Graph theory and network topological metrics may be the potential biomarker in Parkinson’s disease

Combining radiomics and connectomics in MRI studies of the human brain: A systematic literature review

Advances in MRI techniques continue to open new avenues to investigate the structure and function of the human brain. Radiomics, involving the extraction of quantitative image features, and connectomics, involving the estimation of structural and functional neural connections, from large amounts and different types of MRI data sets, represent two key research areas for advancing neuroimaging while exploiting progress in computational and theoretical modelling applied to MRI. This systematic literature review aimed at exploring the combination of radiomics and connectomics in human brain MRI studies, highlighting how the combination of these approaches can provide novel or additional insights into the human brain under normal and pathological conditions. The review was conducted according to the Preferred Reported Item for Systematic Reviews and Meta-Analyses (PRISMA) statement, seeking documents from Scopus and PubMed archives. Eleven studies (out of the initial 675 records) have met the established criteria and reported combined approaches from radiomics and connectomics. Three subgroups of approaches were identified, based on the MRI modalities used to obtain radiomic and connectomic features. The first group of 3 studies combined radiomics and connectomics applied to structural MRI (sMRI) data sets; the second group of 5 studies combined radiomics applied to sMRI data and connectomics applied to diffusion (dMRI) and/or functional MRI (fMRI) data sets; the third group of 3 studies combined radiomics and connectomics applied to fMRI. This review highlighted the recent growing interest in combining MRI-based radiomics and connectomics to explore the human brain for neurological, psychiatric, and oncological conditions. Current methodologies and challenges were discussed, pointing out future research directions to improve or standardize these approaches and the gaps to be filled to advance the field.

High-Order Graphical Topology Analysis of Brain Functional Connectivity Networks Using fMRI

The brain connectivity network can be represented as a graph to reveal its intrinsic topological properties. While classical graph theory provides a powerful framework for examining brain connectivity patterns, it often focuses on low-order graphical indicators and pays less attention to high-order topological metrics, which are crucial to the comprehensive understanding of brain topology. In this paper, we capture high-order topological features via a graphical topology analysis framework for brain connectivity networks derived from functional Magnetic Resonance Imaging (fMRI). Several high-order metrics are examined across varying sparsity levels of binary graphs to trace the evolution of brain networks. Topological phase transitions are primarily investigated that reflect brain criticality, and a novel indicator called "redundant energy" is proposed to measure the chaos level of the brain. Extensive experiments on diverse datasets from healthy controls validate the reproducibility and generalizability of our framework. The results demonstrate that around critical points, classical graph theoretical indicators change sharply, driven by crucial brain regions that have high node curvatures. Further investigations on fMRI of subjects with and without Parkinson's disease uncover significant alterations in high-order topological features which are further associated with the severity of the disease. This study provides a fresh perspective on studying topological architectures of the brain, with the potential to expand our comprehension on brain function in both healthy and diseased states.

Impairment of white matter microstructure and structural network in patients with systemic lupus erythematosus

OBJECTIVE

The study aimed to investigate the damage of white matter (WM) microstructure and structural network in patients with systemic lupus erythematosus (SLE) using diffusion tensor imaging.

METHODS

Tract-based spatial statistics (TBSS) were used to compare the difference in WM fractional anisotropy (FA) between SLE and HCs groups. The differences in WM networks between groups are compared using graph theory. The correlation between clinical data and SLE abnormal WM structure and network was analysed.

RESULTS

The sample included 140 SLE patients and 111 healthy controls (HCs). Due to data missing, excessive head movement amplitude, failure of quality control and other reasons, 127 cases of SLE (103 females, mean age 29.84 years (SD 7.00), median years of education 12.00, interquartile range(9.00,15.00) and a median course of disease (month) 12.00, interquartile range (3.00,24.00)) and 102 cases of HCs (76 females, mean age 30.63 years (SD 7.24), median years of education 15.00, interquartile range(12.00,16.00)) were finally included in the study. The FA values of 5 clusters involving the right retrolenticular part of the internal capsule (RLIC), the genu of corpus callosum (GCC), the body of corpus callosum, the splenium of corpus callosum (SCC), were significantly lower in the SLE group compared to the HCs (P < 0.05 with threshold-free cluster enhancement corrected). The SLEDAI showed a negative correlation with FA in GCC, and HAMD showed a negative correlation with FA in SCC and right RLIC (P < 0.05). Regarding network indicators, Cp, Eglob, and Eloc were significantly decreased, while Lp was significantly increased in the SLE group. The degree centrality (DC) of 6 brain regions and the Enodal of 17 regions were significantly lower in the SLE group. SLEDAI showed a negative correlation with the area under the curve (AUC) of DC and Enodal in the left inferior frontal gyrus triangular (q < 0.05 with false discovery rate corrected), while MMSE showed a positive correlation with the Enodal in the left hippocampus (P < 0.05).

CONCLUSION

The study concludes that changes in WM microstructure and its structural network may contribute to the development of severe neuropsychiatric symptoms in SLE patients. These changes may be the basis of brain damage that leads to the development of NPSLE from SLE without major neuropsychiatric manifestations.

Analyzing Information Exchange in Parkinson's Disease via Eigenvector Centrality: A Source-Level Magnetoencephalography Study

Background: Parkinson's disease (PD) is a progressive neurodegenerative disorder that manifests through motor and non-motor symptoms. Understanding the alterations in brain connectivity associated with PD remains a challenge that is crucial for enhancing diagnosis and clinical management. Methods: This study utilized Magnetoencephalography (MEG) to investigate brain connectivity in PD patients compared to healthy controls (HCs) by applying eigenvector centrality (EC) measures across different frequency bands. Results: Our findings revealed significant differences in EC between PD patients and HCs in the alpha (8-12 Hz) and beta (13-30 Hz) frequency bands. To go into further detail, in the alpha frequency band, PD patients in the frontal lobe showed higher EC values compared to HCs. Additionally, we found statistically significant correlations between EC measures and clinical impairment scores (UPDRS-III). Conclusions: The proposed results suggest that MEG-derived EC measures can reveal important alterations in brain connectivity in PD, potentially serving as biomarkers for disease severity.

Levodopa therapy affects brain functional network dynamics in Parkinson's disease

Levodopa (L-dopa) therapy is the most effective pharmacological treatment for motor symptoms of Parkinson's disease (PD). However, its effect on brain functional network dynamics is still unclear. Here, we recruited 26 PD patients and 24 healthy controls, and acquired their resting-state functional MRI data before (PD-OFF) and after (PD-ON) receiving 400 mg L-dopa. Using the independent component analysis and the sliding-window approach, we estimated the dynamic functional connectivity (dFC) and examined the effect of L-dopa on the temporal properties of dFC states, the variability of dFC and functional network topological organization. We found that PD-ON showed decreased mean dwell time in sparsely connected State 2 than PD-OFF, the transformation of the dFC state is more frequent and the variability of dFC was decreased within the auditory network and sensorimotor network in PD-ON. Our findings provide new insights to understand the dynamic neural activity induced by L-dopa therapy in PD patients.

Explainable biology for improved therapies in precision medicine: AI is not enough

Technological advances and high-throughput bio-chemical assays are rapidly changing ways how we formulate and test biological hypotheses, and how we treat patients. Most complex diseases arise on a background of genetics, lifestyle and environment factors, and manifest themselves as a spectrum of symptoms. To fathom intricate biological processes and their changes from healthy to disease states, we need to systematically integrate and analyze multi-omics datasets, ontologies, and diverse annotations. Without proper management of such complex biological and clinical data, artificial intelligence (AI) algorithms alone cannot be effectively trained, validated, and successfully applied to provide trustworthy and patient-centric diagnosis, prognosis and treatment. Precision medicine requires to use multi-omics approaches effectively, and offers many opportunities for using AI, "big data" analytics, and integrative computational biology workflows. Advances in optical and biochemical assay technologies including sequencing, mass spectrometry and imaging modalities have transformed research by empowering us to simultaneously view all genes expressed, identify proteome-wide changes, and assess interacting partners of each individual protein within a dynamically changing biological system, at an individual cell level. While such views are already having an impact on our understanding of healthy and disease conditions, it remains challenging to extract useful information comprehensively and systematically from individual studies, ensure that signal is separated from noise, develop models, and provide hypotheses for further research. Data remain incomplete and are often poorly connected using fragmented biological networks. In addition, statistical and machine learning models are developed at a cohort level and often not validated at the individual patient level. Combining integrative computational biology and AI has the potential to improve understanding and treatment of diseases by identifying biomarkers and building explainable models characterizing individual patients. From systematic data analysis to more specific diagnostic, prognostic and predictive biomarkers, drug mechanism of action, and patient selection, such analyses influence multiple steps from prevention to disease characterization, and from prognosis to drug discovery. Data mining, machine learning, graph theory and advanced visualization may help identify diagnostic, prognostic and predictive biomarkers, and create causal models of disease. Intertwining computational prediction and modeling with biological experiments leads to faster, more biologically and clinically relevant discoveries. However, computational analysis results and models are going to be only as accurate and useful as correct and comprehensive are the networks, ontologies and datasets used to build them. High quality, curated data portals provide the necessary foundation for translational research. They help to identify better biomarkers, new drugs, precision treatments, and should lead to improved patient outcomes and their quality of life. Intertwining computational prediction and modeling with biological experiments, efficiently and effectively leads to more useful findings faster.

Functional connectivity compensation in Parkinson's disease with freezing of gait

Freezing of gait (FOG) is a disabling motor symptom prevalent in patients with Parkinson's disease (PD); however, its pathophysiological mechanisms are poorly understood. This study aimed to investigate whole-brain functional connectivity (FC) pattern alterations in PD patients with FOG. A total of 18 PD patients, 10 with FOG (PD-FOG) and 8 without FOG (PD-nFOG), and 10 healthy controls were enrolled. High-resolution 3D T1-weighted and resting-state functional MRI (rs-fMRI) data were obtained from all participants. The groups' internetwork connectivity differences were explored with rs-fMRI FC using seed-based analysis and graph theory. Multiple linear regression analysis estimated the relationship between FC changes and clinical measurements. Rs-fMRI analysis demonstrated alterations in FC in various brain regions between the three groups. Freezing of Gait Questionnaire severity was correlated with decreased brain functional connection between Vermis12 and the left temporal occipital fusiform cortex (r = -0.82, P < .001). Graph theory topological metrics indicated a decreased clustering coefficient in the right superior temporal gyrus in the PD-nFOG group. PD-FOG patients exhibited a compensatory increase in connectivity between the left inferior frontal gyrus language network and the postcentral gyrus compared to PD-nFOG patients. Further, the decreased connection between Vermis 12 and the left temporal occipital fusiform cortex may serve as a potential neuroimaging biomarker for tracking PD-FOG and distinguishing between PD subtypes.

Brain networks in newborns and infants with and without sensorineural hearing loss: A functional near-infrared spectroscopy study

BACKGROUND

Understanding the impact of early sensory deficits on brain development is essential for understanding developmental processes and developing potential interventions. While previous studies have looked into the impact of prenatal experiences on language development, there is a lack of research on how these experiences affect early language and brain function development in individuals with sensorineural hearing loss (SNHL).

AIM

To investigate SNHL effects on early brain development and connectivity in 4-month-olds vs healthy newborns and controls.

METHODS

The research involved analyzing the functional brain networks of 65 infants, categorized into three groups: 28 healthy newborns, 22 4-month-old participants with SNHL, and 15 age-matched healthy participants. The resting-state functional connectivity was measured and compared between the groups using functional near-infrared spectroscopy and graph theory to assess the brain network properties.

RESULTS

Significant differences were found in resting-state functional connectivity between participants with SNHL and age-matched controls, indicating a developmental lag in brain connectivity for those with SNHL. Surprisingly, SNHL participants showed better connectivity development compared to healthy newborns, with connectivity strengths of 0.13 ± 0.04 for SNHL, 0.16 ± 0.08 for controls, and 0.098 ± 0.04 for newborns. Graph theory analysis revealed enhanced global brain network properties for the SNHL group, suggesting higher communication efficiency at 4 months. No significant differences were noted in network properties between 4-month-old SNHL participants and neonates. A unique pattern of central hubs was observed in the SNHL group, with 2 hubs in the left hemisphere compared to 6 in controls.

CONCLUSION

4-month-old infants with SNHL have a distinct brain network pattern with efficient long-distance information transmission but less effective local communication compared to age-matched controls.

Disrupted Brain Network Measures in Parkinson's Disease Patients with Severe Hyposmia and Cognitively Normal Ability

Neuroscience has revolved around brain structural changes, functional activity, and connectivity alteration in Parkinson's Disease (PD); however, how the network topology organization becomes altered is still unclear, specifically in Parkinson's patients with severe hyposmia. In this study, we have examined the functional network topological alteration in patients affected by Parkinson's Disease with normal cognitive ability (ODN), Parkinson's Disease with severe hyposmia (ODP), and healthy controls (HCs) using resting-state functional magnetic resonance imaging (rsfMRI) data. We have analyzed brain topological organization using popular graph measures such as network segregation (clustering coefficient, modularity), network integration (participation coefficient, path length), small-worldness, efficiency, centrality, and assortativity. Then, we used a feature ranking approach based on the diagonal adaptation of neighborhood component analysis, aiming to determine a graph measure that is sensitive enough to distinguish between these three different groups. We noted significantly lower segregation and local efficiency and small-worldness in ODP compared to ODN and HCs. On the contrary, we did not find differences in network integration in ODP compared to ODN and HCs, which indicates that the brain network becomes fragmented in ODP. At the brain network level, a progressive increase in the DMN (Default Mode Network) was observed from healthy controls to ODN to ODP, and a continuous decrease in the cingulo-opercular network was observed from healthy controls to ODN to ODP. Further, the feature ranking approach has shown that the whole-brain clustering coefficient and small-worldness are sensitive measures to classify ODP vs. ODN, as well as HCs. Looking at the brain regional network segregation, we have found that the cerebellum and limbic, fronto-parietal, and occipital lobes have higher ODP reductions than ODN and HCs. Our results suggest network topological measures, specifically whole-brain segregation and small-worldness decreases. At the network level, an increase in DMN and a decrease in the cingulo-opercular network could be used as biomarkers to characterize ODN and ODP.

Multimodal data fusion reveals functional and neurochemical correlates of Parkinson's disease

BACKGROUND

Neurotransmitter deficits and spatial associations among neurotransmitter distribution, brain activity, and clinical features in Parkinson's disease (PD) remain unclear. Better understanding of neurotransmitter impairments in PD may provide potential therapeutic targets. Therefore, we aimed to investigate the spatial relationship between PD-related patterns and neurotransmitter deficits.

METHODS

We included 59 patients with PD and 41 age- and sex-matched healthy controls (HCs). The voxel-wise mean amplitude of the low-frequency fluctuation (mALFF) was calculated and compared between the two groups. The JuSpace toolbox was used to test whether spatial patterns of mALFF alterations in patients with PD were associated with specific neurotransmitter receptor/transporter densities.

RESULTS

Compared to HCs, patients with PD showed reduced mALFF in the sensorimotor- and visual-related regions. In addition, mALFF alteration patterns were significantly associated with the spatial distribution of the serotonergic, dopaminergic, noradrenergic, glutamatergic, cannabinoid, and acetylcholinergic neurotransmitter systems (p < 0.05, false discovery rate-corrected).

CONCLUSIONS

Our results revealed abnormal brain activity patterns and specific neurotransmitter deficits in patients with PD, which may provide new insights into the mechanisms and potential targets for pharmacotherapy.

Limbic system plasticity after electroacupuncture intervention in knee osteoarthritis rats

Knee osteoarthritis (KOA) is characterized by debilitating pain. Electroacupuncture (EA), a traditional Chinese medical therapy, has shown promise in KOA pain management. This study investigated the therapeutic potential of EA in KOA and its impact on limbic system neural plasticity. Sixteen rats were randomly assigned into two groups: EA group and sham-EA group. EA or sham-EA interventions were administered at acupoints ST32 (Futu) and ST36 (Zusanli) for three weeks. Post-intervention resting-state fMRI was scanned, assessing parameters including Amplitude of low frequency fluctuations (ALFF), regional homogeneity (ReHo), functional connectivity (FC) and nodal characterizations of network within limbic system. The results showed that EA was strategically directed towards the limbic system, resulting in discernible alterations in neural activity, FC, and network characteristics. Our findings demonstrate that EA had a significant impact on the limbic system neural plasticity in rats with KOA, presenting a novel nonpharmacological approach for KOA treatment.

Optimization of structural connectomes and scaled patterns of structural-functional decoupling in Parkinson's disease

Parkinson's disease (PD) is manifested with disrupted topology of the structural connection network (SCN) and the functional connection network (FCN). However, the SCN and its interactions with the FCN remain to be further investigated. This multimodality study attempted to precisely characterize the SCN using diffusion kurtosis imaging (DKI) and further identify the neuropathological pattern of SCN-FCN decoupling, underscoring the neurodegeneration of PD. Diffusion-weighted imaging and resting-state functional imaging were available for network constructions among sixty-nine patients with PD and seventy demographically matched healthy control (HC) participants. The classification performance and topological prosperities of both the SCN and the FCN were analyzed, followed by quantification of the SCN-FCN couplings across scales. The SCN constructed by kurtosis metrics achieved optimal classification performance (area under the curve 0.89, accuracy 80.55 %, sensitivity 78.40 %, and specificity 80.65 %). Along with diverse alterations of structural and functional network topology, the PD group exhibited decoupling across scales including: reduced global coupling; increased nodal coupling within the sensorimotor network (SMN) and subcortical network (SN); higher intramodular coupling within the SMN and SN and lower intramodular coupling of the default mode network (DMN); decreased coupling between the modules of DMN-fronto-parietal network and DMN-visual network, but increased coupling between the SMN-SN module. Several associations between the coupling coefficient and topological properties of the SCN, as well as between network values and clinical scores, were observed. These findings validated the clinical implementation of DKI for structural network construction with better differentiation ability and characterized the SCN-FCN decoupling as supplementary insight into the pathological process underlying PD.

Analysis of Connectome Graphs Based on Boundary Scale

The purpose of this work is to advance in the computational study of connectome graphs from a topological point of view. Specifically, starting from a sequence of hypergraphs associated to a brain graph (obtained using the Boundary Scale model, BS2), we analyze the resulting scale-space representation using classical topological features, such as Betti numbers and average node and edge degrees. In this way, the topological information that can be extracted from the original graph is substantially enriched, thus providing an insightful description of the graph from a clinical perspective. To assess the qualitative and quantitative topological information gain of the BS2 model, we carried out an empirical analysis of neuroimaging data using a dataset that contains the connectomes of 96 healthy subjects, 52 women and 44 men, generated from MRI scans in the Human Connectome Project. The results obtained shed light on the differences between these two classes of subjects in terms of neural connectivity.

Functional connectome automatically differentiates multiple system atrophy (parkinsonian type) from idiopathic Parkinson's disease at early stages

Differentiating the parkinsonian variant of multiple system atrophy (MSA-P) from idiopathic Parkinson's disease (IPD) is challenging, especially in the early stages. This study aimed to investigate differences and similarities in the brain functional connectomes of IPD and MSA-P patients and use machine learning methods to explore the diagnostic utility of these features. Resting-state fMRI data were acquired from 88 healthy controls, 76 MSA-P patients, and 53 IPD patients using a 3.0 T scanner. The whole-brain functional connectome was constructed by thresholding the Pearson correlation matrices of 116 regions, and topological properties were evaluated through graph theory approaches. Connectome measurements were used as features in machine learning models (random forest [RF]/logistic regression [LR]/support vector machine) to distinguish IPD and MSA-P patients. Regarding graph metrics, early IPD and MSA-P patients shared network topological properties. Both patient groups showed functional connectivity disruptions within the cerebellum-basal ganglia-cortical network, but these disconnections were mainly in the cortico-thalamo-cerebellar circuits in MSA-P patients and the basal ganglia-thalamo-cortical circuits in IPD patients. Among the connectome parameters, t tests combined with the RF method identified 15 features, from which the LR classifier achieved the best diagnostic performance on the validation set (accuracy = 92.31%, sensitivity = 90.91%, specificity = 93.33%, area under the receiver operating characteristic curve = 0.89). MSA-P and IPD patients show similar whole-brain network topological alterations. MSA-P primarily affects cerebellar nodes, and IPD primarily affects basal ganglia nodes; both conditions disrupt the cerebellum-basal ganglia-cortical network. Moreover, functional connectome parameters showed outstanding value in the differential diagnosis of early MSA-P and IPD.

Static and dynamic topological organization of brain functional connectome in acute mild traumatic brain injury

BACKGROUND

Prior studies have detected topological changes of brain functional networks in patients with acute mild traumatic brain injury (mTBI). However, the alterations of dynamic topological characteristics in mTBI have been scarcely elucidated.

PURPOSE

To evaluate static and dynamic functional connectivity topological networks in patients with acute mTBI using resting-state functional magnetic resonance imaging (fMRI).

MATERIAL AND METHODS

A total of 55 patients with acute mTBI and 55 age-, sex-, and education-matched healthy controls (HCs) were enrolled in this study. All participants underwent resting-state fMRI scans, and data were analyzed using graph-theory methods and a sliding window approach. Post-traumatic cognitive performance and resting-state fMRI data were collected within one week after injury. Static and dynamic functional connectivity patterns were determined by independent component analysis. Spearman's correlation analysis was further performed between fMRI changes and Montreal cognitive assessment (MoCA) scores.

RESULTS

Global efficiency was lower (P = 0.02), and local efficiency (P < 0.001) and mean Cp (P < 0.001) were higher in patients with acute mTBI than in HCs. Local efficiency was correlated with visuospatial/executive performance (r = -0.421; P = 0.002) in patients with acute mTBI. Significant differences in nodal efficiency and node degree centrality (P < 0.01) were found between the mTBI and HC groups. For dynamic properties, patients with mTBI showed higher variance (P = 0.016) in global efficiency than HCs.

CONCLUSIONS

The present study shows that patients with mTBI have abnormal brain functional connectome topology, especially the dynamic graph theory characteristics, which provide new insights into the role of topological network properties in patients with acute mTBI.

Amplitude of low-frequency fluctuation-based regional radiomics similarity network: Biomarker for Parkinson's disease

Parkinson's disease (PD) is a highly heterogeneous disorder that is difficult to diagnose. Therefore, reliable biomarkers are needed. We implemented a method constructing a regional radiomics similarity network (R2SN) based on the amplitude of low-frequency fluctuation (ALFF). We classified patients with PD and healthy individuals by using a machine learning approach in accordance with the R2SN connectome. The ALFF-based R2SN exhibited great reproducibility with different brain atlases and datasets. Great classification performances were achieved both in primary (AUC = 0.85 ± 0.02 and accuracy = 0.81 ± 0.03) and independent external validation (AUC = 0.77 and accuracy = 0.70) datasets. The discriminative R2SN edges correlated with the clinical evaluations of patients with PD. The nodes of discriminative R2SN edges were primarily located in the default mode, sensorimotor, executive control, visual and frontoparietal network, cerebellum and striatum. These findings demonstrate that ALFF-based R2SN is a robust potential neuroimaging biomarker for PD and could provide new insights into connectome reorganization in PD.

Graph Theory Measures and Their Application to Neurosurgical Eloquence

Improving patient safety and preserving eloquent brain are crucial in neurosurgery. Since there is significant clinical variability in post-operative lesions suffered by patients who undergo surgery in the same areas deemed compensable, there is an unknown degree of inter-individual variability in brain 'eloquence'. Advances in connectomic mapping efforts through diffusion tractography allow for utilization of non-invasive imaging and statistical modeling to graphically represent the brain. Extending the definition of brain eloquence to graph theory measures of hubness and centrality may help to improve our understanding of individual variability in brain eloquence and lesion responses. While functional deficits cannot be immediately determined intra-operatively, there has been potential shown by emerging technologies in mapping of hub nodes as an add-on to existing surgical navigation modalities to improve individual surgical outcomes. This review aims to outline and review current research surrounding novel graph theoretical concepts of hubness, centrality, and eloquence and specifically its relevance to brain mapping for pre-operative planning and intra-operative navigation in neurosurgery.

Classification of Parkinson's disease using a region-of-interest- and resting-state functional magnetic resonance imaging-based radiomics approach

To investigate the value of combining amplitude of low-frequency fluctuations-based radiomics and the support vector machine classifier method in distinguishing patients with Parkinson's disease from healthy controls. A total of 123 patients with Parkinson's disease and 90 healthy controls from three centers with functional and structural MRI images were included in this study. We extracted radiomics features using the Brainnetome 246 atlas from the mean amplitude of low-frequency fluctuations maps. Two-sample t-tests and recursive feature elimination combined with support vector machine method were applied for feature selection and dimensionality reduction. We used support vector machine classifier to construct model and identify the discriminative features. The automated anatomical labeling 90 atlas and fivefold cross-validation were used to evaluate the robustness and generalization of the classifier. We found our model obtained a high classification performance with an accuracy of 78.07%, and AUC, sensitivity, and specificity of 0.8597, 78.80%, and 76.08%, respectively. We detected 7 discriminative brain subregions. The fivefold cross-validation and automated anatomical labeling 90 atlas also got high classification accuracy, and we found Brainnetome 246 atlas achieved a higher classification performance than the automated anatomical labeling 90 atlas both with tenfold and fivefold cross-validation. Our findings may help the early diagnosis of Parkinson's disease and provide support for research on Parkinson's disease mechanisms and clinical evaluation.

Functional connectivity of fMRI using differential covariance predicts structural connectivity and behavioral reaction times

Recordings from resting state functional Magnetic Resonance Imaging (rs-fMRI) reflect the influence of pathways between brain areas. A wide range of methods have been proposed to measure this functional connectivity (FC), but the lack of “ground truth” has made it difficult to systematically validate them. Most measures of FC produce connectivity estimates that are symmetrical between brain areas. Differential covariance (dCov) is an algorithm for analyzing FC with directed graph edges. When we applied dCov to rs-fMRI recordings from the human connectome project (HCP) and anesthetized mice, dCov-FC accurately identified strong cortical connections from diffusion Magnetic Resonance Imaging (dMRI) in individual humans and viral tract tracing in mice. In addition, those HCP subjects whose dCov-FCs were more integrated, as assessed by a graph-theoretic measure, tended to have shorter reaction times in several behavioral tests. Thus, dCov-FC was able to identify anatomically verified connectivity that yielded measures of brain integration significantly correlated with behavior.

Profiling Parkinson's disease cognitive phenotypes via resting-state magnetoencephalography

Aberrant brain oscillations are a hallmark of Parkinson's disease (PD) pathophysiology and may be related to both motor and nonmotor symptoms. Mild cognitive impairment (MCI) affects many people with PD even at the time of diagnosis and conversion risks to PD dementia (PDD) are very high. Unfortunately, pharmacotherapies are not addressing cognitive symptoms in PD. Profiling PD cognitive phenotypes (e.g., MCI, PDD, etc.) may therefore help inform future treatments. Neurophysiological methods, such as magnetoencephalography (MEG), offer the advantage of observing oscillatory patterns, whose regional and temporal profiles may elucidate how cognitive changes relate to neural mechanisms. We conducted a resting-state MEG cross-sectional study of 89 persons with PD stratified into three phenotypic groups: normal cognition, MCI, and PDD, to identify brain regions and frequencies most associated with each cognitive profile. In addition, a neuropsychological battery was administered to assess each domain of cognition. Our data showed higher power in lower frequency bands (delta and theta) observed along with more severe cognitive impairment and associated with memory, language, attention, and global cognition. Of the total 119 brain parcels assessed during source analysis, widespread group differences were found in the beta band, with significant changes mostly occurring between the normal cognition and MCI groups. Moreover, bilateral frontal and left-hemispheric regions were particularly affected in the other frequencies as cognitive decline becomes more pronounced. Our results suggest that MCI and PDD may be qualitatively distinct cognitive phenotypes, and most dramatic changes seem to have happened when the PD brain shows mild cognitive decline.NEW & NOTEWORTHY Can we better stage cognitive decline in patients with Parkinson's disease (PD)? Here, we provide evidence that mild cognitive impairment, rather than being simply a milder form of dementia, may be a qualitatively distinct phase in its development. We suggest that the most dramatic neurophysiological changes may occur during the time the PD brain transitions from normal cognition to MCI, then compensatory changes further occur as the brain "switches" to a dementia state.

Effect of deep brain stimulation on brain network and white matter integrity in Parkinson's disease

Aims

The effects of subthalamic nucleus (STN)‐deep brain stimulation (DBS) on brain topological metrics, functional connectivity (FC), and white matter integrity were studied in levodopa‐treated Parkinson’s disease (PD) patients before and after DBS.

Methods

Clinical assessment, resting‐state functional MRI (rs‐fMRI), and diffusion tensor imaging (DTI) were performed pre‐ and post‐DBS in 15 PD patients, using a within‐subject design. The rs‐fMRI identified brain network topological metric and FC changes using graph‐theory‐ and seed‐based methods. White matter integrity was determined by DTI and tract‐based spatial statistics.

Results

Unified Parkinson's Disease Rating Scale III (UPDRS‐ III) scores were significantly improved by 35.3% (p < 0.01) after DBS in PD patients, compared with pre‐DBS patients without medication. Post‐DBS PD patients showed a significant decrease in the graph‐theory‐based degree and cost in the middle temporal gyrus and temporo‐occipital part‐Right. Changes in FC were seen in four brain regions, and a decrease in white matter integrity was seen in the left anterior corona radiata. The topological metrics changes were correlated with Beck Depression Inventory II (BDI‐II) and the FC changes with UPDRS‐III scores.

Conclusion

STN‐DBS modulated graph‐theoretical metrics, FC, and white matter integrity. Brain connectivity changes observed with multi‐modal imaging were also associated with postoperative clinical improvement. These findings suggest that the effects of STN‐DBS are caused by brain network alterations.

A novel approach to understanding Parkinsonian cognitive decline using minimum spanning trees, edge cutting, and magnetoencephalography

Graph theory-based approaches are efficient tools for detecting clustering and group-wise differences in high-dimensional data across a wide range of fields, such as gene expression analysis and neural connectivity. Here, we examine data from a cross-sectional, resting-state magnetoencephalography study of 89 Parkinson’s disease patients, and use minimum-spanning tree (MST) methods to relate severity of Parkinsonian cognitive impairment to neural connectivity changes. In particular, we implement the two-sample multivariate-runs test of Friedman and Rafsky (Ann Stat 7(4):697–717, 1979) and find it to be a powerful paradigm for distinguishing highly significant deviations from the null distribution in high-dimensional data. We also generalize this test for use with greater than two classes, and show its ability to localize significance to particular sub-classes. We observe multiple indications of altered connectivity in Parkinsonian dementia that may be of future use in diagnosis and prediction.

Frontoparietal network resilience is associated with protection against cognitive decline in Parkinson's disease

Though Parkinson's disease is primarily defined as a movement disorder, it is also characterized by a range of non-motor symptoms, including cognitive decline. The onset and progression of cognitive decline in individuals with Parkinson's disease is variable, and the neurobiological mechanisms that contribute to, or protect against, cognitive decline in Parkinson's disease are poorly understood. Using resting-state functional magnetic resonance imaging data collected from individuals with Parkinson's disease with and without cognitive decline, we examined the relationship between topological brain-network resilience and cognition in Parkinson's disease. By leveraging network attack analyses, we demonstrate that relative to individuals with Parkinson's disease experiencing cognitive decline, the frontoparietal network in cognitively stable individuals with Parkinson's disease is significantly more resilient to network perturbation. Our findings suggest that the topological robustness of the frontoparietal network is associated with the absence of cognitive decline in individuals with Parkinson's disease.

Functional network analysis of the sub-regions of the primary motor cortex during rest

The cytoarchitectonic properties of the primary motor cortex have shown two distinct sub-regions: Anterior Broadmann area 4 (BA4a) and Posterior Broadmann area 4 (BA4p). Some previous studies have suggested that these two sub-regions are functionally different and showed that in few fMRI experiments, these sub-regions may have different roles in brain functions. Resting-state fMRI (rsfMRI) is advanced technique that allows investigating in detail the functional connectivity and provides a greater understanding of the physiological behavior of different brain regions. In this study, 198 healthy subjects were examined using a region-based rsfMRI analysis to investigate whether BA4a and BA4p have similar or different connections to other brain networks. The finding shows that indeed these two sub-regions have distinct connectivity to different brain networks. BA4a has a greater connection to motor-related areas while BA4p has connections to nonmotor-related areas (such as sensory, attentional, and higher order regions), suggesting that these two sub-regions should be considered as two separate regions of interests.

Application of Functional Magnetic Resonance Imaging in the Diagnosis of Parkinson's Disease: A Histogram Analysis

This study aimed to investigate the value of amplitude of low-frequency fluctuation (ALFF)-based histogram analysis in the diagnosis of Parkinson's disease (PD) and to investigate the regions of the most important discriminative features and their contribution to classification discrimination. Patients with PD (n = 59) and healthy controls (HCs; n = 41) were identified and divided into a primary set (80 cases, including 48 patients with PD and 32 HCs) and a validation set (20 cases, including 11 patients with PD and nine HCs). The Automated Anatomical Labeling (AAL) 116 atlas was used to extract the histogram features of the regions of interest in the brain. Machine learning methods were used in the primary set for data dimensionality reduction, feature selection, model construction, and model performance evaluation. The model performance was further validated in the validation set. After feature data dimension reduction and feature selection, 23 of a total of 1,276 features were entered in the model. The brain regions of the selected features included the frontal, temporal, parietal, occipital, and limbic lobes, as well as the cerebellum and the thalamus. In the primary set, the area under the curve (AUC) of the model was 0.974, the sensitivity was 93.8%, the specificity was 90.6%, and the accuracy was 93.8%. In the validation set, the AUC, sensitivity, specificity, and accuracy were 0.980, 90.9%, 88.9%, and 90.0%, respectively. ALFF-based histogram analysis can be used to classify patients with PD and HCs and to effectively identify abnormal brain function regions in PD patients.

Brain multigraph prediction using topology-aware adversarial graph neural network

Brain graphs (i.e, connectomes) constructed from medical scans such as magnetic resonance imaging (MRI) have become increasingly important tools to characterize the abnormal changes in the human brain. Due to the high acquisition cost and processing time of multimodal MRI, existing deep learning frameworks based on Generative Adversarial Network (GAN) focused on predicting the missing multimodal medical images from a few existing modalities. While brain graphs help better understand how a particular disorder can change the connectional facets of the brain, synthesizing a target brain multigraph (i.e, multiple brain graphs) from a single source brain graph is strikingly lacking. Additionally, existing graph generation works mainly learn one model for each target domain which limits their scalability in jointly predicting multiple target domains. Besides, while they consider the global topological scale of a graph (i.e., graph connectivity structure), they overlook the local topology at the node scale (e.g., how central a node is in the graph). To address these limitations, we introduce topology-aware graph GAN architecture (topoGAN), which jointly predicts multiple brain graphs from a single brain graph while preserving the topological structure of each target graph. Its three key innovations are: (i) designing a novel graph adversarial auto-encoder for predicting multiple brain graphs from a single one, (ii) clustering the encoded source graphs in order to handle the mode collapse issue of GAN and proposing a cluster-specific decoder, (iii) introducing a topological loss to force the prediction of topologically sound target brain graphs. The experimental results using five target domains demonstrated the outperformance of our method in brain multigraph prediction from a single graph in comparison with baseline approaches.

Effective Connectivity During Rest and Music Listening: An EEG Study on Parkinson's Disease

Music-based interventions seem to enhance motor, sensory and cognitive functions in Parkinson’s disease (PD), but the underlying action mechanisms are still largely unknown. This electroencephalography (EEG) study aimed to investigate the effective connectivity patterns characterizing PD in the resting state and during music listening. EEG recordings were obtained from fourteen non-demented PD patients and 12 healthy controls, at rest and while listening to three music tracks. Theta- and alpha-band power spectral density and multivariate partial directed coherence were computed. Power and connectivity measures were compared between patients and controls in the four conditions and in music vs. rest. Compared to controls, patients showed enhanced theta-band power and slightly enhanced alpha-band power, but markedly reduced theta- and alpha-band interactions among EEG channels, especially concerning the information received by the right central channel. EEG power differences were partially reduced by music listening, which induced power increases in controls but not in patients. Connectivity differences were slightly compensated by music, whose effects largely depended on the track. In PD, music enhanced the frontotemporal inter-hemispheric communication. Our findings suggest that PD is characterized by enhanced activity but reduced information flow within the EEG network, being only partially normalized by music. Nevertheless, music capability to facilitate inter-hemispheric communication might underlie its beneficial effects on PD pathophysiology and should be further investigated.

Alterations in intrinsic functional networks in Parkinson's disease patients with depression: A resting-state functional magnetic resonance imaging study

Aims

The aim of this research was to investigate the alterations in functional brain networks and to assess the relationship between depressive impairment and topological network changes in Parkinson's disease (PD) patients with depression (DPD).

Methods

Twenty‐two DPD patients, 23 PD patients without depression (NDPD), and 25 matched healthy controls (HCs) were enrolled. All participants were examined by resting‐state functional magnetic resonance imaging scans. Graph theoretical analysis and network‐based statistic methods were used to analyze brain network topological properties and abnormal subnetworks, respectively.

Results

The DPD group showed significantly decreased local efficiency compared with the HC group (P = .008, FDR corrected). In nodal metrics analyses, the degree of the right inferior occipital gyrus (P = .0001, FDR corrected) was positively correlated with the Hamilton Depression Rating Scale scores in the DPD group. Meanwhile, the temporal visual cortex, including the bilateral middle temporal gyri and right inferior temporal gyrus in the HC and NDPD groups and the left posterior cingulate gyrus in the NDPD group, was defined as hub region, but not in the DPD group. Compared with the HC group, the DPD group had extensive weakening of connections between the temporal‐occipital visual cortex and the prefrontal‐limbic network.

Conclusions

These results suggest that PD depression is associated with disruptions in the topological organization of functional brain networks, mainly involved the temporal‐occipital visual cortex and the posterior cingulate gyrus and may advance our current understanding of the pathophysiological mechanisms underlying DPD.

Altered Structural Brain Networks Related to Adrenergic/Muscarinic Receptor Autoantibodies in Chronic Fatigue Syndrome

BACKGROUND AND PURPOSE

Recent studies suggest that the autoantibodies against adrenergic/muscarinic receptors might be one of the causes and potential markers of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). The purpose of this study was to investigate the structural network changes related to autoantibody titers against adrenergic/muscarinic receptors in ME/CFS by performing a single-subject gray matter similarity-based structural network analysis.

METHODS

We prospectively examined 89 consecutive right-handed ME/CFS patients who underwent both brain MRI including 3D T1-wighted images and a blood analysis of autoantibodies titers against β1 adrenergic receptor (β1 AdR-Ab), β2 AdR-Ab, M3 acetylcholine receptor (M3 AchR-Ab), and M4 AchR-Ab. Single-subject gray matter similarity-based structural networks were extracted from segmented gray matter images for each patient. We calculated local network properties (betweenness centrality, clustering coefficient, and characteristic path length) and global network properties (normalized path length λ, normalized clustering coefficient γ, and small-world network value δ). We investigated the correlations between the autoantibody titers and regional gray matter/white matter volumes, the local network properties, and the global network properties.

RESULTS

Betweenness centrality showed a significant positive correlation with β1-AdR-Ab in the right dorsolateral prefrontal cortex. The characteristic path length showed a significant negative correlation with β2-AdR-Ab in the right precentral gyrus. There were no significant correlations between the antibody titers and the regional gray matter/white matter volumes, and the global network properties.

CONCLUSIONS

Our findings suggest that β1 AdR-Ab and β2 AdR-Ab are potential markers of ME/CFS.