scholarly journals Directed functional and structural connectivity in a large-scale model for the mouse cortex

2021 ◽  
pp. 1-25
Author(s):  
Ronaldo V. Nunes ◽  
Marcelo B. Reyes ◽  
Jorge F. Mejias ◽  
Raphael Y. de Camargo
Keyword(s):  
Functional Connectivity ◽  
Large Scale ◽  
Pearson Correlation ◽  
Structural Connectivity ◽  
Ground Truth ◽  
Scale Model ◽  
Electrophysiological Recording ◽  
Ground Truth Data ◽  
Mouse Cortex ◽  
Electrophysiological Measurements

Abstract Inferring the structural connectivity from electrophysiological measurements is a fundamental challenge in systems neuroscience. Directed functional connectivity measures, such as the Generalized Partial Directed Coherence (GPDC), provide estimates of the causal influence between areas. However, the relation between causality estimates and structural connectivity is still not clear. We analyzed this problem by evaluating the effectiveness of GPDC to estimate the connectivity of a ground-truth, data-constrained computational model of a large-scale network model of the mouse cortex. The model contains 19 cortical areas comprised of spiking neurons, with areas connected by long-range projections with weights obtained from a tract-tracing cortical connectome. We show that GPDC values provide a reasonable estimate of structural connectivity, with an average Pearson correlation over simulations of 0.74. Moreover, even in a typical electrophysiological recording scenario containing five areas, the mean correlation was above 0.6. These results suggest that it may be possible to empirically estimate structural connectivity from functional connectivity even when detailed whole-brain recordings are not achievable.

scholarly journals Inferring large-scale structural connectivity from local activity in a model of the mouse large-scale cortical network

2021 ◽  
Author(s):  
Ronaldo V. Nunes ◽  
Marcelo Bussotti Reyes ◽  
Jorge F. Mejias ◽  
Raphael Y. de Camargo
Keyword(s):  
Functional Connectivity ◽  
Large Scale ◽  
Structural Connectivity ◽  
Ground Truth ◽  
Brain Regions ◽  
Cortical Network ◽  
Ground Truth Data ◽  
Cortical Areas ◽  
Electrophysiological Measurements ◽  
Flow Of Information

AbstractInferring the structural connectivity from electrophysiological measurements is a fundamental challenge in systems neuroscience. Directed functional connectivity measures, such as the Generalized Partial Directed Correlation (GPDC), provide estimates of the causal influence between areas. However, such methods have a limitation because their estimates depend on the number of brain regions simultaneously recorded. We analyzed this problem by evaluating the effectiveness of GPDC to estimate the connectivity of a ground-truth, data-constrained computational model of a large-scale mouse cortical network. The model contains 19 cortical areas modeled using spiking neural populations, and directed weights for long-range projections were obtained from a tract-tracing cortical connectome. We show that the GPDC estimates correlate positively with structural connectivity. Moreover, the correlation between structural and directed functional connectivity is comparable even when using only a few cortical areas for GPDC estimation, a typical scenario for electro-physiological recordings. Finally, GPDC measures also provided a measure of the flow of information among cortical areas.

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 Comparing the temporal relationship of structural and functional connectivity changes in different adult human brain networks: a single-case study

2018 ◽  
Vol 3 ◽  
pp. 50 ◽  
Author(s):  
Takamitsu Watanabe ◽  
Geraint Rees
Keyword(s):  
Functional Connectivity ◽  
Human Brain ◽  
Large Scale ◽  
Single Case ◽  
Brain Networks ◽  
Structural Connectivity ◽  
Time Lags ◽  
Single Case Study ◽  
Adult Human

Background: Despite accumulated evidence for adult brain plasticity, the temporal relationships between large-scale functional and structural connectivity changes in human brain networks remain unclear. Methods: By analysing a unique richly detailed 19-week longitudinal neuroimaging dataset, we tested whether macroscopic functional connectivity changes lead to the corresponding structural alterations in the adult human brain, and examined whether such time lags between functional and structural connectivity changes are affected by functional differences between different large-scale brain networks. Results: In this single-case study, we report that, compared to attention-related networks, functional connectivity changes in default-mode, fronto-parietal, and sensory-related networks occurred in advance of modulations of the corresponding structural connectivity with significantly longer time lags. In particular, the longest time lags were observed in sensory-related networks. In contrast, such significant temporal differences in connectivity change were not seen in comparisons between anatomically categorised different brain areas, such as frontal and occipital lobes. These observations survived even after multiple validation analyses using different connectivity definitions or using parts of the datasets. Conclusions: Although the current findings should be examined in independent datasets with different demographic background and by experimental manipulation, this single-case study indicates the possibility that plasticity of macroscopic brain networks could be affected by cognitive and perceptual functions implemented in the networks, and implies a hierarchy in the plasticity of functionally different brain systems.

scholarly journals A Product Feature Inference Model for Mining Implicit Customer Preferences Within Large Scale Social Media Networks

2015 ◽  
Author(s):  
Suppawong Tuarob ◽  
Conrad S. Tucker
Keyword(s):  
Social Media ◽  
Large Scale ◽  
Ground Truth ◽  
Inference Model ◽  
Underlying Assumption ◽  
Ground Truth Data ◽  
Social Media Networks ◽  
Customer Preferences ◽  
Product Features ◽  
Online Sources

The acquisition and mining of product feature data from online sources such as customer review websites and large scale social media networks is an emerging area of research. In many existing design methodologies that acquire product feature preferences form online sources, the underlying assumption is that product features expressed by customers are explicitly stated and readily observable to be mined using product feature extraction tools. In many scenarios however, product feature preferences expressed by customers are implicit in nature and do not directly map to engineering design targets. For example, a customer may implicitly state “wow I have to squint to read this on the screen”, when the explicit product feature may be a larger screen. The authors of this work propose an inference model that automatically assigns the most probable explicit product feature desired by a customer, given an implicit preference expressed. The algorithm iteratively refines its inference model by presenting a hypothesis and using ground truth data, determining its statistical validity. A case study involving smartphone product features expressed through Twitter networks is presented to demonstrate the effectiveness of the proposed methodology.

scholarly journals Spatiotemporal empirical mode decomposition of resting-state fMRI signals: application to global signal regression

2019 ◽  
Author(s):  
Narges Moradi ◽  
Mehdy Dousty ◽  
Roberto C. Sotero
Keyword(s):  
Functional Connectivity ◽  
Empirical Mode Decomposition ◽  
Resting State ◽  
Large Scale ◽  
Pearson Correlation ◽  
Brain Regions ◽  
Connectivity Matrix ◽  
Correlation Pattern ◽  
Mode Decomposition ◽  
Global Signal

AbstractResting-state functional connectivity MRI (rs-fcMRI) is a common method for mapping functional brain networks. However, estimation of these networks is affected by the presence of a common global systemic noise, or global signal (GS). Previous studies have shown that the common preprocessing steps of removing the GS may create spurious correlations between brain regions. In this paper, we decompose fMRI signals into 5 spatial and 3 temporal intrinsic mode functions (SIMF and TIMF, respectively) by means of the empirical mode decomposition (EMD), which is an adaptive data-driven method widely used to analyze nonlinear and nonstationary phenomena. For each SIMF, brain connectivity matrices were computed by means of the Pearson correlation between TIMFs of different brain areas. Thus, instead of a single connectivity matrix, we obtained 5 × 3 = 15 functional connectivity matrices. Given the high value obtained for large-scale topological measures such as transitivity, in the low spatial maps (SIMF3, SIMF4, and SIMF5), our results suggest that these maps can be considered as spatial global signal masks. Thus, the spatiotemporal EMD of fMRI signals automatically regressed out the GS, although, interestingly, the removed noisy component was voxel-specific. We compared the performance of our method with the conventional GS regression and to the results when the GS was not removed. While the correlation pattern identified by the other methods suffers from a low level of precision, our approach demonstrated a high level of accuracy in extracting the correct correlation between different brain regions.

scholarly journals Inference of Synaptic Connectivity and External Variability in Neural Microcircuits

2019 ◽  
Author(s):  
Cody Baker ◽  
Emmanouil Froudarakis ◽  
Dimitri Yatsenko ◽  
Andreas S. Tolias ◽  
Robert Rosenbaum
Keyword(s):  
Functional Connectivity ◽  
Large Scale ◽  
Network Models ◽  
Ground Truth ◽  
External Input ◽  
Synaptic Connectivity ◽  
Imaging Data ◽  
Common Input ◽  
Simplifying Assumptions

AbstractA major goal in neuroscience is to estimate neural connectivity from large scale extracellular recordings of neural activity in vivo. This is challenging in part because any such activity is modulated by the unmeasured external synaptic input to the network, known as the common input problem. Many different measures of functional connectivity have been proposed in the literature, but their direct relationship to synaptic connectivity is often assumed or ignored. For in vivo data, measurements of this relationship would require a knowledge of ground truth connectivity, which is nearly always unavailable. Instead, many studies use in silico simulations as benchmarks for investigation, but such approaches necessarily rely upon a variety of simplifying assumptions about the simulated network and can depend on numerous simulation parameters. We combine neuronal network simulations, mathematical analysis, and calcium imaging data to address the question of when and how functional connectivity, synaptic connectivity, and latent external input variability can be untangled. We show numerically and analytically that, even though the precision matrix of recorded spiking activity does not uniquely determine synaptic connectivity, it is often closely related to synaptic connectivity in practice under various network models. This relation becomes more pronounced when the spatial structure of neuronal variability is considered jointly with precision.

scholarly journals Thresholding Functional Connectivity Matrices to Recover the Topological Properties of Large-Scale Neuronal Networks

2021 ◽  
Vol 15 ◽  
Author(s):  
Alessio Boschi ◽  
Martina Brofiga ◽  
Paolo Massobrio
Keyword(s):  
Functional Connectivity ◽  
Large Scale ◽  
Neuronal Networks ◽  
Brain Connectivity ◽  
Structural Connectivity ◽  
Synthetic Data ◽  
Connectivity Matrix ◽  
Causal Connection ◽  
Topological Properties ◽  
Functional Connections

The identification of the organization principles on the basis of the brain connectivity can be performed in terms of structural (i.e., morphological), functional (i.e., statistical), or effective (i.e., causal) connectivity. If structural connectivity is based on the detection of the morphological (synaptically mediated) links among neurons, functional and effective relationships derive from the recording of the patterns of electrophysiological activity (e.g., spikes, local field potentials). Correlation or information theory-based algorithms are typical routes pursued to find statistical dependencies and to build a functional connectivity matrix. As long as the matrix collects the possible associations among the network nodes, each interaction between the neuron i and j is different from zero, even though there was no morphological, statistical or causal connection between them. Hence, it becomes essential to find and identify only the significant functional connections that are predictive of the structural ones. For this reason, a robust, fast, and automatized procedure should be implemented to discard the “noisy” connections. In this work, we present a Double Threshold (DDT) algorithm based on the definition of two statistical thresholds. The main goal is not to lose weak but significant links, whose arbitrary exclusion could generate functional networks with a too small number of connections and altered topological properties. The algorithm allows overcoming the limits of the simplest threshold-based methods in terms of precision and guaranteeing excellent computational performances compared to shuffling-based approaches. The presented DDT algorithm was compared with other methods proposed in the literature by using a benchmarking procedure based on synthetic data coming from the simulations of large-scale neuronal networks with different structural topologies.

Measuring Flood Discharge

2017 ◽  
Author(s):  
Marian Muste ◽  
Ton Hoitink
Keyword(s):  
Real Time ◽  
Water Resource Management ◽  
Large Scale ◽  
Water Cycle ◽  
Ground Truth ◽  
Flood Frequency ◽  
Main Concern ◽  
Essential Difference ◽  
Discharge Data ◽  
Ground Truth Data

With a continuous global increase in flood frequency and intensity, there is an immediate need for new science-based solutions for flood mitigation, resilience, and adaptation that can be quickly deployed in any flood-prone area. An integral part of these solutions is the availability of river discharge measurements delivered in real time with high spatiotemporal density and over large-scale areas. Stream stages and the associated discharges are the most perceivable variables of the water cycle and the ones that eventually determine the levels of hazard during floods. Consequently, the availability of discharge records (a.k.a. streamflows) is paramount for flood-risk management because they provide actionable information for organizing the activities before, during, and after floods, and they supply the data for planning and designing floodplain infrastructure. Moreover, the discharge records represent the ground-truth data for developing and continuously improving the accuracy of the hydrologic models used for forecasting streamflows. Acquiring discharge data for streams is critically important not only for flood forecasting and monitoring but also for many other practical uses, such as monitoring water abstractions for supporting decisions in various socioeconomic activities (from agriculture to industry, transportation, and recreation) and for ensuring healthy ecological flows. All these activities require knowledge of past, current, and future flows in rivers and streams. Given its importance, an ability to measure the flow in channels has preoccupied water users for millennia. Starting with the simplest volumetric methods to estimate flows, the measurement of discharge has evolved through continued innovation to sophisticated methods so that today we can continuously acquire and communicate the data in real time. There is no essential difference between the instruments and methods used to acquire streamflow data during normal conditions versus during floods. The measurements during floods are, however, complex, hazardous, and of limited accuracy compared with those acquired during normal flows. The essential differences in the configuration and operation of the instruments and methods for discharge estimation stem from the type of measurements they acquire—that is, discrete and autonomous measurements (i.e., measurements that can be taken any time any place) and those acquired continuously (i.e., estimates based on indirect methods developed for fixed locations). Regardless of the measurement situation and approach, the main concern of the data providers for flooding (as well as for other areas of water resource management) is the timely delivery of accurate discharge data at flood-prone locations across river basins.

scholarly journals Using structural connectivity to augment community structure in EEG functional connectivity

2020 ◽  
Vol 4 (3) ◽  
pp. 761-787 ◽  
Author(s):  
Katharina Glomb ◽  
Emeline Mullier ◽  
Margherita Carboni ◽  
Maria Rubega ◽  
Giannarita Iannotti ◽  
...  
Keyword(s):  
Community Structure ◽  
White Matter ◽  
Functional Connectivity ◽  
Large Scale ◽  
Structural Connectivity ◽  
Brain Regions ◽  
Source Analysis ◽  
Volume Conduction ◽  
Functional Relationships ◽  
The Impact

Recently, EEG recording techniques and source analysis have improved, making it feasible to tap into fast network dynamics. Yet, analyzing whole-cortex EEG signals in source space is not standard, partly because EEG suffers from volume conduction: Functional connectivity (FC) reflecting genuine functional relationships is impossible to disentangle from spurious FC introduced by volume conduction. Here, we investigate the relationship between white matter structural connectivity (SC) and large-scale network structure encoded in EEG-FC. We start by confirming that FC (power envelope correlations) is predicted by SC beyond the impact of Euclidean distance, in line with the assumption that SC mediates genuine FC. We then use information from white matter structural connectivity in order to smooth the EEG signal in the space spanned by graphs derived from SC. Thereby, FC between nearby, structurally connected brain regions increases while FC between nonconnected regions remains unchanged, resulting in an increase in genuine, SC-mediated FC. We analyze the induced changes in FC, assessing the resemblance between EEG-FC and volume-conduction- free fMRI-FC, and find that smoothing increases resemblance in terms of overall correlation and community structure. This result suggests that our method boosts genuine FC, an outcome that is of interest for many EEG network neuroscience questions.

scholarly journals Assessing the tropical forest cover change in northern parts of Sonitpur and Udalguri District of Assam, India

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ranjit Mahato ◽  
Gibji Nimasow ◽  
Oyi Dai Nimasow ◽  
Dhoni Bushi
Keyword(s):  
Protected Areas ◽  
National Park ◽  
Large Scale ◽  
Forest Cover ◽  
Ground Truth ◽  
Forest Cover Change ◽  
Wildlife Sanctuary ◽  
Remotely Sensed Data ◽  
Ground Truth Data ◽  
Increasing Trends

AbstractSonitpur and Udalguri district of Assam possess rich tropical forests with equally important faunal species. The Nameri National Park, Sonai-Rupai Wildlife Sanctuary, and other Reserved Forests are areas of attraction for tourists and wildlife lovers. However, these protected areas are reportedly facing the problem of encroachment and large-scale deforestation. Therefore, this study attempts to estimate the forest cover change in the area through integrating the remotely sensed data of 1990, 2000, 2010, and 2020 with the Geographic Information System. The Maximum Likelihood algorithm-based supervised classification shows acceptable agreement between the classified image and the ground truth data with an overall accuracy of about 96% and a Kappa coefficient of 0.95. The results reveal a forest cover loss of 7.47% from 1990 to 2000 and 7.11% from 2000 to 2010. However, there was a slight gain of 2.34% in forest cover from 2010 to 2020. The net change of forest to non-forest was 195.17 km2 in the last forty years. The forest transition map shows a declining trend of forest remained forest till 2010 and a slight increase after that. There was a considerable decline in the forest to non-forest (11.94% to 3.50%) from 2000–2010 to 2010–2020. Further, a perceptible gain was also observed in the non-forest to the forest during the last four decades. The overlay analysis of forest cover maps show an area of 460.76 km2 (28.89%) as forest (unchanged), 764.21 km2 (47.91%) as non-forest (unchanged), 282.67 km2 (17.72%) as deforestation and 87.50 km2 (5.48%) as afforestation. The study found hotspots of deforestation in the closest areas of National Park, Wildlife Sanctuary, and Reserved Forests due to encroachments for human habitation, agriculture, and timber/fuelwood extractions. Therefore, the study suggests an early declaration of these protected areas as Eco-Sensitive Zone to control the increasing trends of deforestation.

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