Network 'small-world-ness': a quantitative method for determining canonical network equivalence

Machine Learning on Visibility Graph Features Discriminates the Cognitive Event-Related Potentials of Patients with Early Alzheimer's Disease from Healthy Aging

We present a framework for electroencephalography (EEG)-based classification between patients with Alzheimer's Disease (AD) and robust normal elderly (RNE) via a graph theory approach using visibility graphs (VGs). This EEG VG approach is motivated by research that has demonstrated differences between patients with early stage AD and RNE using various features of EEG oscillations or cognitive event-related potentials (ERPs). In the present study, EEG signals recorded during a word repetition experiment were wavelet decomposed into 5 sub-bands (δ,θ,α,β,γ). The raw and band-specific signals were then converted to VGs for analysis. Twelve graph features were tested for differences between the AD and RNE groups, and t-tests employed for feature selection. The selected features were then tested for classification using traditional machine learning and deep learning algorithms, achieving a classification accuracy of 100% with linear and non-linear classifiers. We further demonstrated that the same features can be generalized to the classification of mild cognitive impairment (MCI) converters, i.e., prodromal AD, against RNE with a maximum accuracy of 92.5%. Code is released online to allow others to test and reuse this framework.

Human Cancer Cell Radiation Response Investigated through Topological Analysis of 2D Cell Networks

Clonogenic assays are routinely used to evaluate the response of cancer cells to external radiation fields, assess their radioresistance and radiosensitivity, estimate the performance of radiotherapy. However, classic clonogenic tests focus on the number of colonies forming on a substrate upon exposure to ionizing radiation, and disregard other important characteristics of cells such their ability to generate structures with a certain shape. The radioresistance and radiosensitivity of cancer cells may depend less on the number of cells in a colony and more on the way cells interact to form complex networks. In this study, we have examined whether the topology of 2D cancer-cell graphs is influenced by ionizing radiation. We subjected different cancer cell lines, i.e. H4 epithelial neuroglioma cells, H460 lung cancer cells, PC3 bone metastasis of grade IV of prostate cancer and T24 urinary bladder cancer cells, cultured on planar surfaces, to increasing photon radiation levels up to 6 Gy. Fluorescence images of samples were then processed to determine the topological parameters of the cell-graphs developing over time. We found that the larger the dose, the less uniform the distribution of cells on the substrate-evidenced by high values of small-world coefficient (cc), high values of clustering coefficient (cc), and small values of characteristic path length (cpl). For all considered cell lines, [Formula: see text] for doses higher or equal to 4 Gy, while the sensitivity to the dose varied for different cell lines: T24 cells seem more distinctly affected by the radiation, followed by the H4, H460 and PC3 cells. Results of the work reinforce the view that the characteristics of cancer cells and their response to radiotherapy can be determined by examining their collective behavior-encoded in a few topological parameters-as an alternative to classical clonogenic assays.

Comorbidity Between Internalising and Externalising Disorders Among Adolescents: Symptom Connectivity Features and Psychosocial Outcome

Internalising disorders are highly prevalent conditions in adolescence and tend to co-occur with externalising disorders. The present study used a symptom network approach to examine the interplay between symptoms of internalising disorders among adolescents with comorbid internalising and externalising disorders. Data comes from the National Comorbidity Survey-Adolescent Supplement, a nationally representative survey of adolescents aged 13 to 18 years. The most central symptoms across the disorders in the network were poor self-esteem and worry. The comorbidity between anxiety and depression increases the probability of having comorbid externalising disorders. Adolescents with both internalising and externalising disorders had the highest rate of health service utilisation. Comorbidity group, lifestyle factors, deficits in cognitive and academic competence and coping skills were significant covariates of the mental health outcomes. Understanding comorbidity profile of internalising and externalising disorders and central symptoms that bridge these disorders could have important clinical implications.

Disrupted Topological Organization of White Matter Network in Angelman Syndrome

BACKGROUND

Angelman syndrome (AS) is a genetic disorder that affects neurodevelopment. The investigation of changes in the brain white matter network, which would contribute to a better understanding of the pathogenesis of AS brain, was lacking.

PURPOSE

To investigate both local and global alterations of white matter in patients with AS.

STUDY TYPE

Prospective.

SUBJECTS

A total of 29 AS patients (6.6 ± 1.4 years, 15 [52%] females) and 19 age-matched healthy controls (HC) (7.0 ± 1.5 years, 10 [53%] females).

FIELD STRENGTH/SEQUENCE

A 3-T, three-dimensional (3D) T1-weighted imaging by using gradient-echo-based sequence, single shell diffusion tensor imaging by using spin-echo-based echo-planar imaging.

ASSESSMENT

Network metrics including global efficiency (E_g ), local efficiency (E_loc ), small world coefficient (Swc), rich-club coefficient (Φ), and nodal degree (ND) were estimated from diffusion MR (dMR) data. Connections among highly connected (hub) regions and less connected (peripheral) regions were also assessed. Correlation between the topological parameters and age for each group was also calculated to assess the development of the brain.

STATISTICAL TESTS

Linear regression model, permutation test. P values estimated from the regression model for each brain region were adjusted by false discovery rate (FDR) correction.

RESULTS

AS patients showed significantly lower E_g and higher swc compared to HC. Φ_n significantly increased at higher k-levels in AS patients. In addition, the connections among hub regions and peripheral regions were significantly interrupted in AS patients.

DATA CONCLUSION

The AS brain showed diminished connectivity, reflected by reduced network efficiency compared to HC. Compared to densely connected regions, less connected regions were more vulnerable in AS.

EVIDENCE LEVEL

2 TECHNICAL EFFICACY: Stage 3.

Axonal damage and astrocytosis are biological correlates of grey matter network integrity loss: a cohort study in autosomal dominant Alzheimer disease

Brain development and maturation leads to grey matter networks that can be measured using magnetic resonance imaging. Network integrity is an indicator of information processing capacity which declines in neurodegenerative disorders such as Alzheimer disease (AD). The biological mechanisms causing this loss of network integrity remain unknown. Cerebrospinal fluid (CSF) protein biomarkers are available for studying diverse pathological mechanisms in humans and can provide insight into decline. We investigated the relationships between 10 CSF proteins and network integrity in mutation carriers (N=219) and noncarriers (N=136) of the Dominantly Inherited Alzheimer Network Observational study. Abnormalities in Aβ, Tau, synaptic (SNAP-25, neurogranin) and neuronal calcium-sensor protein (VILIP-1) preceded grey matter network disruptions by several years, while inflammation related (YKL-40) and axonal injury (NfL) abnormalities co-occurred and correlated with network integrity. This suggests that axonal loss and inflammation play a role in structural grey matter network changes.

Key points

Abnormal levels of fluid markers for neuronal damage and inflammatory processes in CSF are associated with grey matter network disruptions.The strongest association was with NfL, suggesting that axonal loss may contribute to disrupted network organization as observed in AD.Tracking biomarker trajectories over the disease course, changes in CSF biomarkers generally precede changes in brain networks by several years.

Fire and Rhizosphere Effects on Bacterial Co-Occurrence Patterns

Fires are common in Mediterranean soils and constitute an important driver of their evolution. Although fire effects on vegetation dynamics are widely studied, their influence on the assembly rules of soil prokaryotes in a small-scale environment has attracted limited attention. In the present study, we reanalyzed the data from Aponte et al. (2022) to test whether the direct and/or indirect effects of fire are reflected in the network of relationships among soil prokaryotes in a Chilean sclerophyllous ecosystem. We focused on bacterial (genus and species level) co-occurrence patterns in the rhizospheres and bulk soils in burned and unburned plots. Four soils were considered: bulk-burnt (BB), bulk-unburnt (BU), rhizosphere-burnt (RB), and rhizosphere-unburnt (RU). The largest differences in network parameters were recorded between RU and BB soils, while RB and BU networks exhibited similar values. The network in the BB soil was the most compact and centralized, while the RU network was the least connected, with no central nodes. The robustness of bacterial communities was enhanced in burnt soils, but this was more pronounced in BB soil. The mechanisms mainly responsible for bacterial community structure were stochastic in all soils, whether burnt or unburnt; however, communities in RB were much more stochastic than in RU.

Connectivity Analysis in EEG Data: A Tutorial Review of the State of the Art and Emerging Trends

Understanding how different areas of the human brain communicate with each other is a crucial issue in neuroscience. The concepts of structural, functional and effective connectivity have been widely exploited to describe the human connectome, consisting of brain networks, their structural connections and functional interactions. Despite high-spatial-resolution imaging techniques such as functional magnetic resonance imaging (fMRI) being widely used to map this complex network of multiple interactions, electroencephalographic (EEG) recordings claim high temporal resolution and are thus perfectly suitable to describe either spatially distributed and temporally dynamic patterns of neural activation and connectivity. In this work, we provide a technical account and a categorization of the most-used data-driven approaches to assess brain-functional connectivity, intended as the study of the statistical dependencies between the recorded EEG signals. Different pairwise and multivariate, as well as directed and non-directed connectivity metrics are discussed with a pros-cons approach, in the time, frequency, and information-theoretic domains. The establishment of conceptual and mathematical relationships between metrics from these three frameworks, and the discussion of novel methodological approaches, will allow the reader to go deep into the problem of inferring functional connectivity in complex networks. Furthermore, emerging trends for the description of extended forms of connectivity (e.g., high-order interactions) are also discussed, along with graph-theory tools exploring the topological properties of the network of connections provided by the proposed metrics. Applications to EEG data are reviewed. In addition, the importance of source localization, and the impacts of signal acquisition and pre-processing techniques (e.g., filtering, source localization, and artifact rejection) on the connectivity estimates are recognized and discussed. By going through this review, the reader could delve deeply into the entire process of EEG pre-processing and analysis for the study of brain functional connectivity and learning, thereby exploiting novel methodologies and approaches to the problem of inferring connectivity within complex networks.

Encoding of everyday objects in older adults: Episodic memory assessment in virtual reality

Introduction

Age-related decline in episodic memory performance in otherwise healthy older adults is indisputably evident. Yet, it has been shown that under certain conditions episodic memory performance in healthy older adults’ barely deviates from those seen in young adults. Here we report on the quality of object encoding in an ecologically valid, virtual-reality based memory assessment in a sample of healthy older and younger adults with comparable memory performance.

Methods

We analyzed encoding by establishing both a serial and semantic clustering index and an object memory association network.

Results

As expected, semantic clustering was superior in older adults without need for additional allocation of executive resources whereas young adults tended more to rely on serial strategies. The association networks suggested a plethora of obvious but also less obvious memory organization principles, some of which indicated converging approaches between the groups as suggested by a subgraph analysis and some of which indicated diverging approaches as suggested by the respective network interconnectivity. A higher interconnectivity was observed in the older adults’ association networks.

Discussion

We interpreted this as a consequence of superior semantic memory organization (extent to which effective semantic strategies diverged within the group). In conclusion, these results might indicate a diminished need for compensatory cognitive effort in healthy older adults when encoding and recalling everyday objects under ecologically valid conditions. Due to an enhanced and multimodal encoding model, superior crystallized abilities might be sufficient to counteract an age-related decline in various other and specific cognitive domains. This approach might potentially elucidate age-related changes in memory performance in both healthy and pathological aging.

Using Network Science and Psycholinguistic Megastudies to Examine the Dimensions of Phonological Similarity

Network science was used to examine different dimensions of phonological similarity in English. Data from a phonological associate task and an identification of words in noise task were used to create a phonological association network and a misperception network. These networks were compared to a network formed by a computational metric widely used to assess phonological similarity (i.e., one-phoneme metric). The phonological association network and the misperception network were topographically more similar to each other than either were to the one-phoneme metric network, but there were several network features in common between the one-phoneme metric network and the phonological association network. To assess the influence of network structure on processing, we compared the influence of degree (i.e., neighborhood density) from each of the networks on visual and auditory lexical decision reaction times obtained from two psycholinguistic megastudies. The effect of degree differed across network types and tasks. We discuss the use of each approach to determine phonological similarity and a possible direction forward for language research through the use of multiplex networks.

Reliable evaluation of functional connectivity and graph theory measures in source-level EEG: How many electrodes are enough?

OBJECTIVE

Using EEG to characterise functional brain networks through graph theory has gained significant interest in clinical and basic research. However, the minimal requirements for reliable measures remain largely unaddressed. Here, we examined functional connectivity estimates and graph theory metrics obtained from EEG with varying electrode densities.

METHODS

EEG was recorded with 128 electrodes in 33 participants. The high-density EEG data were subsequently subsampled into three sparser montages (64, 32, and 19 electrodes). Four inverse solutions, four measures of functional connectivity, and five graph theory metrics were tested.

RESULTS

The correlation between the results obtained with 128-electrode and the subsampled montages decreased as a function of the number of electrodes. As a result of decreased electrode density, the network metrics became skewed: mean network strength and clustering coefficient were overestimated, while characteristic path length was underestimated.

CONCLUSIONS

Several graph theory metrics were altered when electrode density was reduced. Our results suggest that, for optimal balance between resource demand and result precision, a minimum of 64 electrodes should be utilised when graph theory metrics are used to characterise functional brain networks in source-reconstructed EEG data.

SIGNIFICANCE

Characterisation of functional brain networks derived from low-density EEG warrants careful consideration.

From eye movements to scanpath networks: A method for studying individual differences in expository text reading

Eye movements have been examined as an index of attention and comprehension during reading in the literature for over 30 years. Although eye-movement measurements are acknowledged as reliable indicators of readers' comprehension skill, few studies have analyzed eye-movement patterns using network science. In this study, we offer a new approach to analyze eye-movement data. Specifically, we recorded visual scanpaths when participants were reading expository science text, and used these to construct scanpath networks that reflect readers' processing of the text. Results showed that low ability and high ability readers' scanpath networks exhibited distinctive properties, which are reflected in different network metrics including density, centrality, small-worldness, transitivity, and global efficiency. Such patterns provide a new way to show how skilled readers, as compared with less skilled readers, process information more efficiently. Implications of our analyses are discussed in light of current theories of reading comprehension.

Effects of inhaled cannabis high in Δ9-THC or CBD on the aging brain: A translational MRI and behavioral study

With the recent legalization of inhaled cannabis for medicinal and recreational use, the elderly represents one of the newest, rapidly growing cohorts of cannabis users. To understand the neurobiological effects of cannabis on the aging brain, 19-20 months old mice were divided into three groups exposed to vaporized cannabis containing ~10% Δ9-THC, ~10% CBD, or placebo for 30 min each day. Voxel based morphometry, diffusion weighted imaging, and resting state functional connectivity data were gathered after 28 days of exposure and following a two-week washout period. Tail-flick, open field, and novel object preference tests were conducted to explore analgesic, anxiolytic, and cognitive effects of cannabis, respectively. Vaporized cannabis high in Δ9-THC and CBD achieved blood levels reported in human users. Mice showed antinociceptive effects to chronic Δ9-THC without tolerance while the anxiolytic and cognitive effects of Δ9-THC waned with treatment. CBD had no effect on any of the behavioral measures. Voxel based morphometry showed a decrease in midbrain dopaminergic volume to chronic Δ9-THC followed but an increase after a two-week washout. Fractional anisotropy values were reduced in the same area by chronic Δ9-THC, suggesting a reduction in gray matter volume. Cannabis high in CBD but not THC increased network strength and efficiency, an effect that persisted after washout. These data would indicate chronic use of inhaled cannabis high in Δ9-THC can be an effective analgesic but not for treatment of anxiety or cognitive decline. The dopaminergic midbrain system was sensitive to chronic Δ9-THC but not CBD showing robust plasticity in volume and water diffusivity prior to and following drug cessation an effect possibly related to the abuse liability of Δ9-THC. Chronic inhaled CBD resulted in enhanced global network connectivity that persisted after drug cessation. The behavioral consequences of this sustained change in brain connectivity remain to be determined.

Immediate Effects of Vagal Nerve Stimulation in Drug-Resistant Epilepsy Revealed by Magnetoencephalographic Recordings

Objective: Vagus nerve stimulation (VNS) has been a neuromodulatory option for treating drug-resistant epilepsy (DRE), but its mechanism remains unclear. To obtain insight into the mechanism by which VNS reduces epileptic seizures, the immediate effects of VNS in brain networks of DRE patients were investigated when the patients' vagal nerve stimulators were turned on. Methods: The brain network properties of 14 DRE patients with a vagal nerve stimulator and 14 healthy controls were evaluated using magnetoencephalography recordings for 6 main frequency bands. Results: Compared with healthy controls, DRE patients exhibited significant increases in functional connectivity in the theta, alpha, beta, and gamma bands and significant reductions in the small-world measure in the theta and beta bands. During periods when patients' vagal nerve stimulators were turned on, DRE patients showed significant reductions in functional connectivity in the theta and alpha bands and a significant increase in the small-world measure in the theta band when compared with periods when patients' vagal nerve stimulators were turned off. Conclusions: Our results indicate that the brain networks of DRE patients were pathologically hypersynchronous and instantaneous VNS can decrease the synchronization of brain networks of epileptic patients, which might play a key role in the mechanism by which VNS reduces epileptic seizures. In the theta band, instantaneous VNS can increase the network efficiency of DRE patients, and the increment in network efficiency may be helpful for improving brain cognitive function in epileptic patients. Impact statement For the first time, we investigated the immediate effects of vagus nerve stimulation (VNS) in the brain networks of drug-resistant epilepsy patients using magnetoencephalography. Our results show that instantaneous VNS can decrease the hypersynchronization of epileptic networks and increase the network efficiency of epileptic patients. Our results are helpful in understanding the mechanism of action by which VNS reduces epileptic seizures and improves the cognitive function in epileptic patients and the brain network reorganization caused by long-term VNS.

Graph-Based Analysis of Brain Connectivity in Multiple Sclerosis Using Functional MRI: A Systematic Review

(1) Background: Multiple sclerosis (MS) is an immune system disease in which myelin in the nervous system is affected. This abnormal immune system mechanism causes physical disabilities and cognitive impairment. Functional magnetic resonance imaging (fMRI) is a common neuroimaging technique used in studying MS. Computational methods have recently been applied for disease detection, notably graph theory, which helps researchers understand the entire brain network and functional connectivity. (2) Methods: Relevant databases were searched to identify articles published since 2000 that applied graph theory to study functional brain connectivity in patients with MS based on fMRI. (3) Results: A total of 24 articles were included in the review. In recent years, the application of graph theory in the MS field received increased attention from computational scientists. The graph-theoretical approach was frequently combined with fMRI in studies of functional brain connectivity in MS. Lower EDSSs of MS stage were the criteria for most of the studies (4) Conclusions: This review provides insights into the role of graph theory as a computational method for studying functional brain connectivity in MS. Graph theory is useful in the detection and prediction of MS and can play a significant role in identifying cognitive impairment associated with MS.

Revealing the Relational Mechanisms of Research for Development Through Social Network Analysis

Achieving impact through research for development programmes (R4D) requires engagement with diverse stakeholders across the research, development and policy divides. Understanding how such programmes support the emergence of outcomes, therefore, requires a focus on the relational aspects of engagement and collaboration. Increasingly, evaluation of large research collaborations is employing social network analysis (SNA), making use of its relational view of causation. In this paper, we use three applications of SNA within similar large R4D programmes, through our work within evaluation of three Interidsiplinary Hubs of the Global Challenges Research Fund, to explore its potential as an evaluation method. Our comparative analysis shows that SNA can uncover the structural dimensions of interactions within R4D programmes and enable learning about how networks evolve through time. We reflect on common challenges across the cases including navigating different forms of bias that result from incomplete network data, multiple interpretations across scales, and the challenges of making causal inference and related ethical dilemmas. We conclude with lessons on the methodological and operational dimensions of using SNA within monitoring, evaluation and learning (MEL) systems that aim to support both learning and accountability.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1057/s41287-023-00576-y.

Tracking functional network connectivity dynamics in the elderly

Introduction

Functional magnetic resonance imaging (fMRI) has shown that aging disturbs healthy brain organization and functional connectivity. However, how this age-induced alteration impacts dynamic brain function interaction has not yet been fully investigated. Dynamic function network connectivity (DFNC) analysis can produce a brain representation based on the time-varying network connectivity changes, which can be further used to study the brain aging mechanism for people at different age stages.

Method

This presented investigation examined the dynamic functional connectivity representation and its relationship with brain age for people at an elderly stage as well as in early adulthood. Specifically, the resting-state fMRI data from the University of North Carolina cohort of 34 young adults and 28 elderly participants were fed into a DFNC analysis pipeline. This DFNC pipeline forms an integrated dynamic functional connectivity (FC) analysis framework, which consists of brain functional network parcellation, dynamic FC feature extraction, and FC dynamics examination.

Results

The statistical analysis demonstrates that extensive dynamic connection changes in the elderly concerning the transient brain state and the method of functional interaction in the brain. In addition, various machine learning algorithms have been developed to verify the ability of dynamic FC features to distinguish the age stage. The fraction time of DFNC states has the highest performance, which can achieve a classification accuracy of over 88% by a decision tree.

Discussion

The results proved there are dynamic FC alterations in the elderly, and the alteration was found to be correlated with mnemonic discrimination ability and could have an impact on the balance of functional integration and segregation.

Epidemic dynamics in census-calibrated modular contact network

Network-based models are apt for understanding epidemic dynamics due to their inherent ability to model the heterogeneity of interactions in the contemporary world of intense human connectivity. We propose a framework to create a wire-frame that mimics the social contact network of the population in a geography by lacing it with demographic information. The framework results in a modular network with small-world topology that accommodates density variations and emulates human interactions in family, social, and work spaces. When loaded with suitable economic, social, and urban data shaping patterns of human connectance, the network emerges as a potent decision-making instrument for urban planners, demographers, and social scientists. We employ synthetic networks to experiment in a controlled environment and study the impact of zoning, density variations, and population mobility on the epidemic variables using a variant of the SEIR model. Our results reveal that these demographic factors have a characteristic influence on social contact patterns, manifesting as distinct epidemic dynamics. Subsequently, we present a real-world COVID-19 case study for three Indian states by creating corresponding surrogate social contact networks using available census data. The case study validates that the demography-laced modular contact network reduces errors in the estimates of epidemic variables.

Child-oriented word associations improve models of early word learning

How words are associated within the linguistic environment conveys semantic content; however, different contexts induce different linguistic patterns. For instance, it is well known that adults speak differently to children than to other adults. We present results from a new word association study in which adult participants were instructed to produce either unconstrained or child-oriented responses to each cue, where cues included 672 nouns, verbs, adjectives, and other word forms from the McArthur-Bates Communicative Development Inventory (CDI; Fenson et al., 2006). Child-oriented responses consisted of higher frequency words with fewer letters, earlier ages of acquisition, and higher contextual diversity. Furthermore, the correlations among the responses generated for each pair of cues differed between unconstrained (adult-oriented) and child-oriented responses, suggesting that child-oriented associations imply different semantic structure. A comparison of growth models guided by a semantic network structure revealed that child-oriented associations are more predictive of early lexical growth. Additionally, relative to a growth model based on a corpus of naturalistic child-directed speech, the child-oriented associations explain added unique variance to lexical growth. Thus, these new child-oriented word association norms provide novel insight into the semantic context of young children and early lexical development.

Modeling the Evolution of Biological Neural Networks Based on Caenorhabditis elegans Connectomes across Development

Knowledge of the structural properties of biological neural networks can help in understanding how particular responses and actions are generated. Recently, Witvliet et al. published the connectomes of eight isogenic Caenorhabditis elegans hermaphrodites at different postembryonic ages, from birth to adulthood. We analyzed the basic structural properties of these biological neural networks. From birth to adulthood, the asymmetry between in-degrees and out-degrees over the C. elegans neuronal network increased with age, in addition to an increase in the number of nodes and edges. The degree distributions were neither Poisson distributions nor pure power-law distributions. We have proposed a model of network evolution with different initial attractiveness for in-degrees and out-degrees of nodes and preferential attachment, which reproduces the asymmetry between in-degrees and out-degrees and similar degree distributions via the tuning of the initial attractiveness values. In this study, we present the well-preserved structural properties of C. elegans neuronal networks across development, and provide some insight into understanding the evolutionary processes of biological neural networks through a simple network model.

Small world of the miRNA science drives its publication dynamics

Many scientific articles became available in the digital form which allows for querying articles data, and specifically the automated metadata gathering, which includes the affiliation data. This in turn can be used in the quantitative characterization of the scientific field, such as organizations identification, and analysis of the co-authorship graph of those organizations to extract the underlying structure of science. In our work, we focus on the miRNA science field, building the organization co-authorship network to provide the higher-level analysis of scientific community evolution rather than analyzing author-level characteristics. To tackle the problem of the institution name writing variability, we proposed the k-mer/n-gram boolean feature vector sorting algorithm, KOFER in short. This approach utilizes the fact that the contents of the affiliation are rather consistent for the same organization, and to account for writing errors and other organization name variations within the affiliation metadata field, it converts the organization mention within the affiliation to the K-Mer (n-gram) Boolean presence vector. Those vectors for all affiliations in the dataset are further lexicographically sorted, forming groups of organization mentions. With that approach, we clustered the miRNA field affiliation dataset and extracted unique organization names, which allowed us to build the co-authorship graph on the organization level. Using this graph, we show that the growth of the miRNA field is governed by the small-world architecture of the scientific institution network and experiences power-law growth with exponent 2.64 ± 0.23 for organization number, in accordance with network diameter, proposing the growth model for emerging scientific fields. The first miRNA publication rate of an organization interacting with already publishing organization is estimated as 0.184 ± 0.002 year-1.

Structural covariance network of the hippocampus-amygdala complex in medication-naïve patients with first-episode major depressive disorder

Background

The hippocampus and amygdala are densely interconnected structures that work together in multiple affective and cognitive processes that are important to the etiology of major depressive disorder (MDD). Each of these structures consists of several heterogeneous subfields. We aim to explore the topologic properties of the volume-based intrinsic network within the hippocampus-amygdala complex in medication-naïve patients with first-episode MDD.

Methods

High-resolution T1-weighted magnetic resonance imaging scans were acquired from 123 first-episode, medication-naïve, and noncomorbid MDD patients and 81 age-, sex-, and education level-matched healthy control participants (HCs). The structural covariance network (SCN) was constructed for each group using the volumes of the hippocampal subfields and amygdala subregions; the weights of the edges were defined by the partial correlation coefficients between each pair of subfields/subregions, controlled for age, sex, education level, and intracranial volume. The global and nodal graph metrics were calculated and compared between groups.

Results

Compared with HCs, the SCN within the hippocampus-amygdala complex in patients with MDD showed a shortened mean characteristic path length, reduced modularity, and reduced small-worldness index. At the nodal level, the left hippocampal tail showed increased measures of centrality, segregation, and integration, while nodes in the left amygdala showed decreased measures of centrality, segregation, and integration in patients with MDD compared with HCs.

Conclusion

Our results provide the first evidence of atypical topologic characteristics within the hippocampus-amygdala complex in patients with MDD using structure network analysis. It provides more delineate mechanism of those two structures that underlying neuropathologic process in MDD.

Atypical brain network development of infants at elevated likelihood for autism spectrum disorder during the first year of life

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by behavioral features that appear early in life. Although studies have shown that atypical brain functional and structural connectivity are associated with these behavioral traits, the occurrence and initial alterations of brain networks have not been fully investigated. The current study aimed to map early brain network efficiency and information transferring in infants at elevated likelihood (EL) compared to infants at typical likelihood (TL) for ASD in the first year of life. This study used a resting-state functional near-infrared spectroscopy (fNIRS) approach to obtain the length and strength of functional connections in the frontal and temporal areas in 45 5-month-old and 38 10-month-old infants. Modular organization and small-world properties were detected in both EL and TL infants at 5 and 10 months. In 5-month-old EL infants, local and nodal efficiency were significantly greater than age-matched TL infants, indicating overgrown local connections. Furthermore, we used a support vector machine (SVM) model to classify infants with or without EL based on the obtained global properties of the network, achieving an accuracy of 77.6%. These results suggest that infants with EL for ASD exhibit inefficiencies in the organization of brain networks during the first year of life.

Clinical factors associated with microstructural connectome related brain dysmaturation in term neonates with congenital heart disease

Objective

Term congenital heart disease (CHD) neonates display abnormalities of brain structure and maturation, which are possibly related to underlying patient factors, abnormal physiology and perioperative insults. Our primary goal was to delineate associations between clinical factors and postnatal brain microstructure in term CHD neonates using diffusion tensor imaging (DTI) magnetic resonance (MR) acquisition combined with complementary data-driven connectome and seed-based tractography quantitative analyses. Our secondary goal was to delineate associations between mild dysplastic structural brain abnormalities and connectome and seed-base tractography quantitative analyses. These mild dysplastic structural abnormalities have been derived from prior human infant CHD MR studies and neonatal mouse models of CHD that were collectively used to calculate to calculate a brain dysplasia score (BDS) that included assessment of subcortical structures including the olfactory bulb, the cerebellum and the hippocampus.

Methods

Neonates undergoing cardiac surgery for CHD were prospectively recruited from two large centers. Both pre- and postoperative MR brain scans were obtained. DTI in 42 directions was segmented into 90 regions using a neonatal brain template and three weighted methods. Clinical data collection included 18 patient-specific and 9 preoperative variables associated with preoperative scan and 6 intraoperative (e.g., cardiopulmonary bypass and deep hypothermic circulatory arrest times) and 12 postoperative variables associated with postoperative scan. We compared patient specific and preoperative clinical factors to network topology and tractography alterations on a preoperative neonatal brain MRI, and intra and postoperative clinical factors to network topology alterations on postoperative neonatal brain MRI. A composite BDS was created to score abnormal findings involving the cerebellar hemispheres and vermis, supratentorial extra-axial fluid, olfactory bulbs and sulci, hippocampus, choroid plexus, corpus callosum, and brainstem. The neuroimaging outcomes of this study included (1) connectome metrics: cost (number of connections) and global/nodal efficiency (network integration); (2) seed based tractography methods of fractional anisotropy (FA), radial diffusivity, and axial diffusivity. Statistics consisted of multiple regression with false discovery rate correction (FDR) comparing the clinical risk factors and BDS (including subcortical components) as predictors/exposures and the global connectome metrics, nodal efficiency, and seed based- tractography (FA, radial diffusivity, and axial diffusivity) as neuroimaging outcome measures.

Results

A total of 133 term neonates with complex CHD were prospectively enrolled and 110 had analyzable DTI. Multiple patient-specific factors including d-transposition of the great arteries (d-TGA) physiology and severity of impairment of fetal cerebral substrate delivery (i.e., how much the CHD lesion alters typical fetal circulation such that the highest oxygen and nutrient rich blood from the placenta are not directed toward the fetal brain) were predictive of preoperative reduced cost (p < 0.0073) and reduced global/nodal efficiency (p < 0.03). Cardiopulmonary bypass time predicted postoperative reduced cost (p < 0.04) and multiple postoperative factors [extracorporeal membrane oxygenation (ECMO), seizures and cardiopulmonary resuscitation (CPR)] were predictive of postoperative reduced cost and reduced global/nodal efficiency (p < 0.05). Anthropometric measurements (weight, length, and head size) predicted tractography outcomes. Total BDS was not predictive of brain network topology. However, key subcortical components of the BDS score did predict key global and nodal network topology: abnormalities of the cerebellum predicted reduced cost (p < 0.0417) and of the hippocampus predicted reduced global efficiency (p < 0.0126). All three subcortical structures predicted unique alterations of nodal efficiency (p < 0.05), including hippocampal abnormalities predicting widespread reduced nodal efficiency in all lobes of the brain, cerebellar abnormalities predicting increased prefrontal nodal efficiency, and olfactory bulb abnormalities predicting posterior parietal-occipital nodal efficiency.

Conclusion

Patient-specific (d-TGA anatomy, preoperative impairment of fetal cerebral substrate delivery) and postoperative (e.g., seizures, need for ECMO, or CPR) clinical factors were most predictive of diffuse postnatal microstructural dysmaturation in term CHD neonates. Anthropometric measurements (weight, length, and head size) predicted tractography outcomes. In contrast, subcortical components (cerebellum, hippocampus, olfactory) of a structurally based BDS (derived from CHD mouse mutants), predicted more localized and regional postnatal microstructural differences. Collectively, these findings suggest that brain DTI connectome and seed-based tractography are complementary techniques which may facilitate deciphering the mechanistic relative contribution of clinical and genetic risk factors related to poor neurodevelopmental outcomes in CHD.

Abnormal resting-state functional connectome in methamphetamine-dependent patients and its application in machine-learning-based classification

Brain resting-state functional connectivity (rsFC) has been widely analyzed in substance use disorders (SUDs), including methamphetamine (MA) dependence. Most of these studies utilized Pearson correlation analysis to assess rsFC, which cannot determine whether two brain regions are connected by direct or indirect pathways. Moreover, few studies have reported the application of rsFC-based graph theory in MA dependence. We evaluated alterations in Tikhonov regularization-based rsFC and rsFC-based topological attributes in 46 MA-dependent patients, as well as the correlations between topological attributes and clinical variables. Moreover, the topological attributes selected by least absolute shrinkage and selection operator (LASSO) were used to construct a support vector machine (SVM)-based classifier for MA dependence. The MA group presented a subnetwork with increased rsFC, indicating overactivation of the reward circuit that makes patients very sensitive to drug-related visual cues, and a subnetwork with decreased rsFC suggesting aberrant synchronized spontaneous activity in subregions within the orbitofrontal cortex (OFC) system. The MA group demonstrated a significantly decreased area under the curve (AUC) for the clustering coefficient (Cp) (Pperm &lt; 0.001), shortest path length (Lp) (Pperm = 0.007), modularity (Pperm = 0.006), and small-worldness (σ, Pperm = 0.004), as well as an increased AUC for global efficiency (E.glob) (Pperm = 0.009), network strength (Sp) (Pperm = 0.009), and small-worldness (ω, Pperm &lt; 0.001), implying a shift toward random networks. MA-related increased nodal efficiency (E.nodal) and altered betweenness centrality were also discovered in several brain regions. The AUC for ω was significantly positively associated with psychiatric symptoms. An SVM classifier trained by 36 features selected by LASSO from all topological attributes achieved excellent performance, cross-validated prediction area under the receiver operating characteristics curve, accuracy, sensitivity, specificity, and kappa of 99.03 ± 1.79, 94.00 ± 5.78, 93.46 ± 8.82, 94.52 ± 8.11, and 87.99 ± 11.57%, respectively (Pperm &lt; 0.001), indicating that rsFC-based topological attributes can provide promising features for constructing a high-efficacy classifier for MA dependence.

Zoom-In Neural Network Deep-Learning Model for Alzheimer's Disease Assessments

Deep neural networks have been successfully applied to generate predictive patterns from medical and diagnostic data. This paper presents an approach for assessing persons with Alzheimer's disease (AD) mild cognitive impairment (MCI), compared with normal control (NC) persons, using the zoom-in neural network (ZNN) deep-learning algorithm. ZNN stacks a set of zoom-in learning units (ZLUs) in a feedforward hierarchy without backpropagation. The resting-state fMRI (rs-fMRI) dataset for AD assessments was obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). The Automated Anatomical Labeling (AAL-90) atlas, which provides 90 neuroanatomical functional regions, was used to assess and detect the implicated regions in the course of AD. The features of the ZNN are extracted from the 140-time series rs-fMRI voxel values in a region of the brain. ZNN yields the three classification accuracies of AD versus MCI and NC, NC versus AD and MCI, and MCI versus AD and NC of 97.7%, 84.8%, and 72.7%, respectively, with the seven discriminative regions of interest (ROIs) in the AAL-90.

Different Dynamic Nodal Properties Contribute to Cognitive Impairment in Patients with White Matter Hyperintensities

White matter hyperintensities (WMHs) are commonly observed in older adults and are associated with cognitive impairment. Although previous studies have found abnormal functional connectivities in patients with WMHs based on static functional magnetic resonance imaging (fMRI), the topological properties in the context of brain dynamics remain relatively unexplored. Herein, we explored disrupted dynamic topological properties of functional network connectivity in patients with WMHs and its relationship with cognitive impairment. We included 36 healthy controls (HC) and 104 patients with mild WMHs (n = 39), moderate WMHs (n = 37), and severe (n = 28) WMHs. The fMRI data of all participants were analyzed using Anatomical Automatic Labeling (AAL) and a sliding-window approach to generate dynamic functional connectivity matrics. Then, graph theory methods were applied to calculate the topological properties. Comprehensive neuropsychological scales were used to assess cognitive functions. Relationships between cognitive functions and abnormal dynamic topological properties were evaluated by Pearson's correlation. We found that the patients with WMHs had higher temporal variability in regional properties, including betweenness centrality, nodal efficiencies, and nodal clustering coefficient. Furthermore, we found that the degree of centrality was related to executive function and memory, and the local coefficient correlated to executive function. Our results indicate that patients with WMHs have higher temporal variabilities in regional properties and are associated with executive and memory function.

A connectomics-based taxonomy of mammals

Mammalian taxonomies are conventionally defined by morphological traits and genetics. How species differ in terms of neural circuits and whether inter-species differences in neural circuit organization conform to these taxonomies is unknown. The main obstacle to the comparison of neural architectures has been differences in network reconstruction techniques, yielding species-specific connectomes that are not directly comparable to one another. Here, we comprehensively chart connectome organization across the mammalian phylogenetic spectrum using a common reconstruction protocol. We analyse the mammalian MRI (MaMI) data set, a database that encompasses high-resolution ex vivo structural and diffusion MRI scans of 124 species across 12 taxonomic orders and 5 superorders, collected using a unified MRI protocol. We assess similarity between species connectomes using two methods: similarity of Laplacian eigenspectra and similarity of multiscale topological features. We find greater inter-species similarities among species within the same taxonomic order, suggesting that connectome organization reflects established taxonomic relationships defined by morphology and genetics. While all connectomes retain hallmark global features and relative proportions of connection classes, inter-species variation is driven by local regional connectivity profiles. By encoding connectomes into a common frame of reference, these findings establish a foundation for investigating how neural circuits change over phylogeny, forging a link from genes to circuits to behaviour.

Balancing novelty and appropriateness leads to creative associations in children

Creative problem solving is a fundamental skill of human cognition and is conceived as a search process whereby a novel and appropriate solution is generated. However, it is unclear whether children are able to balance novelty and appropriateness to generate creative solutions and what are the underlying computational mechanisms. Here, we asked children, ranging from 10 to 11 years old, to perform a word association task according to three instructions, which triggered a more appropriate (ordinary), novel (random), or balanced (creative) response. Results revealed that children exhibited greater cognitive flexibility in the creative condition compared to the control conditions, as revealed by the structure and resiliency of the semantic networks. Moreover, responses' word embeddings extracted from pretrained deep neural networks showed that semantic distance and category switching index increased in the creative condition with respect to the ordinary condition and decreased compared to the random condition. Critically, we showed how children efficiently solved the exploration/exploitation trade-off to generate creative associations by fitting a computational reinforcement learning (RL) model that simulates semantic search strategies. Our findings provide compelling evidence that children balance novelty and appropriateness to generate creative associations by optimally regulating the level of exploration in the semantic search. This corroborates previous findings on the adult population and highlights the crucial contribution of both components to the overall creative process. In conclusion, these results shed light on the connections between theoretical concepts such as bottom-up/top-down modes of thinking in creativity research and the exploration/exploitation trade-off in human RL research.

Assessment of EEG-based functional connectivity in response to haptic delay

Haptic technologies enable users to physically interact with remote or virtual environments by applying force, vibration, or motion via haptic interfaces. However, the delivery of timely haptic feedback remains a challenge due to the stringent computation and communication requirements associated with haptic data transfer. Haptic delay disrupts the realism of the user experience and interferes with the quality of interaction. Research efforts have been devoted to studying the neural correlates of delayed sensory stimulation to better understand and thus mitigate the impact of delay. However, little is known about the functional neural networks that process haptic delay. This paper investigates the underlying neural networks associated with processing haptic delay in passive and active haptic interactions. Nineteen participants completed a visuo-haptic task using a computer screen and a haptic device while electroencephalography (EEG) data were being recorded. A combined approach based on phase locking value (PLV) functional connectivity and graph theory was used. To assay the effects of haptic delay on functional connectivity, we evaluate a global connectivity property through the small-worldness index and a local connectivity property through the nodal strength index. Results suggest that the brain exhibits significantly different network characteristics when a haptic delay is introduced. Haptic delay caused an increased manifestation of the small-worldness index in the delta and theta bands as well as an increased nodal strength index in the middle central region. Inter-regional connectivity analysis showed that the middle central region was significantly connected to the parietal and occipital regions as a result of haptic delay. These results are expected to indicate the detection of conflicting visuo-haptic information at the middle central region and their respective resolution and integration at the parietal and occipital regions.

Guiding principle of reservoir computing based on "small-world" network

Reservoir computing is a computational framework of recurrent neural networks and is gaining attentions because of its drastically simplified training process. For a given task to solve, however, the methodology has not yet been established how to construct an optimal reservoir. While, "small-world" network has been known to represent networks in real-world such as biological systems and social community. This network is categorized amongst those that are completely regular and totally disordered, and it is characterized by highly-clustered nodes with a short path length. This study aims at providing a guiding principle of systematic synthesis of desired reservoirs by taking advantage of controllable parameters of the small-world network. We will validate the methodology using two different types of benchmark tests-classification task and prediction task.

Spatial clustering in vaccination hesitancy: The role of social influence and social selection

The phenomenon of vaccine hesitancy behavior has gained ground over the last three decades, jeopardizing the maintenance of herd immunity. This behavior tends to cluster spatially, creating pockets of unprotected sub-populations that can be hotspots for outbreak emergence. What remains less understood are the social mechanisms that can give rise to spatial clustering in vaccination behavior, particularly at the landscape scale. We focus on the presence of spatial clustering, and aim to mechanistically understand how different social processes can give rise to this phenomenon. In particular, we propose two hypotheses to explain the presence of spatial clustering: (i) social selection, in which vaccine-hesitant individuals share socio-demographic traits, and clustering of these traits generates spatial clustering in vaccine hesitancy; and (ii) social influence, in which hesitant behavior is contagious and spreads through neighboring societies, leading to hesitant clusters. Adopting a theoretical spatial network approach, we explore the role of these two processes in generating patterns of spatial clustering in vaccination behaviors under a range of spatial structures. We find that both processes are independently capable of generating spatial clustering, and the more spatially structured the social dynamics in a society are, the higher spatial clustering in vaccine-hesitant behavior it realizes. Together, we demonstrate that these processes result in unique spatial configurations of hesitant clusters, and we validate our models of both processes with fine-grain empirical data on vaccine hesitancy, social determinants, and social connectivity in the US. Finally, we propose, and evaluate the effectiveness of two novel intervention strategies to diminish hesitant behavior. Our generative modeling approach informed by unique empirical data provides insights on the role of complex social processes in driving spatial heterogeneity in vaccine hesitancy.

The resting-state topological organization damage of language-related brain regions in post-stroke cognitive impairment

The topology of brain networks is the foundation of cognition. We hypothesized that stroke damaged topological organization resulting in cognitive impairment. The aim was to explore the damage pattern of the resting-state topology in post-stroke cognitive impairment (PSCI) patients. Thirty-seven patients with PSCI and thirty-seven gender- and age-matched healthy controls (HC) were recruited. The structural and functional data were collected from all subjects. The degree centrality (DC), betweenness centrality (BC), and global properties of brain networks were analyzed between groups. Spearman correlation analysis was performed between topological properties that changed significantly and clinical cognitive function scale scores. Compared with HC, the PSCI patients had significantly reduced DC in language-related brain regions and significantly higher DC in the right frontal lobe, hippocampus, and paracentral lobule. The decreased BC was located in the left caudate, thalamus, temporal, and frontal lobes. The increased BC was detected in the left cuneus and right precuneus. In addition, PSCI exhibited increased characteristic path length and decreased small-worldness. PSCI patients had impaired functional topology of the language-related brain regions, mainly in the left hemisphere. The enhanced processing and relaying information of some right high-order cognitive brain regions may be a compensatory mechanism. However, the whole brain's function integration was reduced, and there was an imbalance between efficiency and consumption.

Altered gray matter structural covariance networks in drug-naïve and treated early HIV-infected individuals

Background

While regional brain structure and function alterations in HIV-infected individuals have been reported, knowledge about the topological organization in gray matter networks is limited. This research aims to investigate the effects of early HIV infection and combination antiretroviral therapy (cART) on gray matter structural covariance networks (SCNs) by employing graph theoretical analysis.

Methods

Sixty-five adult HIV+ individuals (25–50 years old), including 34 with cART (HIV+/cART+) and 31 medication-naïve (HIV+/cART–), and 35 demographically matched healthy controls (HCs) underwent high-resolution T1-weighted images. A sliding-window method was employed to create “age bins,” and SCNs (based on cortical thickness) were constructed for each bin by calculating Pearson's correlation coefficients. The group differences of network indices, including the mean nodal path length (Nlp), betweenness centrality (Bc), number of modules, modularity, global efficiency, local efficiency, and small-worldness, were evaluated by ANOVA and post-hoc tests employing the network-based statistics method.

Results

Relative to HCs, less efficiency in terms of information transfer in the parietal and occipital lobe (decreased Bc) and a compensated increase in the frontal lobe (decreased Nlp) were exhibited in both HIV+/cART+ and HIV+/cART– individuals (P &lt; 0.05, FDR-corrected). Compared with HIV+/cART– and HCs, less specialized function segregation (decreased modularity and small-worldness property) and stronger integration in the network (increased Eglob and little changed path length) were found in HIV+/cART+ group (P &lt; 0.05, FDR-corrected).

Conclusion

Early HIV+ individuals exhibited a decrease in the efficiency of information transmission in sensory regions and a compensatory increase in the frontal lobe. HIV+/cART+ showed a less specialized regional segregation function, but a stronger global integration function in the network.

Transdiagnostic connectome signatures from resting-state fMRI predict individual-level intellectual capacity

Medication and other therapies for psychiatric disorders show unsatisfying efficacy, in part due to the significant clinical/ biological heterogeneity within each disorder and our over-reliance on categorical clinical diagnoses. Alternatively, dimensional transdiagnostic studies have provided a promising pathway toward realizing personalized medicine and improved treatment outcomes. One factor that may influence response to psychiatric treatments is cognitive function, which is reflected in one's intellectual capacity. Intellectual capacity is also reflected in the organization and structure of intrinsic brain networks. Using a large transdiagnostic cohort (n = 1721), we sought to discover neuroimaging biomarkers by developing a resting-state functional connectome-based prediction model for a key intellectual capacity measure, Full-Scale Intelligence Quotient (FSIQ), across the diagnostic spectrum. Our cross-validated model yielded an excellent prediction accuracy (r = 0.5573, p < 0.001). The robustness and generalizability of our model was further validated on three independent cohorts (n = 2641). We identified key transdiagnostic connectome signatures underlying FSIQ capacity involving the dorsal-attention, frontoparietal and default-mode networks. Meanwhile, diagnosis groups showed disorder-specific biomarker patterns. Our findings advance the neurobiological understanding of cognitive functioning across traditional diagnostic categories and provide a new avenue for neuropathological classification of psychiatric disorders.

The trend of disruption in the functional brain network topology of Alzheimer's disease

Alzheimer's disease (AD) is a progressive disorder associated with cognitive dysfunction that alters the brain's functional connectivity. Assessing these alterations has become a topic of increasing interest. However, a few studies have examined different stages of AD from a complex network perspective that cover different topological scales. This study used resting state fMRI data to analyze the trend of functional connectivity alterations from a cognitively normal (CN) state through early and late mild cognitive impairment (EMCI and LMCI) and to Alzheimer's disease. The analyses had been done at the local (hubs and activated links and areas), meso (clustering, assortativity, and rich-club), and global (small-world, small-worldness, and efficiency) topological scales. The results showed that the trends of changes in the topological architecture of the functional brain network were not entirely proportional to the AD progression. There were network characteristics that have changed non-linearly regarding the disease progression, especially at the earliest stage of the disease, i.e., EMCI. Further, it has been indicated that the diseased groups engaged somatomotor, frontoparietal, and default mode modules compared to the CN group. The diseased groups also shifted the functional network towards more random architecture. In the end, the methods introduced in this paper enable us to gain an extensive understanding of the pathological changes of the AD process.

Longitudinal resting-state electroencephalography in patients with chronic pain undergoing interdisciplinary multimodal pain therapy

ABSTRACT

Chronic pain is a major healthcare issue posing a large burden on individuals and society. Converging lines of evidence indicate that chronic pain is associated with substantial changes of brain structure and function. However, it remains unclear which neuronal measures relate to changes of clinical parameters over time and could thus monitor chronic pain and treatment responses. We therefore performed a longitudinal study in which we assessed clinical characteristics and resting-state electroencephalography data of 41 patients with chronic pain before and 6 months after interdisciplinary multimodal pain therapy. We specifically assessed electroencephalography measures that have previously been shown to differ between patients with chronic pain and healthy people. These included the dominant peak frequency; the amplitudes of neuronal oscillations at theta, alpha, beta, and gamma frequencies; as well as graph theory-based measures of brain network organization. The results show that pain intensity, pain-related disability, and depression were significantly improved after interdisciplinary multimodal pain therapy. Bayesian hypothesis testing indicated that these clinical changes were not related to changes of the dominant peak frequency or amplitudes of oscillations at any frequency band. Clinical changes were, however, associated with an increase in global network efficiency at theta frequencies. Thus, changes in chronic pain might be reflected by global network changes in the theta band. These longitudinal insights further the understanding of the brain mechanisms of chronic pain. Beyond, they might help to identify biomarkers for the monitoring of chronic pain.

Neuropsychological networks in cognitively healthy older adults and dementia patients

Neuropsychological tests have commonly been used to determine the organization of cognitive functions by identifying latent variables. In contrast, an approach which has seldom been employed is network analysis. We characterize the network structure of a set of representative neuropsychological test scores in cognitively healthy older adults and MCI and dementia patients using network analysis. We employed the neuropsychological battery from the National Alzheimer's Coordinating Center which included healthy controls (n = 7623), mild cognitive impairment patients (n = 5981) and dementia patients (n = 2040), defined according to the Clinical Dementia Rating. The results showed that, according to several network analysis measures, the most central cognitive function is executive function followed by attention, language, and memory. At the test level, the most central test was the Trail Making Test B, which measures cognitive flexibility. Importantly, these results and most other network measures, such as the community organization and graph representation, were similar across the three diagnostic groups. Therefore, network analysis can help to establish a ranking of cognitive functions and tests based on network centrality and suggests that this organization is preserved in dementia. Central nodes might be particularly relevant both from a theoretical and clinical point of view, as they are more associated with other nodes, and their disruption is likely to have a larger effect on the overall network than peripheral nodes. The present analysis may provide a proof of principle for the application of network analysis to cognitive data.

Synchronization dynamics on power grids in Europe and the United States

Dynamical simulation of the cascade failures on the Europe and United States (U.S.) high-voltage power grids has been done via solving the second-order Kuramoto equation. We show that synchronization transition happens by increasing the global coupling parameter K with metasatble states depending on the initial conditions so that hysteresis loops occur. We provide analytic results for the time dependence of frequency spread in the large-K approximation and by comparing it with numerics of d=2,3 lattices, we find agreement in the case of ordered initial conditions. However, different power-law (PL) tails occur, when the fluctuations are strong. After thermalizing the systems we allow a single line cut failure and follow the subsequent overloads with respect to threshold values T. The PDFs p(N_{f}) of the cascade failures exhibit PL tails near the synchronization transition point K_{c}. Near K_{c} the exponents of the PLs for the U.S. power grid vary with T as 1.4≤τ≤2.1, in agreement with the empirical blackout statistics, while on the Europe power grid we find somewhat steeper PLs characterized by 1.4≤τ≤2.4. Below K_{c}, we find signatures of T-dependent PLs, caused by frustrated synchronization, reminiscent of Griffiths effects. Here we also observe stability growth following the blackout cascades, similar to intentional islanding, but for K>K_{c} this does not happen. For T<T_{c}, bumps appear in the PDFs with large mean values, known as "dragon king" blackout events. We also analyze the delaying or stabilizing effects of instantaneous feedback or increased dissipation and show how local synchronization behaves on geographic maps.

An exploration on the topologies of SARS-CoV-2/human protein-protein interaction network

Network biology is an important finding that uncovers the significant elements in viral infection control. Since viruses use the proteins on their surfaces to attach and enter into the host cell, the establishment of virus-host protein interactions is a potent regulator of the global organization of the viral life cycle after virus entry into host cells. In this instance, a topological study on the SARS-CoV-2/Human Protein-Protein Interaction Network (PPIN) evacuates much information about the protein-protein interactions. By making some interruptions to the interaction between proteins and hosts, we can quickly reduce the spread of the disease and get an insight into the target protein for drug development. This paper mainly focused on the graphical and structural complexity of the SARS-CoV-2/Human PPIN. For this purpose, the various primary (distance, radius, diameter, etc…) and advanced levels of graph measures (density, modularity, clustering coefficient, etc…) as well as a few fractal (box dimension, multifractal analysis) and entropy measures have been used. In addition, several graph descriptions and distribution graphs of PPIN offered to gain a thorough understanding of the SARS-CoV-2/Human PPIN. Conclusively, based on our work, we have discovered that PPIN is moderately complex and identified that hiring Nsp8 as a target node will positively affect the PPIN and has pointed out that mathematically found target proteins are matched with already suggested target proteins in the previous survey.Communicated by Ramaswamy H. Sarma.

Spontaneous Activity Predicts Survival of Developing Cortical Neurons

Spontaneous activity plays a crucial role in brain development by coordinating the integration of immature neurons into emerging cortical networks. High levels and complex patterns of spontaneous activity are generally associated with low rates of apoptosis in the cortex. However, whether spontaneous activity patterns directly encode for survival of individual cortical neurons during development remains an open question. Here, we longitudinally investigated spontaneous activity and apoptosis in developing cortical cultures, combining extracellular electrophysiology with calcium imaging. These experiments demonstrated that the early occurrence of calcium transients was strongly linked to neuronal survival. Silent neurons exhibited a higher probability of cell death, whereas high frequency spiking and burst behavior were almost exclusively detected in surviving neurons. In local neuronal clusters, activity of neighboring neurons exerted a pro-survival effect, whereas on the functional level, networks with a high modular topology were associated with lower cell death rates. Using machine learning algorithms, cell fate of individual neurons was predictable through the integration of spontaneous activity features. Our results indicate that high frequency spiking activity constrains apoptosis in single neurons through sustained calcium rises and thereby consolidates networks in which a high modular topology is reached during early development.

Diurnal variations of resting-state fMRI data: A graph-based analysis

Circadian rhythms (lasting approximately 24 h) control and entrain various physiological processes, ranging from neural activity and hormone secretion to sleep cycles and eating habits. Several studies have shown that time of day (TOD) is associated with human cognition and brain functions. In this study, utilizing a chronotype-based paradigm, we applied a graph theory approach on resting-state functional MRI (rs-fMRI) data to compare whole-brain functional network topology between morning and evening sessions and between morning-type (MT) and evening-type (ET) participants. Sixty-two individuals (31 MT and 31 ET) underwent two fMRI sessions, approximately 1 hour (morning) and 10 h (evening) after their wake-up time, according to their declared habitual sleep-wake pattern on a regular working day. In the global analysis, the findings revealed the effect of TOD on functional connectivity (FC) patterns, including increased small-worldness, assortativity, and synchronization across the day. However, we identified no significant differences based on chronotype categories. The study of the modular structure of the brain at mesoscale showed that functional networks tended to be more integrated with one another in the evening session than in the morning session. Local/regional changes were affected by both factors (i.e., TOD and chronotype), mostly in areas associated with somatomotor, attention, frontoparietal, and default networks. Furthermore, connectivity and hub analyses revealed that the somatomotor, ventral attention, and visual networks covered the most highly connected areas in the morning and evening sessions: the latter two were more active in the morning sessions, and the first was identified as being more active in the evening. Finally, we performed a correlation analysis to determine whether global and nodal measures were associated with subjective assessments across participants. Collectively, these findings contribute to an increased understanding of diurnal fluctuations in resting brain activity and highlight the role of TOD in future studies on brain function and the design of fMRI experiments.

Human lung-cancer-cell radioresistance investigated through 2D network topology

Radiation therapy (RT) is now considered to be a main component of cancer therapy, alongside surgery, chemotherapy and monoclonal antibody-based immunotherapy. In RT, cancer tissues are exposed to ionizing radiation causing the death of malignant cells and favoring cancer regression. However, the efficiency of RT may be hampered by cell-radioresistance (RR)—that is a feature of tumor cells of withstanding RT. To improve the RT performance, it is decisive developing methods that can help to quantify cell sensitivity to radiation. In acknowledgment of the fact that none of the existing methods to assess RR are based on cell graphs topology, in this work we have examined how 2D cell networks, within a single colony, from different human lung cancer lines (H460, A549 and Calu-1) behave in response to doses of ionizing radiation ranging from 0 to 8 Gy. We measured the structure of resulting cell-graphs using well-assessed networks-analysis metrics, such as the clustering coefficient (cc), the characteristic path length (cpl), and the small world coefficient (SW). Findings of the work illustrate that the clustering characteristics of cell-networks show a marked sensitivity to the dose and cell line. Higher-than-one values of SW coefficient, clue of a discontinuous and inhomogeneous cell spatial layout, are associated to elevated levels of radiation and to a lower radio-resistance of the treated cell line. Results of the work suggest that topology could be used as a quantitative parameter to assess the cell radio-resistance and measure the performance of cancer radiotherapy.

Inferring the underlying multivariate structure from bivariate networks with highly correlated nodes

Complex systems are often described mathematically as networks. Inferring the actual interactions from observed dynamics of the nodes of the networks is a challenging inverse task. It is crucial to distinguish direct and indirect interactions to allow for a robust identification of the underlying network. If strong and weak links are simultaneously present in the observed network, typical multivariate approaches to address this challenge fail. By means of correlation and partial correlation, we illustrate the challenges that arise and demonstrate how to overcome these. The challenge of strong and weak links translates into ill-conditioned matrices that need to be inverted to obtain the partial correlations, and therefore the correct network topology. Our novel procedure enables robust identification of multivariate network topologies in the presence of highly correlated processes. In applications, this is crucial to avoid erroneous conclusions about network structures and characteristics. Our novel approach applies to other types of interaction measures between processes in a network.