Gibbs distribution for statistical analysis of graphical data with a sample application to fcMRI brain images

An executive-functions-based reading training enhances sensory-motor systems integration during reading fluency in children with dyslexia

The Simple View of Reading model suggests that intact language processing and word decoding lead to proficient reading comprehension, with recent studies pointing at executive functions as an important component contributing to reading proficiency. Here, we aimed to determine the underlying mechanism(s) for these changes. Participants include 120 8- to 12-year-old children (n = 55 with dyslexia, n = 65 typical readers) trained on an executive functions-based reading program, including pre/postfunctional MRI and behavioral data collection. Across groups, improved word reading was related to stronger functional connections within executive functions and sensory networks. In children with dyslexia, faster and more accurate word reading was related to stronger functional connections within and between sensory networks. These results suggest greater synchronization of brain systems after the intervention, consistent with the "neural noise" hypothesis in children with dyslexia and support the consideration of including executive functions as part of the Simple View of Reading model.

Cognitive deficits and altered functional brain network organization in pediatric brain tumor patients

Survivors of pediatric brain tumors experience significant cognitive deficits from their diagnosis and treatment. The exact mechanisms of cognitive injury are poorly understood, and validated predictors of long-term cognitive outcome are lacking. Resting state functional magnetic resonance imaging allows for the study of the spontaneous fluctuations in bulk neural activity, providing insight into brain organization and function. Here, we evaluated cognitive performance and functional network architecture in pediatric brain tumor patients. Forty-nine patients (7-18 years old) with a primary brain tumor diagnosis underwent resting state imaging during regularly scheduled clinical visits. All patients were tested with a battery of cognitive assessments. Extant data from 139 typically developing children were used as controls. We found that obtaining high-quality imaging data during routine clinical scanning was feasible. Functional network organization was significantly altered in patients, with the largest disruptions observed in patients who received propofol sedation. Awake patients demonstrated significant decreases in association network segregation compared to controls. Interestingly, there was no difference in the segregation of sensorimotor networks. With a median follow-up of 3.1 years, patients demonstrated cognitive deficits in multiple domains of executive function. Finally, there was a weak correlation between decreased default mode network segregation and poor picture vocabulary score. Future work with longer follow-up, longitudinal analyses, and a larger cohort will provide further insight into this potential predictor.

Comparison of Resting State Functional Connectivity in Persons With and Without HIV: A Cross-sectional Study

BACKGROUND

This study examined the effects of human immunodeficiency virus (HIV) on resting state functional connectivity (RSFC) in a large cohort of people with HIV (PWH) and healthy controls without HIV (PWoH). Within PWH analyses focused on the effects of viral suppression and cognitive impairment on RSFC.

METHODS

A total of 316 PWH on stable combination antiretroviral therapy and 209 demographically matched PWoH were scanned at a single institution. Effects of the virus were examined by grouping PWH by detectable (viral load > 20 copies/mL; VLD) and undetectable (VLU) viral loads and as being cognitively impaired (CI) (Global Deficit Score ≥ 0.5) or cognitively normal (CN). Regression analysis, object oriented data analysis, and spring embedded graph models were applied to RSFC measures from 298 established brain regions of interest comprising 13 brain networks to examine group differences.

RESULTS

No significant RSFC differences were observed between PWH and PWoH. Within PWH, there were no significant differences in RSFC between VLD and VLU subgroups and CI and CN subgroups.

CONCLUSIONS

There were no significant effects of HIV on RSFC in our relatively large cohort of PWH and PWoH. Future studies could increase the sample size and combine with other imaging modalities.

Preoperative functional connectivity by magnetic resonance imaging for refractory neocortical epilepsy

Objective

Patients with refractory epilepsy experience extensive and invasive clinical testing for seizure onset zones treatable by surgical resection. However, surgical resection can fail to provide therapeutic benefit, and patients with neocortical epilepsy have the poorest therapeutic outcomes. This case series studied patients with neocortical epilepsy who were referred for surgical treatment. Prior to surgery, patients volunteered for resting-state functional magnetic resonance imaging (rs-fMRI) in addition to imaging for the clinical standard of care. This work examined the variability of functional connectivity in patients, estimated from rs-fMRI, for associations with surgical outcomes.

Methods

This work examined pre-operative structural imaging, pre-operative rs-fMRI, and post-operative structural imaging from seven epilepsy patients. Review of the clinical record provided Engel classifications for surgical outcomes. A novel method assessed pre-operative rs-fMRI from patients using comparative rs-fMRI from a large cohort of healthy control subjects and estimated Gibbs distributions for functional connectivity in patients compared to healthy controls.

Results

Three patients had Engel classification Ia, one patient had Engel classification IIa, and three patients had Engel classification IV. Metrics for variability of functional connectivity, including absolute differences of the functional connectivity of each patient from healthy control averages and probabilistic scores for absolute differences, were higher for patients classified as Engel IV, for whom epilepsy surgery provided no meaningful improvement.

Significance

This work continues on-going efforts to use rs-fMRI to characterize abnormal functional connectivity in the brain. Preliminary evidence indicates that the topography of variant functional connectivity in epilepsy patients may be clinically relevant for identifying patients unlikely to have favorable outcomes after epilepsy surgery. Widespread topographic variations of functional connectivity also support the hypothesis that epilepsy is a disease of brain resting-state networks.

Clustering of heterogeneous populations of networks

Statistical methods for reconstructing networks from repeated measurements typically assume that all measurements are generated from the same underlying network structure. This need not be the case, however. People's social networks might be different on weekdays and weekends, for instance. Brain networks may differ between healthy patients and those with dementia or other conditions. Here we describe a Bayesian analysis framework for such data that allows for the fact that network measurements may be reflective of multiple possible structures. We define a finite mixture model of the measurement process and derive a Gibbs sampling procedure that samples exactly from the full posterior distribution of model parameters. The end result is a clustering of the measured networks into groups with similar structure. We demonstrate the method on both real and synthetic network populations.

Functional Connectivity Decreases with Metabolic Stress in Sickle Cell Disease

OBJECTIVE

Children with sickle cell disease (SCD) experience cognitive deficits even when unaffected by stroke. Using functional connectivity magnetic resonance imaging (MRI) as a potential biomarker of cognitive function, we tested our hypothesis that children with SCD would have decreased functional connectivity, and that children experiencing the greatest metabolic stress, indicated by elevated oxygen extraction fraction, would have the lowest connectivity.

METHODS

We prospectively obtained brain MRIs and cognitive testing in healthy controls and children with SCD.

RESULTS

We analyzed data from 60 participants (20 controls and 40 with sickle cell disease). There was no difference in global cognition or cognitive subdomains between cohorts. However, we found decreased functional connectivity within the sensory-motor, lateral sensory-motor, auditory, salience, and subcortical networks in participants with SCD compared with controls. Further, as white matter oxygen extraction fraction increased, connectivity within the visual (p = 0.008, parameter estimate = -0.760 [95% CI = -1.297, -0.224]), default mode (p = 0.012, parameter estimate = -0.417 [95% CI = -0.731, -0.104]), and cingulo-opercular (p = 0.009, parameter estimate = -0.883 [95% CI = -1.517, -0.250]) networks decreased.

INTERPRETATION

We conclude that there is diminished functional connectivity within these anatomically contiguous networks in children with SCD compared with controls, even when differences are not seen with cognitive testing. Increased white matter oxygen extraction fraction was associated with decreased connectivity in select networks. These data suggest that elevated oxygen extraction fraction and disrupted functional connectivity are potentially presymptomatic neuroimaging biomarkers for cognitive decline in SCD. ANN NEUROL 2020;88:995-1008.

Regional, not global, functional connectivity contributes to isolated focal dystonia

OBJECTIVE

To test the hypothesis that there is shared regional or global functional connectivity dysfunction in a large cohort of patients with isolated focal dystonia affecting different body regions compared to control participants. In this case-control study, we obtained resting-state MRI scans (three or four 7.3-minute runs) with eyes closed in participants with focal dystonia (cranial [17], cervical [13], laryngeal [18], or limb [10]) and age- and sex-matched controls.

METHODS

Rigorous preprocessing for all analyses was performed to minimize effect of head motion during scan acquisition (dystonia n = 58, control n = 47 analyzed). We assessed regional functional connectivity by computing a seed-correlation map between putamen, pallidum, and sensorimotor cortex and all brain voxels. We assessed significant group differences on a cluster-wise basis. In a separate analysis, we applied 300 seed regions across the cortex, cerebellum, basal ganglia, and thalamus to comprehensively sample the whole brain. We obtained participant whole-brain correlation matrices by computing the correlation between seed average time courses for each seed pair. Weighted object-oriented data analysis assessed group-level whole-brain differences.

RESULTS

Participants with focal dystonia had decreased functional connectivity at the regional level, within the striatum and between lateral primary sensorimotor cortex and ventral intraparietal area, whereas whole-brain correlation matrices did not differ between focal dystonia and control groups. Rigorous quality control measures eliminated spurious large-scale functional connectivity differences between groups.

CONCLUSION

Regional functional connectivity differences, not global network level dysfunction, contributes to common pathophysiologic mechanisms in isolated focal dystonia. Rigorous quality control eliminated spurious large-scale network differences between patients with focal dystonia and control participants.

Little Change in Functional Brain Networks Following Acute Levodopa in Drug-Naïve Parkinson's Disease

OBJECTIVE

The objective of this study was to investigate the effects of levodopa on functional brain networks in Parkinson's disease.

METHODS

We acquired resting state functional magnetic resonance imaging in 30 drug-naïve participants with Parkinson's disease and 20 age-matched healthy controls. Each participant was studied following administration of a single oral dose of either levodopa or placebo in a randomized, double-blind, crossover design.

RESULTS

The greatest observed differences in functional connectivity were between Parkinson's disease versus control participants, independent of pharmacologic intervention. By contrast, the effects of levodopa were much smaller and detectable only in the Parkinson's disease group. Moreover, although levodopa administration in the Parkinson's disease group measurably improved motor performance, it did not increase the similarity of functional connectivity in Parkinson's disease to the control group.

CONCLUSIONS

We found that a single, small dose of levodopa did not normalize functional connectivity in drug-naïve Parkinson's disease. © 2019 International Parkinson and Movement Disorder Society.

Detecting associations between intact connectomes and clinical covariates using recursive partitioning object-oriented data analysis

Many neuroscientists are interested in how connectomes (graphical representations of functional connectivity between areas of the brain) change in relation to covariates. In statistics, changes like this are analyzed using regression, where the outcomes or dependent variables are regressed onto the covariates. However, when the outcome is a complex object, such as connectome graphs, classical regression models cannot be used. The regression approach developed here to work with complex graph outcomes combines recursive partitioning with the Gibbs distribution. We will only discuss the application to connectomes, but the method is generally applicable to any graphical outcome. The method, called Gibbs-RPart, partitions the covariate space into a set of nonoverlapping regions such that the connectomes within regions are more similar than they are to the connectomes in other regions. This paper extends the object-oriented data analysis paradigm for graph-valued data based on the Gibbs distribution, which we have applied previously to hypothesis testing to compare populations of connectomes from distinct groups (see the work of La Rosa et al).

Emergent Functional Network Effects in Parkinson Disease

The hallmark pathology underlying Parkinson disease (PD) is progressive synucleinopathy, beginning in caudal brainstem that later spreads rostrally. However, the primarily subcortical pathology fails to account for the wide spectrum of clinical manifestations in PD. To reconcile these observations, resting-state functional connectivity (FC) can be used to examine dysfunction across distributed brain networks. We measured FC in a large, single-site study of nondemented PD (N = 107; OFF medications) and healthy controls (N = 46) incorporating rigorous quality control measures and comprehensive sampling of cortical, subcortical and cerebellar regions. We employed novel statistical approaches to determine group differences across the entire connectome, at the network-level, and for select brain regions. Group differences respected well-characterized network delineations producing a striking "block-wise" pattern of network-to-network effects. Surprisingly, these results demonstrate that the greatest FC differences involve sensorimotor, thalamic, and cerebellar networks, with notably smaller striatal effects. Split-half replication demonstrates the robustness of these results. Finally, block-wise FC correlations with behavior suggest that FC disruptions may contribute to clinical manifestations in PD. Overall, these results indicate a concerted breakdown of functional network interactions, remote from primary pathophysiology, and suggest that FC deficits in PD are related to emergent network-level phenomena rather than focal pathology.

The power of language: Functional brain network topology of deaf and hearing in relation to sign language experience

Prolonged auditory sensory deprivation leads to brain reorganization. This is indicated by functional enhancement in remaining sensory systems and known as cross-modal plasticity. In this study we investigated differences in functional brain network topology between deaf and hearing individuals. We also studied altered functional network responses between deaf and hearing individuals with a recording paradigm containing an eyes-closed and eyes-open condition. Electroencephalography activity was recorded in a group of sign language-trained deaf (N = 71) and hearing people (N = 122) living in rural Africa. Functional brain networks were constructed from the functional connectivity between fourteen electrodes distributed over the scalp. Functional connectivity was quantified with the phase lag index based on bandpass filtered epochs of brain signal. We studied the functional connectivity between the auditory, somatosensory and visual cortex and performed whole-brain minimum spanning tree analysis to capture network backbone characteristics. Functional connectivity between different regions involved in sensory information processing tended to be stronger in deaf people during the eyes-closed condition in both the alpha and beta frequency band. Furthermore, we found differences in functional backbone topology between deaf and hearing individuals. The backbone topology altered during transition from the eyes-closed to eyes-open condition irrespective of deafness, but was more pronounced in deaf individuals. The transition of backbone strength was different between individuals with congenital, pre-lingual or post-lingual deafness. Functional backbone characteristics correlated with the experience of sign language. Overall, our study revealed more insights in functional network reorganization caused by auditory deprivation and cross-modal plasticity. It further supports the idea of a brain plasticity potential in deaf and hearing people. The association between network organization and acquired sign language experience reflects the ability of ongoing brain adaptation in people with hearing disabilities.

Modified structural network backbone in the contralesional hemisphere chronically after stroke in rat brain

Functional outcome after stroke depends on the local site of ischemic injury and on remote effects within connected networks, frequently extending into the contralesional hemisphere. However, the pattern of large-scale contralesional network remodeling remains largely unresolved. In this study, we applied diffusion-based tractography and graph-based network analysis to measure structural connectivity in the contralesional hemisphere chronically after experimental stroke in rats. We used the minimum spanning tree method, which accounts for variations in network density, for unbiased characterization of network backbones that form the strongest connections in a network. Ultrahigh-resolution diffusion MRI scans of eight post-mortem rat brains collected 70 days after right-sided stroke were compared against scans from 10 control brains. Structural network backbones of the left (contralesional) hemisphere, derived from 42 atlas-based anatomical regions, were found to be relatively stable across stroke and control animals. However, several sensorimotor regions showed increased connection strength after stroke. Sensorimotor function correlated with specific contralesional sensorimotor network backbone measures of global integration and efficiency. Our findings point toward post-stroke adaptive reorganization of the contralesional sensorimotor network with recruitment of distinct sensorimotor regions, possibly through strengthening of connections, which may contribute to functional recovery.

Influences on the Test-Retest Reliability of Functional Connectivity MRI and its Relationship with Behavioral Utility

Best practices are currently being developed for the acquisition and processing of resting-state magnetic resonance imaging data used to estimate brain functional organization—or “functional connectivity.” Standards have been proposed based on test–retest reliability, but open questions remain. These include how amount of data per subject influences whole-brain reliability, the influence of increasing runs versus sessions, the spatial distribution of reliability, the reliability of multivariate methods, and, crucially, how reliability maps onto prediction of behavior. We collected a dataset of 12 extensively sampled individuals (144 min data each across 2 identically configured scanners) to assess test–retest reliability of whole-brain connectivity within the generalizability theory framework. We used Human Connectome Project data to replicate these analyses and relate reliability to behavioral prediction. Overall, the historical 5-min scan produced poor reliability averaged across connections. Increasing the number of sessions was more beneficial than increasing runs. Reliability was lowest for subcortical connections and highest for within-network cortical connections. Multivariate reliability was greater than univariate. Finally, reliability could not be used to improve prediction; these findings are among the first to underscore this distinction for functional connectivity. A comprehensive understanding of test–retest reliability, including its limitations, supports the development of best practices in the field.

Behavioral interventions for reducing head motion during MRI scans in children

A major limitation to structural and functional MRI (fMRI) scans is their susceptibility to head motion artifacts. Even submillimeter movements can systematically distort functional connectivity, morphometric, and diffusion imaging results. In patient care, sedation is often used to minimize head motion, but it incurs increased costs and risks. In research settings, sedation is typically not an ethical option. Therefore, safe methods that reduce head motion are critical for improving MRI quality, especially in high movement individuals such as children and neuropsychiatric patients. We investigated the effects of (1) viewing movies and (2) receiving real-time visual feedback about head movement in 24 children (5-15 years old). Children completed fMRI scans during which they viewed a fixation cross (i.e., rest) or a cartoon movie clip, and during some of the scans they also received real-time visual feedback about head motion. Head motion was significantly reduced during movie watching compared to rest and when receiving feedback compared to receiving no feedback. However, these results depended on age, such that the effects were largely driven by the younger children. Children older than 10 years showed no significant benefit. We also found that viewing movies significantly altered the functional connectivity of fMRI data, suggesting that fMRI scans during movies cannot be equated to standard resting-state fMRI scans. The implications of these results are twofold: (1) given the reduction in head motion with behavioral interventions, these methods should be tried first for all clinical and structural MRIs in lieu of sedation; and (2) for fMRI research scans, these methods can reduce head motion in certain groups, but investigators must keep in mind the effects on functional MRI data.

Cognitive Training for Adults With Bothersome Tinnitus: A Randomized Clinical Trial

Importance

Individuals with tinnitus have poorer working memory, slower processing speeds and reaction times, and deficiencies in selective attention, all of which interfere with readiness and performance. Brain Fitness Program-Tinnitus (BFP-T) is a cognitive training program specially designed to exploit neuroplasticity for preservation and expansion of cognitive health in adults with tinnitus.

Objective

To evaluate the effect of the BFP-T on tinnitus.

Design, Setting, and Participants

This open-label, intention-to-treat randomized clinical trial prescreened 191 patients with tinnitus and 64 healthy controls (HCs) from June 1, 2012, through October 31, 2013. Participants were 40 adults with bothersome tinnitus for more than 6 months and 20 age-matched HCs. Patients with tinnitus were randomized to a BFP-T or non-BFP-T control group. The BFP-T was completed online, and assessments were completed at Washington University School of Medicine.

Interventions

Participants in the intervention group were required to complete the BFP-T online 1 hour per day 5 days per week for 8 weeks. Tinnitus assessment, neuroimaging, and cognitive testing were completed at baseline and 8 weeks later. The HCs underwent neuroimaging and cognitive assessments.

Main Outcomes and Measures

The primary outcome measure was the change in Tinnitus Handicap Inventory (THI) score. Behavioral measures, neuroimaging, and cognitive tests were performed before and after the intervention.

Results

A total of 40 patients with tinnitus and 20 HCs participated in the study (median [range] age, 56 [35-64] years in the BFP-T group, 52 [24-64] years in the non-BFP-T group, and 50 [30-64] years in the HC group; 13 [65%] in the BFP-T group, 14 [70%] in the non-BFP-T group, and 13 [65%] in the HC group were males; and 16 [80%] in the BFP-T group, 16 [80%] in the non-BFP-T group, and 15 [75%] in the HC group were white). There was a reduction in the THI score in the BFP-T group (median, 7; range, -16 to 64) and non-BFP-T group (median, 11; range, -6 to 26), but this reduction was not significantly different between the 2 groups (median difference, 0; 95% CI, -10 to 8). There was no difference in cognitive test scores and other behavioral measures. There was a significant difference between baseline and follow-up in functional connectivity in cognitive control regions in the BFP-T group but not in HCs or individuals with untreated tinnitus. Of the 20 patients in the BFP-T group, 10 (50%) self-reported improvement attributable to the intervention, and 6 (30%) reported to be much improved in the domains of tinnitus, memory, attention, and concentration.

Conclusions and Relevance

These findings suggest that the computer-based cognitive training program is associated with self-reported changes in attention, memory, and perception of tinnitus. A possible mechanistic explanation for these changes could be neuroplastic changes in key brain systems involved in cognitive control. Cognitive training programs might have a role in the future treatment of patients with tinnitus.

Trial Registration

clinicaltrials.gov Identifier: NCT01458821.

The Feasibility of Using Metacognitive Strategy Training to Improve Cognitive Performance and Neural Connectivity in Women with Chemotherapy-Induced Cognitive Impairment

OBJECTIVE

To evaluate the feasibility and preliminary effect of metacognitive strategy training (MCST) on cognitive performance and on neural connectivity in the frontoparietal network in women with chemotherapy-induced cognitive impairment (CICI) following treatment for breast cancer.

METHODS

A single-group pre/post study was conducted. After completing the baseline assessment battery and neuroimaging, the participants completed a 12-session MCST intervention. Following the completion of the intervention, the subjects completed the same assessment battery and neuroimaging as was completed at baseline within 4 weeks after the intervention. The key inclusion/exclusion criteria for this study were: completed chemotherapy for treatment of breast cancer, no other neurological or psychiatric diagnoses, self-reported CICI, and no contraindications to the use of MRI.

RESULTS

MCST had a small-to-large positive effect on all primary (cognitive) and secondary (quality of life and psychosocial) behavioral outcome measures (r = -0.12 to -0.88). There was also a positive change in functional connectivity in a frontoparietal cognitive control network connection in 6 of the 10 subjects, which was correlated to changes in the behavioral measures.

CONCLUSIONS

This study found that MCST was associated with a positive effect on cognitive performance and neural connectivity in women with CICI following treatment for breast cancer.