Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reproducibility of graph-theoretic brain network metrics: a systematic review.

ABSTRACT: This systematic review aimed to assess the reproducibility of graph-theoretic brain network metrics. Primary research studies of test-retest reliability conducted on healthy human subjects were included that quantified test-retest reliability using either the intraclass correlation coefficient (ICC) or the coefficient of variance. The MEDLINE, Web of Knowledge, Google Scholar, and OpenGrey databases were searched up to February 2014. Risk of bias was assessed with 10 criteria weighted toward methodological quality. Twenty-three studies were included in the review (n=499 subjects) and evaluated for various characteristics, including sample size (5-45), retest interval (<1 h to >1 year), acquisition method, and test-retest reliability scores. For at least one metric, ICCs reached the fair range (ICC 0.40-0.59) in one study, the good range (ICC 0.60-0.74) in five studies, and the excellent range (ICC>0.74) in 16 studies. Heterogeneity of methods prevented further quantitative analysis. Reproducibility was good overall. For the metrics having three or more ICCs reported for both functional and structural networks, six of seven were higher in structural networks, indicating that structural networks may be more reliable over time. The authors were also able to highlight and discuss a number of methodological factors affecting reproducibility.

SUBMITTER: Welton T

PROVIDER: S-EPMC4432917 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Test-Retest Reliability of Graph Theoretic Metrics in Adolescent Brains.

Project description:Graph theory analysis of structural brain networks derived from diffusion tensor imaging (DTI) has become a popular analytical method in neuroscience, enabling advanced investigations of neurological and psychiatric disorders. The purpose of this study was to investigate (1) the effects of edge weighting schemes and (2) the effects of varying interscan periods on graph metrics within the adolescent brain. We compared a binary (B) network definition with three weighting schemes: fractional anisotropy (FA), streamline count, and streamline count with density and length correction (SDL). Two commonly used global and two local graph metrics were examined. The analysis was conducted with two groups of adolescent volunteers who received DTI scans either 12 weeks apart (16.62 ± 1.10 years) or within the same scanning session (30 min apart) (16.65 ± 1.14 years). The intraclass correlation coefficient was used to assess test-retest reliability and the coefficient of variation (CV) was used to assess precision. On average, each edge scheme produced reliable results at both time intervals. Weighted measures outperformed binary measures, with SDL weights producing the most reliable metrics. All edge schemes except FA displayed high CV values, leaving FA as the only edge scheme that consistently showed high precision while also producing reliable results. Overall findings suggest that FA weights are more suited for DTI connectome studies in adolescents.

| S-EPMC6444894 | biostudies-literature

Reproducibility of structural brain connectivity and network metrics using probabilistic diffusion tractography.

Project description:The structural connectivity network constructed using probabilistic diffusion tractography can be characterized by the network metrics. In this study, short-term test-retest reproducibility of structural networks and network metrics were evaluated on 30 subjects in terms of within- and between-subject coefficient of variance (CVws, CVbs), and intra class coefficient (ICC) using various connectivity thresholds. The short-term reproducibility under various connectivity thresholds were also investigated when subject groups have same or different sparsity. In summary, connectivity threshold of 0.01 can exclude around 80% of the edges with CVws?=?73.2?±?37.7%, CVbs?=?119.3?±?44.0% and ICC?=?0.62?±?0.19. The rest 20% edges have CVws?<?45%, CVbs?<?90%, ICC?=?0.75?±?0.12. The presence of 1% difference in the sparsity can cause additional within-subject variations on network metrics. In conclusion, applying connectivity thresholds on structural network to exclude spurious connections for the network analysis should be considered as necessities. Our findings suggest that a connectivity threshold over 0.01 can be applied without significant effect on the short-term when network metrics are evaluated at the same sparsity in subject group. When the sparsity is not the same, the procedure of integration over various connectivity thresholds can provide reliable estimation of network metrics.

| S-EPMC6070542 | biostudies-literature

Effect of Resting-State fNIRS Scanning Duration on Functional Brain Connectivity and Graph Theory Metrics of Brain Network.

Project description:As an emerging brain imaging technique, functional near infrared spectroscopy (fNIRS) has attracted widespread attention for advancing resting-state functional connectivity (FC) and graph theoretical analyses of brain networks. However, it remains largely unknown how the duration of the fNIRS signal scanning is related to stable and reproducible functional brain network features. To answer this question, we collected resting-state fNIRS signals (10-min duration, two runs) from 18 participants and then truncated the hemodynamic time series into 30-s time bins that ranged from 1 to 10 min. Measures of nodal efficiency, nodal betweenness, network local efficiency, global efficiency, and clustering coefficient were computed for each subject at each fNIRS signal acquisition duration. Analyses of the stability and between-run reproducibility were performed to identify optimal time length for each measure. We found that the FC, nodal efficiency and nodal betweenness stabilized and were reproducible after 1 min of fNIRS signal acquisition, whereas network clustering coefficient, local and global efficiencies stabilized after 1 min and were reproducible after 5 min of fNIRS signal acquisition for only local and global efficiencies. These quantitative results provide direct evidence regarding the choice of the resting-state fNIRS scanning duration for functional brain connectivity and topological metric stability of brain network connectivity.

| S-EPMC5517460 | biostudies-literature

Detrimental network effects in privacy: A graph-theoretic model for node-based intrusions.

Project description:Despite proportionality being one of the tenets of data protection laws, we currently lack a robust analytical framework to evaluate the reach of modern data collections and the network effects at play. Here, we propose a graph-theoretic model and notions of node- and edge-observability to quantify the reach of networked data collections. We first prove closed-form expressions for our metrics and quantify the impact of the graph's structure on observability. Second, using our model, we quantify how (1) from 270,000 compromised accounts, Cambridge Analytica collected 68.0M Facebook profiles; (2) from surveilling 0.01% of the nodes in a mobile phone network, a law enforcement agency could observe 18.6% of all communications; and (3) an app installed on 1% of smartphones could monitor the location of half of the London population through close proximity tracing. Better quantifying the reach of data collection mechanisms is essential to evaluate their proportionality.

| S-EPMC9868678 | biostudies-literature

GraTeLPy: graph-theoretic linear stability analysis.

Project description:BackgroundA biochemical mechanism with mass action kinetics can be represented as a directed bipartite graph (bipartite digraph), and modeled by a system of differential equations. If the differential equations (DE) model can give rise to some instability such as multistability or Turing instability, then the bipartite digraph contains a structure referred to as a critical fragment. In some cases the existence of a critical fragment indicates that the DE model can display oscillations for some parameter values. We have implemented a graph-theoretic method that identifies the critical fragments of the bipartite digraph of a biochemical mechanism.ResultsGraTeLPy lists all critical fragments of the bipartite digraph of a given biochemical mechanism, thus enabling a preliminary analysis on the potential of a biochemical mechanism for some instability based on its topological structure. The correctness of the implementation is supported by multiple examples. The code is implemented in Python, relies on open software, and is available under the GNU General Public License.ConclusionsGraTeLPy can be used by researchers to test large biochemical mechanisms with mass action kinetics for their capacity for multistability, oscillations and Turing instability.

| S-EPMC4016541 | biostudies-literature

Graph theoretic network analysis reveals protein pathways underlying cell death following neurotropic viral infection.

Project description:Complex protein networks underlie any cellular function. Certain proteins play a pivotal role in many network configurations, disruption of whose expression proves fatal to the cell. An efficient method to tease out such key proteins in a network is still unavailable. Here, we used graph-theoretic measures on protein-protein interaction data (interactome) to extract biophysically relevant information about individual protein regulation and network properties such as formation of function specific modules (sub-networks) of proteins. We took 5 major proteins that are involved in neuronal apoptosis post Chandipura Virus (CHPV) infection as seed proteins in a database to create a meta-network of immediately interacting proteins (1(st) order network). Graph theoretic measures were employed to rank the proteins in terms of their connectivity and the degree upto which they can be organized into smaller modules (hubs). We repeated the analysis on 2(nd) order interactome that includes proteins connected directly with proteins of 1(st) order. FADD and Casp-3 were connected maximally to other proteins in both analyses, thus indicating their importance in neuronal apoptosis. Thus, our analysis provides a blueprint for the detection and validation of protein networks disrupted by viral infections.

| S-EPMC4585883 | biostudies-literature

Reproducibility and robustness of graph measures of the associative-semantic network.

Project description:Graph analysis is a promising tool to quantify brain connectivity. However, an essential requirement is that the graph measures are reproducible and robust. We have studied the reproducibility and robustness of various graph measures in group based and in individual binary and weighted networks derived from a task fMRI experiment during explicit associative-semantic processing of words and pictures. The nodes of the network were defined using an independent study and the connectivity was based on the partial correlation of the time series between any pair of nodes. The results showed that in case of binary networks, global graph measures exhibit a good reproducibility and robustness for networks which are not too sparse and these figures of merit depend on the graph measure and on the density of the network. Furthermore, group based binary networks should be derived from groups of sufficient size and the lower the density the more subjects are required to obtain robust values. Local graph measures are very variable in terms of reproducibility and should be interpreted with care. For weighted networks, we found good reproducibility (average test-retest variability <5% and ICC values >0.4) when using subject specific networks and this will allow us to relate network properties to individual subject information.

| S-EPMC4264875 | biostudies-literature

Graph Theoretic Analysis of Brain Connectomics in Multiple Sclerosis: Reliability and Relationship with Cognition.

Project description:Research suggests that disruption of brain networks might explain cognitive deficits in multiple sclerosis (MS). The reliability and effectiveness of graph theoretic network metrics as measures of cognitive performance were tested in 37 people with MS and 23 controls. Specifically, relationships with cognitive performance (linear regression against the paced auditory serial addition test-3 seconds [PASAT-3], symbol digit modalities test [SDMT], and attention network test) and 1-month reliability (using the intraclass correlation coefficient [ICC]) of network metrics were measured using both resting-state functional and diffusion magnetic resonance imaging data. Cognitive impairment was directly related to measures of brain network segregation and inversely related to network integration (prediction of PASAT-3 by small worldness, modularity, characteristic path length, R2?=?0.55; prediction of SDMT by small worldness, global efficiency, and characteristic path length, R2?=?0.60). Reliability of the measures for 1 month in a subset of nine participants was mostly rated as good (ICC >0.6) for both controls and MS patients in both functional and diffusion data, but was highly dependent on the chosen parcellation and graph density, with the 0.2-0.5 density range being the most reliable. This suggests that disrupted network organization predicts cognitive impairment in MS and its measurement is reliable for a 1-month period. These new findings support the hypothesis of network disruption as a major determinant of cognitive deficits in MS and the future possibility of the application of derived metrics as surrogate outcomes in trials of therapies for cognitive impairment.

| S-EPMC7196369 | biostudies-literature

Information-theoretic metrics for visualizing gene-environment interactions.

Project description:The purpose of our work was to develop heuristics for visualizing and interpreting gene-environment interactions (GEIs) and to assess the dependence of candidate visualization metrics on biological and study-design factors. Two information-theoretic metrics, the k-way interaction information (KWII) and the total correlation information (TCI), were investigated. The effectiveness of the KWII and TCI to detect GEIs in a diverse range of simulated data sets and a Crohn disease data set was assessed. The sensitivity of the KWII and TCI spectra to biological and study-design variables was determined. Head-to-head comparisons with the relevance-chain, multifactor dimensionality reduction, and the pedigree disequilibrium test (PDT) methods were obtained. The KWII and TCI spectra, which are graphical summaries of the KWII and TCI for each subset of environmental and genotype variables, were found to detect each known GEI in the simulated data sets. The patterns in the KWII and TCI spectra were informative for factors such as case-control misassignment, locus heterogeneity, allele frequencies, and linkage disequilibrium. The KWII and TCI spectra were found to have excellent sensitivity for identifying the key disease-associated genetic variations in the Crohn disease data set. In head-to-head comparisons with the relevance-chain, multifactor dimensionality reduction, and PDT methods, the results from visual interpretation of the KWII and TCI spectra performed satisfactorily. The KWII and TCI are promising metrics for visualizing GEIs. They are capable of detecting interactions among numerous single-nucleotide polymorphisms and environmental variables for a diverse range of GEI models.

| S-EPMC2265645 | biostudies-literature

The structural connectome in traumatic brain injury: A meta-analysis of graph metrics.

Project description:Although recent structural connectivity studies of traumatic brain injury (TBI) have used graph theory to evaluate alterations in global integration and functional segregation, pooled analysis is needed to examine the robust patterns of change in graph metrics across studies. Following a systematic search, 15 studies met the inclusion criteria for review. Of these, ten studies were included in a random-effects meta-analysis of global graph metrics, and subgroup analyses examined the confounding effects of severity and time since injury. The meta-analysis revealed significantly higher values of normalised clustering coefficient (gö=ö1.445, CI=[0.512, 2.378], pö=ö0.002) and longer characteristic path length (gö=ö0.514, CI=[0.190, 0.838], pö=ö0.002) in TBI patients compared with healthy controls. Our findings suggest that the TBI structural network has shifted away from the balanced small-world network towards a regular lattice. Therefore, these graph metrics may be useful markers of neurocognitive dysfunction in TBI. We conclude that the pattern of change revealed by our analysis should be used to guide hypothesis-driven research into the role of graph metrics as diagnostic and prognostic biomarkers.

| S-EPMC7615245 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data