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Yassin A, Haidar A, Cherifi H, Seba H, Togni O. An evaluation tool for backbone extraction techniques in weighted complex networks. Sci Rep 2023; 13:17000. [PMID: 37813946 PMCID: PMC10562457 DOI: 10.1038/s41598-023-42076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/05/2023] [Indexed: 10/11/2023] Open
Abstract
Networks are essential for analyzing complex systems. However, their growing size necessitates backbone extraction techniques aimed at reducing their size while retaining critical features. In practice, selecting, implementing, and evaluating the most suitable backbone extraction method may be challenging. This paper introduces netbone, a Python package designed for assessing the performance of backbone extraction techniques in weighted networks. Its comparison framework is the standout feature of netbone. Indeed, the tool incorporates state-of-the-art backbone extraction techniques. Furthermore, it provides a comprehensive suite of evaluation metrics allowing users to evaluate different backbones techniques. We illustrate the flexibility and effectiveness of netbone through the US air transportation network analysis. We compare the performance of different backbone extraction techniques using the evaluation metrics. We also show how users can integrate a new backbone extraction method into the comparison framework. netbone is publicly available as an open-source tool, ensuring its accessibility to researchers and practitioners. Promoting standardized evaluation practices contributes to the advancement of backbone extraction techniques and fosters reproducibility and comparability in research efforts. We anticipate that netbone will serve as a valuable resource for researchers and practitioners enabling them to make informed decisions when selecting backbone extraction techniques to gain insights into the structural and functional properties of complex systems.
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Affiliation(s)
- Ali Yassin
- Laboratoire d'Informatique de Bourgogne, University of Burgundy, Dijon, France.
| | - Abbas Haidar
- Computer Science Department, Lebanese University, Beirut, Lebanon
| | - Hocine Cherifi
- ICB UMR 6303 CNRS, Univ. Bourgogne - Franche-Comté, Dijon, France
| | - Hamida Seba
- UCBL, CNRS, INSA Lyon, LIRIS, UMR5205, Univ Lyon, 69622, Villeurbanne, France
| | - Olivier Togni
- Laboratoire d'Informatique de Bourgogne, University of Burgundy, Dijon, France
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Powell JR, Hopfinger JB, Giovanello KS, Walton SR, DeLellis SM, Kane SF, Means GE, Mihalik JP. Mild traumatic brain injury history is associated with lower brain network resilience in soldiers. Brain Commun 2023; 5:fcad201. [PMID: 37545546 PMCID: PMC10400114 DOI: 10.1093/braincomms/fcad201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/12/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
Special Operations Forces combat soldiers sustain frequent blast and blunt neurotrauma, most often classified as mild traumatic brain injuries. Exposure to repetitive mild traumatic brain injuries is associated with persistent behavioural, cognitive, emotional and neurological symptoms later in life. Identifying neurophysiological changes associated with mild traumatic brain injury exposure, in the absence of present-day symptoms, is necessary for detecting future neurological risk. Advancements in graph theory and functional MRI have offered novel ways to analyse complex whole-brain network connectivity. Our purpose was to determine how mild traumatic brain injury history, lifetime incidence and recency affected whole-brain graph theoretical outcome measures. Healthy male Special Operations Forces combat soldiers (age = 33.2 ± 4.3 years) underwent multimodal neuroimaging at a biomedical research imaging centre using 3T Siemens Prisma or Biograph MRI scanners in this cross-sectional study. Anatomical and functional scans were preprocessed. The blood-oxygen-level-dependent signal was extracted from each functional MRI time series using the Big Brain 300 atlas. Correlations between atlas regions were calculated and Fisher z-transformed to generate subject-level correlation matrices. The Brain Connectivity Toolbox was used to obtain functional network measures for global efficiency (the average inverse shortest path length), local efficiency (the average global efficiency of each node and its neighbours), and assortativity coefficient (the correlation coefficient between the degrees of all nodes on two opposite ends of a link). General linear models were fit to compare mild traumatic brain injury lifetime incidence and recency. Nonparametric ANOVAs were used for tests on non-normally distributed data. Soldiers with a history of mild traumatic brain injury had significantly lower assortativity than those who did not self-report mild traumatic brain injury (t148 = 2.44, P = 0.016). The assortativity coefficient was significantly predicted by continuous mild traumatic brain injury lifetime incidence [F1,144 = 6.51, P = 0.012]. No differences were observed between recency groups, and no global or local efficiency differences were observed between mild traumatic brain injury history and lifetime incidence groups. Brain networks with greater assortativity have more resilient, interconnected hubs, while those with lower assortativity indicate widely distributed, vulnerable hubs. Greater lifetime mild traumatic brain injury incidence predicted lower assortativity in our study sample. Less resilient brain networks may represent a lack of physiological recovery in mild traumatic brain injury patients, who otherwise demonstrate clinical recovery, more vulnerability to future brain injury and increased risk for accelerated age-related neurodegenerative changes. Future longitudinal studies should investigate whether decreased brain network resilience may be a predictor for long-term neurological dysfunction.
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Affiliation(s)
- Jacob R Powell
- Matthew Gfeller Center, Department of Exercise and Sport Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joseph B Hopfinger
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kelly S Giovanello
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel R Walton
- Physical Medicine and Rehabilitation, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Stephen M DeLellis
- Fort Liberty Research Institute, The Geneva Foundation, Tacoma, WA 98402, USA
| | - Shawn F Kane
- Matthew Gfeller Center, Department of Exercise and Sport Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gary E Means
- United States Army Special Operations Command, Fort Liberty, NC 28303, USA
| | - Jason P Mihalik
- Correspondence to: Jason P. Mihalik Matthew Gfeller Center, Department of Exercise and Sport Science The University of North Carolina at Chapel Hill, 2201 Stallings-Evans Sports Medicine Center Campus Box 8700, Chapel Hill, NC 27599, USA E-mail:
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Ferrari-Díaz M, Bravo-Chávez RI, Silva-Pereyra J, Fernández T, García-Peña C, Rodríguez-Camacho M. Verbal intelligence and leisure activities are associated with cognitive performance and resting-state electroencephalogram. Front Aging Neurosci 2022; 14:921518. [PMID: 36268192 PMCID: PMC9577299 DOI: 10.3389/fnagi.2022.921518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
Cognitive reserve (CR) is the adaptability of cognitive processes that helps to explain differences in the susceptibility of cognitive or daily functions to resist the onslaught of brain-related injury or the normal aging process. The underlying brain mechanisms of CR studied through electroencephalogram (EEG) are scarcely reported. To our knowledge, few studies have considered a combination of exclusively dynamic proxy measures of CR. We evaluated the association of CR with cognition and resting-state EEG in older adults using three of the most frequently used dynamic proxy measures of CR: verbal intelligence, leisure activities, and physical activities. Multiple linear regression analyses with the CR proxies as independent variables and cognitive performance and the absolute power (AP) on six resting-state EEG components (beta, alpha1, alpha2, gamma, theta, and delta) as outcomes were performed. Eighty-eight healthy older adults aged 60–77 (58 female) were selected from previous study data. Verbal intelligence was a significant positive predictor of perceptual organization, working memory, processing speed, executive functions, and central delta power. Leisure activities were a significant positive predictor of posterior alpha2 power. The dynamic proxy variables of CR are differently associated with cognitive performance and resting-state EEG. Implementing leisure activities and tasks to increase vocabulary may promote better cognitive performance through compensation or neural efficiency mechanisms.
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Affiliation(s)
- Martina Ferrari-Díaz
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Ricardo Iván Bravo-Chávez
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
| | - Juan Silva-Pereyra
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
- *Correspondence: Juan Silva-Pereyra,
| | - Thalía Fernández
- Departamento de Neurobiología Conductual y Cognitiva, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Mexico
| | - Carmen García-Peña
- Departamento de Investigación, Instituto Nacional de Geriatría, Ciudad de México, Mexico
| | - Mario Rodríguez-Camacho
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico
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Perinelli A, Assecondi S, Tagliabue CF, Mazza V. Power shift and connectivity changes in healthy aging during resting-state EEG. Neuroimage 2022; 256:119247. [PMID: 35477019 DOI: 10.1016/j.neuroimage.2022.119247] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/20/2022] [Accepted: 04/23/2022] [Indexed: 12/15/2022] Open
Abstract
The neural activity of human brain changes in healthy individuals during aging. The most frequent variation in patterns of neural activity are a shift from posterior to anterior areas and a reduced asymmetry between hemispheres. These patterns are typically observed during task execution and by using functional magnetic resonance imaging data. In the present study we investigated whether analogous effects can also be detected during rest and by means of source-space time series reconstructed from electroencephalographic recordings. By analyzing oscillatory power distribution across the brain we indeed found a shift from posterior to anterior areas in older adults. We additionally examined this shift by evaluating connectivity and its changes with age. The findings indicated that inter-area connections among frontal, parietal and temporal areas were strengthened in older individuals. A more complex pattern was shown in intra-area connections, where age-related activity was enhanced in parietal and temporal areas, and reduced in frontal areas. Finally, the resulting network exhibits a loss of modularity with age. Overall, the results extend to resting-state condition the evidence of an age-related shift of brain activity from posterior to anterior areas, thus suggesting that this shift is a general feature of the aging brain rather than being task-specific. In addition, the connectivity results provide new information on the reorganization of resting-state brain activity in aging.
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Affiliation(s)
- Alessio Perinelli
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Corso Bettini 31, 38068 Rovereto, TN, Italy.
| | - Sara Assecondi
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Corso Bettini 31, 38068 Rovereto, TN, Italy
| | - Chiara F Tagliabue
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Corso Bettini 31, 38068 Rovereto, TN, Italy
| | - Veronica Mazza
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Corso Bettini 31, 38068 Rovereto, TN, Italy
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Tagliabue CF, Varesio G, Mazza V. Inter- and Intra-Hemispheric Age-Related Remodeling in Visuo-Spatial Working Memory. Front Aging Neurosci 2022; 13:807907. [PMID: 35111040 PMCID: PMC8803153 DOI: 10.3389/fnagi.2021.807907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Electroencephalography (EEG) studies investigating visuo-spatial working memory (vWM) in aging typically adopt an event-related potential (ERP) analysis approach that has shed light on the age-related changes during item retention and retrieval. However, this approach does not fully enable a detailed description of the time course of the neural dynamics related to aging. The most frequent age-related changes in brain activity have been described by two influential models of neurocognitive aging, the Hemispheric Asymmetry Reduction in Older Adults (HAROLD) and the Posterior-Anterior Shift in Aging (PASA). These models posit that older adults tend to recruit additional brain areas (bilateral as predicted by HAROLD and anterior as predicted by PASA) when performing several cognitive tasks. We tested younger (N = 36) and older adults (N = 35) in a typical vWM task (delayed match-to-sample) where participants have to retain items and then compare them to a sample. Through a data-driven whole scalp EEG analysis we aimed at characterizing the temporal dynamics of the age-related activations predicted by the two models, both across and within different stages of stimulus processing. Behaviorally, younger outperformed older adults. The EEG analysis showed that older adults engaged supplementary bilateral posterior and frontal sites when processing different levels of memory load, in line with both HAROLD and PASA-like activations. Interestingly, these age-related supplementary activations dynamically developed over time. Indeed, they varied across different stages of stimulus processing, with HAROLD-like modulations being mainly present during item retention, and PASA-like activity during both retention and retrieval. Overall, the present results suggest that age-related neural changes are not a phenomenon indiscriminately present throughout all levels of cognitive processing.
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