velocity, namely axonal diameter and myelin content. Using the model proposed by Rushton, we used these measures to calculate the conduction velocity and estimated the associated delays using tractography. We observed that both the axonal diameter and conduction velocity distributions presented a rather constant trend across different connection lengths, with resulting delays that scale linearly with the connection length. Relying on insights from graph theory and Kuramoto simulations, our results support the approximation of constant conduction velocity but also show path- and region-specific differences.

scholarly journals On the structural connectivity of large-scale models of brain networks at cellular level

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giuseppe Giacopelli ◽  
Domenico Tegolo ◽  
Emiliano Spera ◽  
Michele Migliore
Keyword(s):  
Large Scale ◽  
Brain Networks ◽  
Structural Connectivity ◽  
Network Models ◽  
Brain Regions ◽  
Cellular Level ◽  
Scale Model ◽  
Mathematical Framework ◽  
Underlying Mechanisms ◽  
Experimental Findings

AbstractThe brain’s structural connectivity plays a fundamental role in determining how neuron networks generate, process, and transfer information within and between brain regions. The underlying mechanisms are extremely difficult to study experimentally and, in many cases, large-scale model networks are of great help. However, the implementation of these models relies on experimental findings that are often sparse and limited. Their predicting power ultimately depends on how closely a model’s connectivity represents the real system. Here we argue that the data-driven probabilistic rules, widely used to build neuronal network models, may not be appropriate to represent the dynamics of the corresponding biological system. To solve this problem, we propose to use a new mathematical framework able to use sparse and limited experimental data to quantitatively reproduce the structural connectivity of biological brain networks at cellular level.

scholarly journals Bayesian Optimisation of Large-Scale Biophysical Networks

2017 ◽  
Author(s):  
J. Hadida ◽  
S.N. Sotiropoulos ◽  
R.G. Abeysuriya ◽  
M.W. Woolrich ◽  
S. Jbabdi
Keyword(s):  
Large Scale ◽  
Model Comparison ◽  
Structural Information ◽  
Structural Connectivity ◽  
Network Models ◽  
Network Architectures ◽  
Diffusion Tractography ◽  
Biophysical Models ◽  
Local Extrema ◽  
And Function

AbstractThe relationship between structure and function in the human brain is well established, but not yet well characterised. Large-scale biophysical models allow us to investigate this relationship, by leveraging structural information (e.g. derived from diffusion tractography) in order to couple dynamical models of local neuronal activity into networks of interacting regions distributed across the cortex. In practice however, these models are difficult to parametrise, and their simulation is often delicate and computationally expensive. This undermines the experimental aspect of scientific modelling, and stands in the way of comparing different parametrisations, network architectures, or models in general, with confidence. Here, we advocate the use of Bayesian optimisation for assessing the capabilities of biophysical network models, given a set of desired properties (e.g. band-specific functional connectivity); and in turn the use of this assessment as a principled basis for incremental modelling and model comparison. We adapt an optimisation method designed to cope with costly, high-dimensional, non-convex problems, and demonstrate its use and effectiveness. We find that this method is able to converge to regions of high functional similarity with real MEG data, with very few samples given the number of parameters, without getting stuck in local extrema, and while building and exploiting a map of uncertainty defined smoothly across the parameter space. We compare the results obtained using different methods of structural connectivity estimation from diffusion tractography, and find that one method leads to better simulations.

An HPC Framework for Large Scale Simulations and Visualizations of Oil Spill Trajectories

2013 ◽  
Author(s):  
Jian Tao ◽  
Werner Benger ◽  
Kelin Hu ◽  
Edwin Mathews ◽  
Marcel Ritter ◽  
...  
Keyword(s):  
Oil Spill ◽  
Large Scale ◽  
Large Scale Simulations

Methods of Network Planning and Management when Implementing Territory Planning Projects

2019 ◽  
pp. 49-54
Keyword(s):  
Large Scale ◽  
Housing Stock ◽  
Network Planning ◽  
Network Models ◽  
Point Of View ◽  
Residential Areas ◽  
Basic Principles ◽  
Planning And Management ◽  
Planning Project ◽  
Complex Process

The success of the Program of housing stock renovation in Moscow depends on the efficiency of resource management. One of the main urban planning documents that determine the nature of the reorganization of residential areas included in the Program of renovation is the territory planning project. The implementation of the planning project is a complex process that has a time point of its beginning and end, and also includes a set of interdependent parallel-sequential activities. From an organizational point of view, it is convenient to use network planning and management methods for project implementation. These methods are based on the construction of network models, including its varieties – a Gantt chart. A special application has been developed to simulate the implementation of planning projects. The article describes the basic principles and elements of modeling. The list of the main implementation parameters of the Program of renovation obtained with the help of the developed software for modeling is presented. The variants of using the results obtained for a comprehensive analysis of the implementation of large-scale urban projects are proposed.

scholarly journals Measuring sleep regularity: Theoretical properties and practical usage of existing metrics

SLEEP ◽  
2021 ◽  
Author(s):  
Dorothee Fischer ◽  
Elizabeth B Klerman ◽  
Andrew J K Phillips
Keyword(s):  
Large Scale ◽  
Research Question ◽  
Group Differences ◽  
Regularity Index ◽  
Wake Patterns ◽  
Health Related ◽  
Phase Deviation ◽  
Unbiased Estimates ◽  
Large Scale Simulations ◽  
Larger Sample

Abstract Study Objectives Sleep regularity predicts many health-related outcomes. Currently, however, there is no systematic approach to measuring sleep regularity. Traditionally, metrics have assessed deviations in sleep patterns from an individual’s average. Traditional metrics include intra-individual standard deviation (StDev), Interdaily Stability (IS), and Social Jet Lag (SJL). Two metrics were recently proposed that instead measure variability between consecutive days: Composite Phase Deviation (CPD) and Sleep Regularity Index (SRI). Using large-scale simulations, we investigated the theoretical properties of these five metrics. Methods Multiple sleep-wake patterns were systematically simulated, including variability in daily sleep timing and/or duration. Average estimates and 95% confidence intervals were calculated for six scenarios that affect measurement of sleep regularity: ‘scrambling’ the order of days; daily vs. weekly variation; naps; awakenings; ‘all-nighters’; and length of study. Results SJL measured weekly but not daily changes. Scrambling did not affect StDev or IS, but did affect CPD and SRI; these metrics, therefore, measure sleep regularity on multi-day and day-to-day timescales, respectively. StDev and CPD did not capture sleep fragmentation. IS and SRI behaved similarly in response to naps and awakenings but differed markedly for all-nighters. StDev and IS required over a week of sleep-wake data for unbiased estimates, whereas CPD and SRI required larger sample sizes to detect group differences. Conclusions Deciding which sleep regularity metric is most appropriate for a given study depends on a combination of the type of data gathered, the study length and sample size, and which aspects of sleep regularity are most pertinent to the research question.

scholarly journals Pairwise maximum entropy model explains the role of white matter structure in shaping emergent co-activation states

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Arian Ashourvan ◽  
Preya Shah ◽  
Adam Pines ◽  
Shi Gu ◽  
Christopher W. Lynn ◽  
...  
Keyword(s):  
White Matter ◽  
Maximum Entropy ◽  
Large Scale ◽  
Structural Connectivity ◽  
Quantitative Relationship ◽  
Brain Regions ◽  
Maximum Entropy Model ◽  
Entropy Model ◽  
Activation Patterns ◽  
Co Activation

AbstractA major challenge in neuroscience is determining a quantitative relationship between the brain’s white matter structural connectivity and emergent activity. We seek to uncover the intrinsic relationship among brain regions fundamental to their functional activity by constructing a pairwise maximum entropy model (MEM) of the inter-ictal activation patterns of five patients with medically refractory epilepsy over an average of ~14 hours of band-passed intracranial EEG (iEEG) recordings per patient. We find that the pairwise MEM accurately predicts iEEG electrodes’ activation patterns’ probability and their pairwise correlations. We demonstrate that the estimated pairwise MEM’s interaction weights predict structural connectivity and its strength over several frequencies significantly beyond what is expected based solely on sampled regions’ distance in most patients. Together, the pairwise MEM offers a framework for explaining iEEG functional connectivity and provides insight into how the brain’s structural connectome gives rise to large-scale activation patterns by promoting co-activation between connected structures.

scholarly journals Accelerating In-Transit Co-Processing for Scientific Simulations Using Region-Based Data-Driven Analysis

Algorithms ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 154
Author(s):  
Marcus Walldén ◽  
Masao Okita ◽  
Fumihiko Ino ◽  
Dimitris Drikakis ◽  
Ioannis Kokkinakis
Keyword(s):  
Large Scale ◽  
Data Driven ◽  
Data Sets ◽  
Output Constraints ◽  
Data Driven Approach ◽  
Scientific Simulations ◽  
Multiple Metrics ◽  
In Transit ◽  
Multiple Compression ◽  
Large Scale Simulations

Increasing processing capabilities and input/output constraints of supercomputers have increased the use of co-processing approaches, i.e., visualizing and analyzing data sets of simulations on the fly. We present a method that evaluates the importance of different regions of simulation data and a data-driven approach that uses the proposed method to accelerate in-transit co-processing of large-scale simulations. We use the importance metrics to simultaneously employ multiple compression methods on different data regions to accelerate the in-transit co-processing. Our approach strives to adaptively compress data on the fly and uses load balancing to counteract memory imbalances. We demonstrate the method’s efficiency through a fluid mechanics application, a Richtmyer–Meshkov instability simulation, showing how to accelerate the in-transit co-processing of simulations. The results show that the proposed method expeditiously can identify regions of interest, even when using multiple metrics. Our approach achieved a speedup of 1.29× in a lossless scenario. The data decompression time was sped up by 2× compared to using a single compression method uniformly.

Brain stem – from general view to computational model based on switchboard rules of operation

2019 ◽  
Vol 16 (1) ◽  
Author(s):  
Włodzisław Duch ◽  
Dariusz Mikołajewski
Keyword(s):  
Brain Stem ◽  
Large Scale ◽  
Ionic Channels ◽  
General View ◽  
The Central Nervous System ◽  
Network States ◽  
Large Scale Simulations ◽  
Influence Of Noise ◽  
The Brain ◽  
Sufficient Precision

Abstract Despite great progress in understanding the functions and structures of the central nervous system (CNS) the brain stem remains one of the least understood systems. We know that the brain stem acts as a decision station preparing the organism to act in a specific way, but such functions are rather difficult to model with sufficient precision to replicate experimental data due to the scarcity of data and complexity of large-scale simulations of brain stem structures. The approach proposed in this article retains some ideas of previous models, and provides more precise computational realization that enables qualitative interpretation of the functions played by different network states. Simulations are aimed primarily at the investigation of general switching mechanisms which may be executed in brain stem neural networks, as far as studying how the aforementioned mechanisms depend on basic neural network features: basic ionic channels, accommodation, and the influence of noise.

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