A MATLAB toolbox for multivariate analysis of brain networks

Differences in Brain Network Topology Based on Alcohol Use History in Adolescents

Approximately 6 million youth aged 12 to 20 consume alcohol monthly in the United States. The effect of alcohol consumption in adolescence on behavior and cognition is heavily researched; however, little is known about how alcohol consumption in adolescence may alter brain function, leading to long-term developmental detriments. In order to investigate differences in brain connectivity associated with alcohol use in adolescents, brain networks were constructed using resting-state functional magnetic resonance imaging data collected by the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA) from 698 youth (12-21 years; 117 hazardous drinkers and 581 no/low drinkers). Analyses assessed differences in brain network topology based on alcohol consumption in eight predefined brain networks, as well as in whole-brain connectivity. Within the central executive network (CEN), basal ganglia network (BGN), and sensorimotor network (SMN), no/low drinkers demonstrated stronger and more frequent connections between highly globally efficient nodes, with fewer and weaker connections between highly clustered nodes. Inverse results were observed within the dorsal attention network (DAN), visual network (VN), and frontotemporal network (FTN), with no/low drinkers demonstrating weaker connections between nodes with high efficiency and increased frequency of clustered nodes compared to hazardous drinkers. Cross-sectional results from this study show clear organizational differences between adolescents with no/low or hazardous alcohol use, suggesting that aberrant connectivity in these brain networks is associated with risky drinking behaviors.

Brain working memory network indices as landmarks of intelligence

Identifying the neural correlates of intelligence has long been a goal in neuroscience. Recently, the field of network neuroscience has attracted researchers' attention as a means for answering this question. In network neuroscience, the brain is considered as an integrated system whose systematic properties provide profound insights into health and behavioral outcomes. However, most network studies of intelligence have used univariate methods to investigate topological network measures, with their focus limited to a few measures. Furthermore, most studies have focused on resting state networks despite the fact that brain activation during working memory tasks has been linked to intelligence. Finally, the literature is still missing an investigation of the association between network assortativity and intelligence. To address these issues, here we employ a recently developed mixed-modeling framework for analyzing multi-task brain networks to elucidate the most critical working memory task network topological properties corresponding to individuals' intelligence differences. We used a data set of 379 subjects (22-35 y/o) from the Human Connectome Project (HCP). Each subject's data included composite intelligence scores, and fMRI during resting state and a 2-back working memory task. Following comprehensive quality control and preprocessing of the minimally preprocessed fMRI data, we extracted a set of the main topological network features, including global efficiency, degree, leverage centrality, modularity, and clustering coefficient. The estimated network features and subject's confounders were then incorporated into the multi-task mixed-modeling framework to investigate how brain network changes between working memory and resting state relate to intelligence score. Our results indicate that the general intelligence score (cognitive composite score) is associated with a change in the relationship between connection strength and multiple network topological properties, including global efficiency, leverage centrality, and degree difference during working memory as it is compared to resting state. More specifically, we observed a higher increase in the positive association between global efficiency and connection strength for the high intelligence group when they switch from resting state to working memory. The strong connections might form superhighways for a more efficient global flow of information through the brain network. Furthermore, we found an increase in the negative association between degree difference and leverage centrality with connection strength during working memory tasks for the high intelligence group. These indicate higher network resilience and assortativity along with higher circuit-specific information flow during working memory for those with a higher intelligence score. Although the exact neurobiological implications of our results are speculative at this point, our results provide evidence for the significant association of intelligence with hallmark properties of brain networks during working memory.

Altered Default Mode Network Associated with Pesticide Exposure in Latinx Children from Rural Farmworker Families

Pesticide exposure has been associated with adverse cognitive and neurological effects. However, neuroimaging studies aimed at examining the impacts of pesticide exposure on brain networks underlying abnormal neurodevelopment in children remain limited. It has been demonstrated that pesticide exposure in children is associated with disrupted brain anatomy in regions that make up the default mode network (DMN), a subnetwork engaged across a diverse set of cognitive processes, particularly higher-order cognitive tasks. This study tested the hypothesis that functional brain network connectivity/topology in Latinx children from rural farmworker families (FW children) would differ from urban Latinx children from non-farmworker families (NFW children). We also tested the hypothesis that probable historic childhood exposure to pesticides among FW children would be associated with network connectivity/topology in a manner that parallels differences between FW and NFW children. We used brain networks from functional magnetic resonance imaging (fMRI) data from 78 children and a mixed-effects regression framework to test our hypotheses. We found that network topology was differently associated with the connection probability between FW and NFW children in the DMN. Our results also indicated that, among 48 FW children, historic reports of exposure to pesticides from prenatal to 96 months old were significantly associated with DMN topology, as hypothesized. Although the cause of the differences in brain networks between FW and NFW children cannot be determined using a cross-sectional study design, the observed associations between network connectivity/topology and historic exposure reports in FW children provide compelling evidence for a contribution of pesticide exposure on altering the DMN network organization in this vulnerable population. Although longitudinal follow-up of the children is necessary to further elucidate the cause and reveal the ultimate neurological implications, these findings raise serious concerns about the potential adverse health consequences from developmental neurotoxicity associated with pesticide exposure in this vulnerable population.

Longitudinal relationship of baseline functional brain networks with intentional weight loss in older adults

OBJECTIVE

The goal of this study was to determine whether the degree of weight loss after 6 months of a behavior-based intervention is related to baseline connectivity within two functional networks (FNs) of interest, FN1 and FN2, in a group of older adults with obesity.

METHODS

Baseline functional magnetic resonance imaging data were collected following an overnight fast in 71 older adults with obesity involved in a weight-loss intervention. Functional brain networks in a resting state and during a food-cue task were analyzed using a mixed-regression framework to examine the relationships between baseline networks and 6-month change in weight.

RESULTS

During the resting condition, the relationship of baseline brain functional connectivity and network clustering in FN1, which includes the visual cortex and sensorimotor areas, was significantly associated with 6-month weight loss. During the food-cue condition, 6-month weight loss was significantly associated with the relationship between baseline brain connectivity and network global efficiency in FN2, which includes executive control, attention, and limbic regions.

CONCLUSION

These findings provide further insight into complex functional circuits in the brain related to successful weight loss and may ultimately aid in developing tailored behavior-based treatment regimens that target specific brain circuitry.

Current Status and Future Directions of Neuromonitoring With Emerging Technologies in Neonatal Care

Neonatology has experienced a significant reduction in mortality rates of the preterm population and critically ill infants over the last few decades. Now, the emphasis is directed toward improving long-term neurodevelopmental outcomes and quality of life. Brain-focused care has emerged as a necessity. The creation of neonatal neurocritical care units, or Neuro-NICUs, provides strategies to reduce brain injury using standardized clinical protocols, methodologies, and provider education and training. Bedside neuromonitoring has dramatically improved our ability to provide assessment of newborns at high risk. Non-invasive tools, such as continuous electroencephalography (cEEG), amplitude-integrated electroencephalography (aEEG), and near-infrared spectroscopy (NIRS), allow screening for seizures and continuous evaluation of brain function and cerebral oxygenation at the bedside. Extended and combined uses of these techniques, also described as multimodal monitoring, may allow practitioners to better understand the physiology of critically ill neonates. Furthermore, the rapid growth of technology in the Neuro-NICU, along with the increasing use of telemedicine and artificial intelligence with improved data mining techniques and machine learning (ML), has the potential to vastly improve decision-making processes and positively impact outcomes. This article will cover the current applications of neuromonitoring in the Neuro-NICU, recent advances, potential pitfalls, and future perspectives in this field.

A mixed-modeling framework for whole-brain dynamic network analysis

The emerging area of dynamic brain network analysis has gained considerable attention in recent years. However, development of multivariate statistical frameworks that allow for examining the associations between phenotypic traits and dynamic patterns of system-level properties of the brain, and drawing statistical inference about such associations, has largely lagged behind. To address this need we developed a mixed-modeling framework that allows for assessing the relationship between any desired phenotype and dynamic patterns of whole-brain connectivity and topology. This novel framework also allows for simulating dynamic brain networks with respect to desired covariates. Unlike current tools, which largely use data-driven methods, our model-based method enables aligning neuroscientific hypotheses with the analytic approach. We demonstrate the utility of this model in identifying the relationship between fluid intelligence and dynamic brain networks by using resting-state fMRI (rfMRI) data from 200 participants in the Human Connectome Project (HCP) study. We also demonstrate the utility of this model to simulate dynamic brain networks at both group and individual levels. To our knowledge, this approach provides the first model-based statistical method for examining dynamic patterns of system-level properties of the brain and their relationships to phenotypic traits as well as simulating dynamic brain networks.

In recent years, a growing body of studies have aimed at analyzing the brain as a complex dynamic system by using various neuroimaging data. This has opened new avenues to answer compelling questions about the brain function in health and disease. However, methods that allow for providing statistical inference about how the complex interactions of the brain are associated with desired phenotypes are to be developed for a more profound insight. This study introduces a promising regression-based model to relate dynamic brain networks to desired phenotypes and provide statistical inference. Moreover, it can be used for simulating dynamic brain networks with respect to desired phenotypes at the group and individual levels.

Mixed Modeling Frameworks for Analyzing Whole-Brain Network Data

Brain network analyses have exploded in recent years and hold great potential in helping us understand normal and abnormal brain function. Network science approaches have facilitated these analyses and our understanding of how the brain is structurally and functionally organized. However, the development of statistical methods that allow relating this organization to health outcomes has lagged behind. We have attempted to address this need by developing mixed modeling frameworks that allow relating system-level properties of brain networks to outcomes of interest. These frameworks serve as a synergistic fusion of multivariate statistical approaches with network science, providing a needed analytic (modeling and inferential) foundation for whole-brain network data. In this chapter we delineate these approaches that have been developed for single-task and multitask (longitudinal) brain network data, illustrate their utility with data applications, detail their implementation with a user-friendly Matlab toolbox, and discuss ongoing work to adapt the methods to (within-task) dynamic network analysis.

Influence of Heart Rate Variability on Abstinence-Related Changes in Brain State in Everyday Drinkers

Alcohol consumption is now common practice worldwide, and functional brain networks are beginning to reveal the complex interactions observed with alcohol consumption and abstinence. The autonomic nervous system (ANS) has a well-documented relationship with alcohol use, and a growing body of research is finding links between the ANS and functional brain networks. This study recruited everyday drinkers in an effort to uncover the relationship between alcohol abstinence, ANS function, and whole brain functional brain networks. Participants (n = 29), 24-60 years-of-age, consumed moderate levels of alcohol regularly (males 2.4 (±0.26) drinks/day, females 2.3 (±0.96) drinks/day). ANS function, specifically cardiac vagal tone, was assessed using the Porges-Bohrer method for calculating respiratory sinus arrhythmia (PB_RSA). Functional brain networks were generated from resting-state MRI scans obtained following 3-day periods of typical consumption and abstinence. A multi-task mixed-effects regression model determined the influences of HRV and drinking state on functional network connectivity. Results showed differences in the relationship between the strength of network connections and clustering coefficients across drinking states, moderated by PB_RSA. Increases in connection strength between highly clustered nodes during abstinence as PB_RSA increases demonstrates a greater possible range of topological configurations at high PB_RSA values. This novel finding begins to shed light on the complex interactions between typical alcohol abstinence and physiological responses of the central and autonomic nervous system.

Functional Brain Networks: Unique Patterns with Hedonic Appetite and Confidence to Resist Eating in Older Adults with Obesity

OBJECTIVE

The purpose of this study was to determine whether baseline measures of hedonic hunger-the Power of Food Scale-and self-control for food consumption-the Weight Efficacy Lifestyle Questionnaire-were associated with network topology within two sets of brain regions (regions of interest [ROIs] 1 and 2) in a group of older adults with obesity. These previously identified brain regions were shown in a different cohort of older adults to be critical for discriminating weight loss success and failure.

METHODS

Baseline functional magnetic resonance imaging data (resting state and food cue task) were collected in a novel cohort of 67 older adults with obesity (65-85 years, BMI = 35-42 kg/m² ) participating in an 18-month randomized clinical trial on weight regain.

RESULTS

The Power of Food Scale was most related to ROI 1, which includes the visual cortex and sensorimotor processing areas during only the food cue state. During both the food cue and resting conditions, the Weight Efficacy Lifestyle Questionnaire was associated with ROI 2, which includes areas of the attention network and limbic circuitry.

CONCLUSIONS

Our findings show critical, distinct links between brain network topology with self-reported measures that capture hedonic hunger and the confidence that older adults have in resisting the consumption of food because of both intrapersonal and social/environmental cues.

Using Low-Dimensional Manifolds to Map Relationships Between Dynamic Brain Networks

As the field of dynamic brain networks continues to expand, new methods are needed to allow for optimal handling and understanding of this explosion in data. We propose here a novel approach that embeds dynamic brain networks onto a two-dimensional (2D) manifold based on similarities and differences in network organization. Each brain network is represented as a single point on the low dimensional manifold with networks of similar topology being located in close proximity. The rich spatio-temporal information has great potential for visualization, analysis, and interpretation of dynamic brain networks. The fact that each network is represented by a single point makes it possible to switch between the low-dimensional space and the full connectivity of any given brain network. Thus, networks in a specific region of the low-dimensional space can be examined to identify network features, such as the location of brain network hubs or the interconnectivity between brain circuits. In this proof-of-concept manuscript, we show that these low dimensional manifolds contain meaningful information, as they were able to successfully discriminate between cognitive tasks and study populations. This work provides evidence that embedding dynamic brain networks onto low dimensional manifolds has the potential to help us better visualize and understand dynamic brain networks with the hope of gaining a deeper understanding of normal and abnormal brain dynamics.

Analysis of brain subnetworks within the context of their whole-brain networks

Analyzing the structure and function of the brain from a network perspective has increased considerably over the past two decades, with regional subnetwork analyses becoming prominent in the recent literature. However, despite the fact that the brain, as a complex system of interacting subsystems (i.e., subnetworks), cannot be fully understood by analyzing its constituent parts as independent elements, most studies extract subnetworks from the whole and treat them as independent networks. This approach entails neglecting their interactions with other brain regions and precludes identifying potential compensatory mechanisms outside the analyzed subnetwork. In this study, using simulated and empirical data, we show that the analysis of brain subnetworks within the context of their whole-brain networks, that is, including their interactions with other brain regions, can yield different outcomes when compared to analyzing them as independent networks. We also provide a multivariate mixed-effects modeling framework that allows analyzing subnetworks within the context of their whole-brain networks, and show that it can better disentangle global (whole-brain) and local (subnetwork) differences when compared to standard t-test analyses. T-test analyses may produce misleading results in identifying complex global and local level differences. The provided multivariate model is an extension of a previously developed model for global, system-level hypotheses about the brain. The modified version detailed here provides the same utilities as the original model-quantifying the relationship between phenotypes and brain connectivity, comparing brain networks among groups, predicting brain connectivity from phenotypes, and simulating brain networks-but for local, subnetwork-level hypotheses.

A MATLAB toolbox for multivariate analysis of brain networks

Complex brain networks formed via structural and functional interactions among brain regions are believed to underlie information processing and cognitive function. A growing number of studies indicate that altered brain network topology is associated with physiological, behavioral, and cognitive abnormalities. Graph theory is showing promise as a method for evaluating and explaining brain networks. However, multivariate frameworks that provide statistical inferences about how such networks relate to covariates of interest, such as disease phenotypes, in different study populations are yet to be developed. We have developed a freely available MATLAB toolbox with a graphical user interface that bridges this important gap between brain network analyses and statistical inference. The modeling framework implemented in this toolbox utilizes a mixed-effects multivariate regression framework that allows assessing brain network differences between study populations as well as assessing the effects of covariates of interest such as age, disease phenotype, and risk factors on the density and strength of brain connections in global (i.e., whole-brain) and local (i.e., subnetworks) brain networks. Confounding variables, such as sex, are controlled for through the implemented framework. A variety of neuroimaging data such as fMRI, EEG, and DTI can be analyzed with this toolbox, which makes it useful for a wide range of studies examining the structure and function of brain networks. The toolbox uses SAS, R, or Python (depending on software availability) to perform the statistical modeling. We also provide a clustering-based data reduction method that helps with model convergence and substantially reduces modeling time for large data sets.