Statistical mechanics of community detection

Inverse relationship between nodal strength and nodal power: Insights from separate resting fMRI and EEG datasets

BACKGROUND

Regional neural response and network properties have traditionally been studied separately. However, growing evidence suggests a close interplay between regional activity and inter-regional connectivity. This study aimed to examine the relationship between global functional connectivity and regional spontaneous activity, termed the global-to-local relationship.

NEW METHOD

Resting-state fMRI data were parcellated using MOSI (modular analysis and similarity measurements), enabling multi-resolution functional partitioning. For each parcellated cluster, the mean amplitude of low-frequency fluctuations (node power) and its average functional connectivity with the remaining cortex (node strength) were computed. Correlation analyses assessed their relationship. A supplementary analysis was conducted on EEG data (1-30 Hz).

RESULTS

A significant negative correlation between node strength and regional power was observed in MRI datasets. One-sample t-tests confirmed robustness across different MOSI resolutions, with individual P values at the level 10-4 to 10-5. The negative relationship was also found in EEG data but was restricted to delta (1-4 Hz) and theta (4-8 Hz) bands.

COMPARISON WITH EXISTING METHODS

This study introduces two key novel aspects. First, it applies MOSI to the entire cortex, enhancing the comprehensiveness of network analysis. Second, it examines the global influence on regional neural activity, rather than limiting the focus to a specific network.

CONCLUSIONS

A robust negative relationship between node strength and node power was consistently observed across both MRI and EEG datasets, particularly in lower frequency bands (up to 8 Hz). These findings suggest a framework for investigating how global connectivity shapes regional neural activity, with inhibitory coupling as a potential underlying mechanism.

Dual temporal pathway model of emotion processing based on dynamic network reconfiguration analysis of EEG signals

Emotion is crucial for the quality of daily life. Recent findings suggest that the cooperation and integration of multiple brain regions are essential for effective emotion processing. Additionally, network reconfiguration has been observed during various cognitive tasks. However, it remains unclear how the brain responds to different emotional categories under natural stimuli from the perspective of network reconfiguration, or whether this reconfiguration can predict subjective rating scores. To address this question, 28 video clips were used to evoke eight distinct emotion categories, and the participants' electroencephalogram (EEG) signals were recorded. Dynamic network reconfiguration analysis was performed on brain networks extracted from band-limited EEG signals using the phase locking value (PLV) across multiple non-overlapping time windows. Robust dynamic community detection was applied to these networks, followed by quantification of integration and segregation at both node- and community-level changes. Multidimensional rating scores were collected for each clip. The analysis revealed that the metrics of dynamic network reconfiguration could predict subjective ratings. Specifically, longer EEG segments improved predictions for positive emotions, whereas shorter segments were more effective for negative emotions. Our study provides empirical evidence integrating the dual-process model and the theory of constructed emotion. Based on observed spatiotemporal patterns of global integration and segregation across the brain, we propose the dual temporal pathway model for emotional processing across various emotion categories, highlighting fast and slow neural processes associated with negative and positive emotions, respectively. These findings offer valuable support for developing temporally targeted diagnostic and therapeutic strategies for emotion-related brain disorders.

TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses

RNA-guided systems provide remarkable versatility, enabling diverse biological functions. Through iterative structural and sequence homology-based mining starting with a guide RNA-interaction domain of Cas9, we identified a family of RNA-guided DNA-targeting proteins in phage and parasitic bacteria. Each system consists of a tandem interspaced guide RNA (TIGR) array and a TIGR-associated (Tas) protein containing a nucleolar protein (Nop) domain, sometimes fused to HNH (TasH)- or RuvC (TasR)-nuclease domains. We show that TIGR arrays are processed into 36-nucleotide RNAs (tigRNAs) that direct sequence-specific DNA binding through a tandem-spacer targeting mechanism. TasR can be reprogrammed for precise DNA cleavage, including in human cells. The structure of TasR reveals striking similarities to box C/D small nucleolar ribonucleoproteins and IS110 RNA-guided transposases, providing insights into the evolution of diverse RNA-guided systems.

Machine learning and complex network analysis of drug effects on neuronal microelectrode biosensor data

Biosensors, such as microelectrode arrays that record in vitro neuronal activity, provide powerful platforms for studying neuroactive substances. This study presents a machine learning workflow to analyze drug-induced changes in neuronal biosensor data using complex network measures from graph theory. Microelectrode array recordings of neuronal networks exposed to bicuculline, a GABA[Formula: see text] receptor antagonist known to induce hypersynchrony, demonstrated the workflow's ability to detect and characterize pharmacological effects. The workflow integrates network-based features with synchrony, optimizing preprocessing parameters, including spike train bin sizes, segmentation window sizes, and correlation methods. It achieved high classification accuracy (AUC up to 90%) and used Shapley Additive Explanations to interpret feature importance rankings. Significant reductions in network complexity and segregation, hallmarks of epileptiform activity induced by bicuculline, were revealed. While bicuculline's effects are well established, this framework is designed to be broadly applicable for detecting both strong and subtle network alterations induced by neuroactive compounds. The results demonstrate the potential of this methodology for advancing biosensor applications in neuropharmacology and drug discovery.

Validation of an Adaptive Assessment of Executive Functions (Adaptive Cognitive Evaluation-Explorer): Longitudinal and Cross-Sectional Analyses of Cognitive Task Performance

BACKGROUND

Executive functions (EFs) predict positive life outcomes and educational attainment. Consequently, it is imperative that our measures of EF constructs are both reliable and valid, with advantages for research tools that offer efficiency and remote capabilities.

OBJECTIVE

The objective of this study was to evaluate reliability and validity evidence for a mobile, adaptive measure of EFs called Adaptive Cognitive Evaluation-Explorer (ACE-X).

METHODS

We collected data from 2 cohorts of participants: a test-retest sample (N=246, age: mean 35.75, SD 11.74 y) to assess consistency of ACE-X task performance over repeated administrations and a validation sample involving child or adolescent (5436/6052, 89.82%; age: mean 12.78, SD 1.60 years) and adult participants (484/6052, 8%; age: mean 38.11, SD 14.96 years) to examine consistency of metrics, internal structures, and invariance of ACE-X task performance. A subset of participants (132/6052, 2.18%; age: mean 37.04, SD 13.23 years) also completed a similar set of cognitive tasks using the Inquisit platform to assess the concurrent validity of ACE-X.

RESULTS

Intraclass correlation coefficients revealed most ACE-X tasks were moderately to very reliable across repeated assessments (intraclass correlation coefficient=0.45-0.79; P<.001). Moreover, in comparisons of internal structures of ACE-X task performance, model fit indices suggested that a network model based on partial correlations was the best fit to the data (χ228=40.13; P=.06; comparative fit index=0.99; root mean square error of approximation=0.03, 90% CI 0.00-0.05; Bayesian information criterion=5075.87; Akaike information criterion=4917.71) and that network edge weights are invariant across both younger and older adult participants. A Spinglass community detection algorithm suggested ACE-X task performance can be described by 3 communities (selected in 85% of replications): set reconfiguration, attentional control, and interference resolution. On the other hand, Pearson correlation coefficients indicated mixed results for the concurrent validity comparisons between ACE-X and Inquisit (r=-.05-.62, P<.001-.76).

CONCLUSIONS

These findings suggest that ACE-X is a reliable and valid research tool for understanding EFs and their relations to outcome measures.

Inhomogeneous graph trend filtering via a l 2,0 -norm cardinality penalty

We study estimation of piecewise smooth signals over a graph. We propose aℓ 2,0 -norm penalized Graph Trend Filtering (GTF) model to estimate piecewise smooth graph signals that exhibit inhomogeneous levels of smoothness across the nodes. We prove that the proposed GTF model is simultaneously a k-means clustering on the signal over the nodes and a minimum graph cut on the edges of the graph, where the clustering and the cut share the same assignment matrix. We propose two methods to solve the proposed GTF model: a spectral decomposition method and a method based on simulated annealing. In the experiment on synthetic and real-world datasets, we show that the proposed GTF model has a better performances compared with existing approaches on the tasks of denoising, support recovery and semi-supervised classification. We also show that the proposed GTF model can be solved more efficiently than existing models for the dataset with a large edge set.

Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data

BACKGROUND

The circadian clock is a central driver of many biological and behavioral processes, regulating the levels of many genes and proteins, termed clock controlled genes and proteins (CCGs/CCPs), to impart biological timing at the molecular level. While transcriptomic and proteomic data has been analyzed to find potential CCGs and CCPs, multi-omic modeling of circadian data, which has the potential to enhance the understanding of circadian control of biological timing, remains relatively rare due to several methodological hurdles. To address this gap, a dual-approach co-expression analysis framework (D-CAF) was created to perform co-expression analysis that is robust to Gaussian noise perturbations on time-series measurements of both transcripts and proteins.

RESULTS

Applying this D-CAF framework to previously gathered transcriptomic and proteomic data from mouse macrophages gathered over circadian time, we identified small, highly significant clusters of oscillating transcripts and proteins in the unweighted similarity matrices and larger, less significant clusters of of oscillating transcripts and proteins using the weighted similarity network. Functional enrichment analysis of these clusters identified novel immunological response pathways that appear to be under circadian control.

CONCLUSIONS

Overall, our findings suggest that D-CAF is a tool that can be used by the circadian community to integrate multi-omic circadian data to improve our understanding of the mechanisms of circadian regulation of molecular processes.

Perceptual and semantic maps in individual humans share structural features that predict creative abilities

Building perceptual and associative links between internal representations is a fundamental neural process, allowing individuals to structure their knowledge about the world and combine it to enable efficient and creative behavior. In this context, the representational similarity between pairs of represented entities is thought to reflect their associative linkage at different levels of sensory processing, ranging from lower-order perceptual levels up to higher-order semantic levels. While recently specific structural features of semantic representational maps were linked with creative abilities of individual humans, it remains unclear if these features are also shared on lower level, perceptual maps. Here, we address this question by presenting 148 human participants with psychophysical scaling tasks, using two sets of independent and qualitatively distinct stimuli, to probe representational map structures in the lower-order auditory and the higher-order semantic domain. We quantify individual representational features with graph-theoretical measures and demonstrate a robust correlation of representational structures in the perceptual auditory and semantic modality. We delineate these shared representational features to predict multiple verbal standard measures of creativity, observing that both, semantic and auditory features, reflect creative abilities. Our findings indicate that the general, modality-overarching representational geometry of an individual is a relevant underpinning of creative thought.

Parallel median consensus clustering in complex networks

We develop an algorithm that finds the consensus among many different clustering solutions of a graph. We formulate the problem as a median set partitioning problem and propose a greedy optimization technique. Unlike other approaches that find median set partitions, our algorithm takes graph structure into account and finds a comparable quality solution much faster than the other approaches. For graphs with known communities, our consensus partition captures the actual community structure more accurately than alternative approaches. To make it applicable to large graphs, we remove sequential dependencies from our algorithm and design a parallel algorithm. Our parallel algorithm achieves 35x speedup when utilizing 64 processing cores for large real-world graphs representing mass cytometry data from single-cell experiments.

Detectability constraints on meso-scale structure in complex networks

Community, core-periphery, disassortative and other node partitions allow us to understand the organisation and function of large networks. In this work we study common meso-scale structures using the idea of block modularity. We find that the configuration model imposes strong restrictions on core-periphery and related structures in directed and undirected networks. We derive inequalities expressing when such structures can be detected under the configuration model which are closely related to the resolution limit. Nestedness is closely related to core-periphery and is similarly restricted to only be detectable under certain conditions. We then derive a general equivalence between optimising block modularity and maximum likelihood estimation of the parameters of the degree corrected Stochastic Block Model. This allows us to contrast the two approaches, how they formalise the structure detection problem and understand these constraints in inferential versus descriptive approaches to meso-scale structure detection.

Longitudinal evolution of the transdiagnostic prodrome to severe mental disorders: a dynamic temporal network analysis informed by natural language processing and electronic health records

Modelling the prodrome to severe mental disorders (SMD), including unipolar mood disorders (UMD), bipolar mood disorders (BMD) and psychotic disorders (PSY), should consider both the evolution and interactions of symptoms and substance use (prodromal features) over time. Temporal network analysis can detect causal dependence between and within prodromal features by representing prodromal features as nodes, with their connections (edges) indicating the likelihood of one feature preceding the other. In SMD, node centrality could reveal insights into important prodromal features and potential intervention targets. Community analysis can identify commonly occurring feature groups to define SMD at-risk states. This retrospective (2-year) cohort study aimed to develop a global transdiagnostic SMD network of the temporal relationships between prodromal features and to examine within-group differences with sub-networks specific to UMD, BMD and PSY. Electronic health records (EHRs) from South London and Maudsley (SLaM) NHS Foundation Trust were included from 6462 individuals with SMD diagnoses (UMD:2066; BMD:740; PSY:3656). Validated natural language processing algorithms extracted the occurrence of 61 prodromal features every three months from two years to six months before SMD onset. Temporal networks of prodromal features were constructed using generalised vector autoregression panel analysis, adjusting for covariates. Edge weights (partial directed correlation coefficients, z) were reported in autocorrelative, unidirectional and bidirectional relationships. Centrality was calculated as the sum of (non-autoregressive) connections leaving (out-centrality, cout) or entering (in-centrality, cin) a node. The three sub-networks (UMD, BMD, PSY) were compared using permutation analysis, and community analysis was performed using Spinglass. The SMD network revealed strong autocorrelations (0.04 ≤ z ≤ 0.10), predominantly positive connections, and identified aggression (cout = 0.103) and tearfulness (cin = 0.134) as the most central features. Sub-networks for UMD, BMD, and PSY showed minimal differences, with 3.5% of edges differing between UMD and PSY, 0.8% between UMD and BMD, and 0.4% between BMD and PSY. Community analysis identified one positive psychotic community (delusional thinking-hallucinations-paranoia) and two behavioural communities (aggression-cannabis use-cocaine use-hostility, aggression-agitation-hostility) as the most common. This study represents the most extensive temporal network analysis conducted on the longitudinal interplay of SMD prodromal features. The findings provide further evidence to support transdiagnostic early detection services across SMD, refine assessments to detect individuals at risk and identify central features as potential intervention targets.

Linking new national active biomonitoring data with stream macroinvertebrate communities suggests large-scale effects of toxic contamination on freshwater ecosystems

Since recent years, an increasingly large number of toxic chemicals enters watercourses threatening freshwater biodiversity. But ecological studies still poorly document the quantitative patterns linking exposure to complex mixture of toxic chemicals and species communities' integrity in the field. In this context, French monitoring authorities have recently deployed at a national scale in situ biotests using the feeding inhibition of the crustacean Gammarus as toxicity indicator. In this paper, we conjointly exploit this new type of biomonitoring dataset and ecological data for macroinvertebrates to gain information about the structuring influence of toxicity on aquatic communities. Especially, we used multivariate analyses with variation partitioning for testing the hypothesis that toxicity (feeding inhibition index) can explain variations in the taxonomical composition between 76 stations on French streams while, for different spatial scales, estimating the confounding influences of other environmental and spatial factors. Our results showed that changes in the toxicity indicator were significantly associated with specific changes in the taxonomic composition of stream macroinvertebrate communities. That association was weakly confounded with the effects of environmental and spatial factors, especially at the largest spatial scale considered. That taxon turnover linked to toxicity was associated with reduced richness at the community scale, and the replacement of native taxa by alien taxa. Overall, our study thus supports the hypothesis that toxic contamination modifies the structure of stream communities and ergo threatens aquatic biodiversity.

Graph-Theoretical Prediction and Analysis of Biologically Relevant Substructures in an Open and Closed Conformation of Respiratory Complex I

Protein complexes are functional modules within the hierarchy of the cellular organization. Large protein complexes often consist of smaller functional modules, which are biologically relevant substructures with specific functions. The first protein complex of the respiratory chain, complex I, consists of functional modules for the electron transfer from NADH to quinone and the translocation of protons across the inner mitochondrial membrane. Complex I is well-characterized and biological modules have been experimentally assigned. Nevertheless, there is an ongoing discussion about the coupling of the electron transfer and the proton translocation, and about the proton translocation pathways.We modelled a mammalian complex I in open and closed conformations as complex graphs, with vertices representing protein chains and edges representing chain-chain contacts. Using a graph-theoretical method, we computed the structural modules of complex I, which indicated functional, biological substructures. We described characteristic structural features of complex I and observed a rearrangement of the structural modules. The changes in the structural modules indicated the formation of a functional module in the membrane arm of complex I during the conformational change.

Coexisting patterns of posttraumatic stress disorder and depression symptoms in college students who experienced childhood maltreatment: Different types of maltreatment exposure

BACKGROUND

Childhood maltreatment is often associated with comorbid posttraumatic stress disorder (PTSD) and depression, but the impact of different types of maltreatment on this comorbidity is not well understood.

METHODS

Using network analysis, we examined differences in comorbidity patterns of PTSD and depression symptoms among college students who experienced different forms of childhood maltreatment. We selected a subsample of 2968 students (Mage = 19.38, SD = ±1.45) who reported exposure to childhood maltreatment from a larger sample of 5231 students.

RESULTS

This study showed that symptoms of negative emotions and cognitive change, intrusive symptoms, and increased alertness might play a significant role in the diagnosis and prognosis of comorbid PTSD and depression. The most central nodes in the network of physical maltreatment were flashbacks, and irritability, whereas the most central nodes in the network of emotional and compound trauma, were low mood and sadness. Moreover, network structure and strength differed significantly between maltreatment types, and differences in specific symptom associations were also observed.

CONCLUSION

Network analysis provides insights into which symptoms contribute to the development of comorbidities in individuals with different childhood maltreatment types, as well as how specific symptoms are interconnected in the network. This information can aid in developing targeted and effective interventions for different maltreatment forms.

Discovering prominent differences in structural and functional connectomes using a multinomial stochastic block model

Understanding the differences between functional and structural human brain connectivity has been a focus of an extensive amount of neuroscience research. We employ a novel approach using the multinomial stochastic block model (MSBM) to explicitly extract components that characterize prominent differences across graphs. We analyze structural and functional connectomes derived from high-resolution diffusion-weighted MRI and fMRI scans of 250 Human Connectome Project subjects, analyzed at group connectivity level across 50 subjects. The inferred brain partitions revealed consistent, spatially homogeneous clustering patterns across inferred resolutions demonstrating the MSBM's reliability in identifying brain areas with prominent structure-function differences. Prominent differences in low-resolution brain maps (K = {3, 4} clusters) were attributed to weak functional connectivity in the bilateral anterior temporal lobes, while higher resolution results (K ≥ 25) revealed stronger interhemispheric functional than structural connectivity. Our findings emphasize significant differences in high-resolution functional and structural connectomes, revealing challenges in extracting meaningful connectivity measurements from both modalities, including tracking fibers through the corpus callosum and attenuated functional connectivity in anterior temporal lobe fMRI data, which we attribute to increased noise levels. The MSBM emerges as a valuable tool for understanding differences across graphs, with potential future applications and avenues beyond the current focus on characterizing modality-specific distinctions in connectomics data.

Transcranial ultrasound stimulation effect in the redundant and synergistic networks consistent across macaques

Low-intensity transcranial ultrasound stimulation (TUS) is a noninvasive technique that safely alters neural activity, reaching deep brain areas with good spatial accuracy. We investigated the effects of TUS in macaques using a recent metric, the synergy minus redundancy rank gradient, which quantifies different kinds of neural information processing. We analyzed this high-order quantity on the fMRI data after TUS in two targets: the supplementary motor area (SMA-TUS) and the frontal polar cortex (FPC-TUS). The TUS produced specific changes at the limbic network at FPC-TUS and the motor network at SMA-TUS and altered the sensorimotor, temporal, and frontal networks in both targets, mostly consistent across macaques. Moreover, there was a reduction in the structural and functional coupling after both stimulations. Finally, the TUS changed the intrinsic high-order network topology, decreasing the modular organization of the redundancy at SMA-TUS and increasing the synergistic integration at FPC-TUS.

Predicting modular functions and neural coding of behavior from a synaptic wiring diagram

A long-standing goal in neuroscience is to understand how a circuit's form influences its function. Here, we reconstruct and analyze a synaptic wiring diagram of the larval zebrafish brainstem to predict key functional properties and validate them through comparison with physiological data. We identify modules of strongly connected neurons that turn out to be specialized for different behavioral functions, the control of eye and body movements. The eye movement module is further organized into two three-block cycles that support the positive feedback long hypothesized to underlie low-dimensional attractor dynamics in oculomotor control. We construct a neural network model based directly on the reconstructed wiring diagram that makes predictions for the cellular-resolution coding of eye position and neural dynamics. These predictions are verified statistically with calcium imaging-based neural activity recordings. This work demonstrates how connectome-based brain modeling can reveal previously unknown anatomical structure in a neural circuit and provide insights linking network form to function.

Prefrontal multistimulus integration within a dedicated disambiguation circuit guides interleaving contingency judgment learning

Understanding how cortical network dynamics support learning is a challenge. This study investigates the role of local neural mechanisms in the prefrontal cortex during contingency judgment learning (CJL). To better understand brain network mechanisms underlying CJL, we introduce ambiguity into associative learning after fear acquisition, inducing a generalized fear response to an ambiguous stimulus sharing nontrivial similarities with the conditioned stimulus. Real-time recordings at single-neuron resolution from the prelimbic (PL) cortex show distinct PL network dynamics across CJL phases. Fear acquisition triggers PL network reorganization, led by a disambiguation circuit managing spurious and predictive relationships during cue-danger, cue-safety, and cue-neutrality contingencies. Mice with PL-targeted memory deficiency show malfunctioning disambiguation circuit function, while naive mice lacking unconditioned stimulus exposure lack the disambiguation circuit. This study shows that fear conditioning induces prefrontal cortex cognitive map reorganization and that subsequent CJL relies on the disambiguation circuit's ability to learn predictive relationships.

A multilayer network analysis of Alzheimer's disease pathogenesis: Roles for p-tau, synaptic peptides, and physical activity

INTRODUCTION

In the aging brain, cognitive abilities emerge from the coordination of complex pathways arising from a balance between protective lifestyle and environmental factors and accumulation of neuropathologies.

METHODS

As part of the Rush Memory and Aging Project (n = 440), we measured accelerometer-based actigraphy, cognitive performance, and after brain autopsy, selected reaction monitoring mass spectrometry. Multilevel network analysis was used to examine the relationships among the molecular machinery of vesicular neurotransmission, Alzheimer's disease (AD) neuropathology, cognition, and late-life physical activity.

RESULTS

Synaptic peptides involved in neuronal secretory function were the most influential contributors to the multilayer network, reflecting the complex interdependencies among AD pathology, synaptic processes, and late-life cognition. Older adults with lower physical activity evidenced stronger adverse relationships among phosphorylated tau peptides, markers of synaptic integrity, and tangle pathology.

DISCUSSION

Network-based approaches simultaneously model interdependent biological processes and advance understanding of the role of physical activity in age-associated cognitive impairment.

HIGHLIGHTS

Network-based approaches simultaneously model interdependent biological processes. Secretory synaptic peptides were influential contributors to the multilayer network. Older adults with lower physical activity had adverse relationships among pathology. There was interdependence among phosphorylated tau, synaptic integrity, and tangles. Network methods elucidate the role of physical activity in cognitive impairment.

Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics

Modeling the network topology of the human brain within the mesoscale has become an increasing focus within the neuroscientific community due to its variation across diverse cognitive processes, in the presence of neuropsychiatric disease or injury, and over the lifespan. Much research has been done on the creation of algorithms to detect these mesoscopic structures, called communities or modules, but less has been done to conduct inference on these structures. The literature on analysis of these community detection algorithms has focused on comparing them within the same subject. These approaches, however, either do not accomodate a more general association between community structure and an outcome or cannot accommodate additional covariates that may confound the association of interest. We propose a semiparametric kernel machine regression model for either a continuous or binary outcome, where covariate effects are modeled parametrically and brain connectivity measures are measured nonparametrically. By incorporating notions of similarity between network community structures into a kernel distance function, the high-dimensional feature space of brain networks, defined on input pairs, can be generalized to non-linear spaces, allowing for a wider class of distance-based algorithms. We evaluate our proposed methodology on both simulated and real datasets.

Scalable identification of lineage-specific gene regulatory networks from metacells with NetID

The identification of gene regulatory networks (GRNs) is crucial for understanding cellular differentiation. Single-cell RNA sequencing data encode gene-level covariations at high resolution, yet data sparsity and high dimensionality hamper accurate and scalable GRN reconstruction. To overcome these challenges, we introduce NetID leveraging homogenous metacells while avoiding spurious gene-gene correlations. Benchmarking demonstrates superior performance of NetID compared to imputation-based methods. By incorporating cell fate probability information, NetID facilitates the prediction of lineage-specific GRNs and recovers known network motifs governing bone marrow hematopoiesis, making it a powerful toolkit for deciphering gene regulatory control of cellular differentiation from large-scale single-cell transcriptome data.

Multiclass classification of Autism Spectrum Disorder, attention deficit hyperactivity disorder, and typically developed individuals using fMRI functional connectivity analysis

Neurodevelopmental conditions, such as Autism Spectrum Disorder (ASD) and Attention Deficit Hyperactivity Disorder (ADHD), present unique challenges due to overlapping symptoms, making an accurate diagnosis and targeted intervention difficult. Our study employs advanced machine learning techniques to analyze functional magnetic resonance imaging (fMRI) data from individuals with ASD, ADHD, and typically developed (TD) controls, totaling 120 subjects in the study. Leveraging multiclass classification (ML) algorithms, we achieve superior accuracy in distinguishing between ASD, ADHD, and TD groups, surpassing existing benchmarks with an area under the ROC curve near 98%. Our analysis reveals distinct neural signatures associated with ASD and ADHD: individuals with ADHD exhibit altered connectivity patterns of regions involved in attention and impulse control, whereas those with ASD show disruptions in brain regions critical for social and cognitive functions. The observed connectivity patterns, on which the ML classification rests, agree with established diagnostic approaches based on clinical symptoms. Furthermore, complex network analyses highlight differences in brain network integration and segregation among the three groups. Our findings pave the way for refined, ML-enhanced diagnostics in accordance with established practices, offering a promising avenue for developing trustworthy clinical decision-support systems.

Dual-Approach Co-expression Analysis Framework (D-CAF) Enables Identification of Novel Circadian Regulation From Multi-Omic Timeseries Data

The circadian clock is a central driver of many biological and behavioral processes, regulating the levels of many genes and proteins, termed clock controlled genes and proteins (CCGs/CCPs), to impart biological timing at the molecular level. While transcriptomic and proteomic data has been analyzed to find potential CCGs and CCPs, multi-omic modeling of circadian data, which has the potential to enhance the understanding of circadian control of biological timing, remains relatively rare due to several methodological hurdles. To address this gap, a Dual-approach Co-expression Analysis Framework (D-CAF) was created to perform perturbation-robust co-expression analysis on time-series measurements of both transcripts and proteins. Applying this D-CAF framework to previously gathered transcriptomic and proteomic data from mouse macrophages gathered over circadian time, we identified small, highly significant clusters of oscillating transcripts and proteins in the unweighted similarity matrices and larger, less significant clusters of of oscillating transcripts and proteins using the weighted similarity network. Functional enrichment analysis of these clusters identified novel immunological response pathways that appear to be under circadian control. Overall, our findings suggest that D-CAF is a tool that can be used by the circadian community to integrate multi-omic circadian data to improve our understanding of the mechanisms of circadian regulation of molecular processes.

Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart

Metagenomic Hi-C (metaHi-C) has shown remarkable potential for retrieving high-quality metagenome-assembled genomes from complex microbial communities. Nevertheless, existing metaHi-C-based contig binning methods solely rely on Hi-C interactions between contigs, disregarding crucial biological information such as the presence of single-copy marker genes. To overcome this limitation, we introduce ImputeCC, an integrative contig binning tool optimized for metaHi-C datasets. ImputeCC integrates both Hi-C interactions and the discriminative power of single-copy marker genes to group marker-gene-containing contigs into preliminary bins. It also introduces a novel constrained random walk with restart algorithm to enhance Hi-C connectivity among contigs. Comprehensive assessments using both mock and real metaHi-C datasets from diverse environments demonstrate that ImputeCC consistently outperforms other Hi-C-based contig binning tools. A genus-level analysis of the sheep gut microbiota reconstructed by ImputeCC underlines its capability to recover key species from dominant genera and identify previously unknown genera.

Bayan algorithm: Detecting communities in networks through exact and approximate optimization of modularity

Community detection is a classic network problem with extensive applications in various fields. Its most common method is using modularity maximization heuristics which rarely return an optimal partition or anything similar. Partitions with globally optimal modularity are difficult to compute, and therefore have been underexplored. Using structurally diverse networks, we compare 30 community detection methods including our proposed algorithm that offers optimality and approximation guarantees: the Bayan algorithm. Unlike existing methods, Bayan globally maximizes modularity or approximates it within a factor. Our results show the distinctive accuracy and stability of maximum-modularity partitions in retrieving planted partitions at rates higher than most alternatives for a wide range of parameter settings in two standard benchmarks. Compared to the partitions from 29 other algorithms, maximum-modularity partitions have the best medians for description length, coverage, performance, average conductance, and well clusteredness. These advantages come at the cost of additional computations which Bayan makes possible for small networks (networks that have up to 3000 edges in their largest connected component). Bayan is several times faster than using open-source and commercial solvers for modularity maximization, making it capable of finding optimal partitions for instances that cannot be optimized by any other existing method. Our results point to a few well-performing algorithms, among which Bayan stands out as the most reliable method for small networks. A python implementation of the Bayan algorithm (bayanpy) is publicly available through the package installer for python.

Comparing the Clique Percolation algorithm to other overlapping community detection algorithms in psychological networks: A Monte Carlo simulation study

In psychological networks, one limitation of the most used community detection algorithms is that they can only assign each node (symptom) to a unique community, without being able to identify overlapping symptoms. The clique percolation (CP) is an algorithm that identifies overlapping symptoms but its performance has not been evaluated in psychological networks. In this study, we compare the CP with model parameters chosen based on fuzzy modularity (CPMod) with two other alternatives, the ratio of the two largest communities (CPRat), and entropy (CPEnt). We evaluate their performance to: (1) identify the correct number of latent factors (i.e., communities); and (2) identify the observed variables with substantive (and equally sized) cross-loadings (i.e., overlapping symptoms). We carried out simulations under 972 conditions (3x2x2x3x3x3x3): (1) data categories (continuous, polytomous and dichotomous); (2) number of factors (two and four); (3) number of observed variables per factor (four and eight); (4) factor correlations (0.0, 0.5, and 0.7); (5) size of primary factor loadings (0.40, 0.55, and 0.70); (6) proportion of observed variables with substantive cross-loadings (0.0%, 12.5%, and 25.0%); and (7) sample size (300, 500, and 1000). Performance was evaluated through the Omega index, Mean Bias Error (MBE), Mean Absolute Error (MAE), sensitivity, specificity, and mean number of isolated nodes. We also evaluated two other methods, Exploratory Factor Analysis and the Walktrap algorithm modified to consider overlap (EFA-Ov and Walk-Ov, respectively). The Walk-Ov displayed the best performance across most conditions and is the recommended option to identify communities with overlapping symptoms in psychological networks.

A comparative anatomical network analysis of the human and chimpanzee brains

Spatial interactions among anatomical elements help to identify topological factors behind morphological variation and can be investigated through network analysis. Here, a whole-brain network model of the chimpanzee (Pan troglodytes, Blumenbach 1776) is presented, based on macroanatomical divisions, and compared with a previous equivalent model of the human brain. The goal was to contrast which regions are essential in the geometric balance of the brains of the two species, to compare underlying phenotypic patterns of spatial variation, and to understand how these patterns might have influenced the evolution of human brain morphology. The human and chimpanzee brains share morphologically complex inferior-medial regions and a topological organization that matches the spatial constraints exerted by the surrounding braincase. These shared topological features are interesting because they can be traced back to the Chimpanzee-Human Last Common Ancestor, 7-10 million years ago. Nevertheless, some key differences are found in the human and chimpanzee brains. In humans, the temporal lobe, particularly its deep and medial limbic aspect (the parahippocampal gyrus), is a crucial node for topological complexity. Meanwhile, in chimpanzees, the cerebellum is, in this sense, more embedded in an intricate spatial position. This information helps to interpret brain macroanatomical change in fossil hominids.

Age-related differences in resting-state, task-related, and structural brain connectivity: graph theoretical analyses and visual search performance

Previous magnetic resonance imaging (MRI) research suggests that aging is associated with a decrease in the functional interconnections within and between groups of locally organized brain regions (modules). Further, this age-related decrease in the segregation of modules appears to be more pronounced for a task, relative to a resting state, reflecting the integration of functional modules and attentional allocation necessary to support task performance. Here, using graph-theoretical analyses, we investigated age-related differences in a whole-brain measure of module connectivity, system segregation, for 68 healthy, community-dwelling individuals 18-78 years of age. We obtained resting-state, task-related (visual search), and structural (diffusion-weighted) MRI data. Using a parcellation of modules derived from the participants' resting-state functional MRI data, we demonstrated that the decrease in system segregation from rest to task (i.e., reconfiguration) increased with age, suggesting an age-related increase in the integration of modules required by the attentional demands of visual search. Structural system segregation increased with age, reflecting weaker connectivity both within and between modules. Functional and structural system segregation had qualitatively different influences on age-related decline in visual search performance. Functional system segregation (and reconfiguration) influenced age-related decline in the rate of visual evidence accumulation (drift rate), whereas structural system segregation contributed to age-related slowing of encoding and response processes (nondecision time). The age-related differences in the functional system segregation measures, however, were relatively independent of those associated with structural connectivity.

Finding Similarities in Differences Between Autistic Adults: Two Replicated Subgroups

Autism is heterogeneous, which complicates providing tailored support and future prospects. We aim to identify subgroups in autistic adults with average to high intelligence, to clarify if certain subgroups might need support. We included 14 questionnaire variables related to aging and/or autism (e.g., demographic, psychological, and lifestyle). Community detection analysis was used for subgroup identification in an original sample of 114 autistic adults with an adulthood diagnosis (autism) and 58 non-autistic adults as comparison group (COMP), and a replication sample (NAutism = 261; NCOMP = 287), both aged 30-89 years. Next, we identified subgroups and assessed external validity (for cognitive and psychological difficulties, and quality of life [QoL]) in the autism samples. To test specificity, we repeated the analysis after adding 123 adults with ADHD, aged 30-80 years. As expected, the autism and COMP groups formed distinct subgroups. Among autistic adults, we identified three subgroups of which two were replicated. One of these subgroups seemed most vulnerable on the cluster variables; this subgroup also reported the most cognitive and psychological difficulties, and lowest QoL. Adding the ADHD group did not alter results. Within autistic adults, one subgroup could especially benefit from support and specialized care, although this must be tested in future studies.

A simplex path integral and a simplex renormalization group for high-order interactions. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024;87:087601. [PMID: 39077989 DOI: 10.1088/1361-6633/ad5c99] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Modern theories of phase transitions and scale invariance are rooted in path integral formulation and renormalization groups (RGs). Despite the applicability of these approaches in simple systems with only pairwise interactions, they are less effective in complex systems with undecomposable high-order interactions (i.e. interactions among arbitrary sets of units). To precisely characterize the universality of high-order interacting systems, we propose a simplex path integral and a simplex RG (SRG) as the generalizations of classic approaches to arbitrary high-order and heterogeneous interactions. We first formalize the trajectories of units governed by high-order interactions to define path integrals on corresponding simplices based on a high-order propagator. Then, we develop a method to integrate out short-range high-order interactions in the momentum space, accompanied by a coarse graining procedure functioning on the simplex structure generated by high-order interactions. The proposed SRG, equipped with a divide-and-conquer framework, can deal with the absence of ergodicity arising from the sparse distribution of high-order interactions and can renormalize a system with intertwined high-order interactions at thep-order according to its properties at theq-order (p⩽q). The associated scaling relation and its corollaries provide support to differentiate among scale-invariant, weakly scale-invariant, and scale-dependent systems across different orders. We validate our theory in multi-order scale-invariance verification, topological invariance discovery, organizational structure identification, and information bottleneck analysis. These experiments demonstrate the capability of our theory to identify intrinsic statistical and topological properties of high-order interacting systems during system reduction.

Targeted co-expression networks for the study of traits

Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used approach for the generation of gene co-expression networks. However, networks generated with this tool usually create large modules with a large set of functional annotations hard to decipher. We have developed TGCN, a new method to create Targeted Gene Co-expression Networks. This method identifies the transcripts that best predict the trait of interest based on gene expression using a refinement of the LASSO regression. Then, it builds the co-expression modules around those transcripts. Algorithm properties were characterized using the expression of 13 brain regions from the Genotype-Tissue Expression project. When comparing our method with WGCNA, TGCN networks lead to more precise modules that have more specific and yet rich biological meaning. Then, we illustrate its applicability by creating an APP-TGCN on The Religious Orders Study and Memory and Aging Project dataset, aiming to identify the molecular pathways specifically associated with APP role in Alzheimer's disease. Main biological findings were further validated in two independent cohorts. In conclusion, we provide a new framework that serves to create targeted networks that are smaller, biologically relevant and useful in high throughput hypothesis driven research. The TGCN R package is available on Github: https://github.com/aliciagp/TGCN .

A Novel Registration Framework for Aligning Longitudinal Infant Brain Tensor Images

Registering longitudinal infant brain images is challenging, as the infant brain undergoes rapid changes in size, shape and tissue contrast in the first months and years of life. Diffusion tensor images (DTI) have relatively consistent tissue properties over the course of infancy compared to commonly used T1 or T2-weighted images, presenting great potential for infant brain registration. Moreover, groupwise registration has been widely used in infant neuroimaging studies to reduce bias introduced by predefined atlases that may not be well representative of samples under study. To date, however, no methods have been developed for groupwise registration of tensor-based images. Here, we propose a novel registration approach to groupwise align longitudinal infant DTI images to a sample-specific common space. Longitudinal infant DTI images are first clustered into more homogenous subgroups based on image similarity using Louvain clustering. DTI scans are then aligned within each subgroup using standard tensor-based registration. The resulting images from all subgroups are then further aligned onto a sample-specific common space. Results show that our approach significantly improved registration accuracy both globally and locally compared to standard tensor-based registration and standard fractional anisotropy-based registration. Additionally, clustering based on image similarity yielded significantly higher registration accuracy compared to no clustering, but comparable registration accuracy compared to clustering based on chronological age. By registering images groupwise to reduce registration bias and capitalizing on the consistency of features in tensor maps across early infancy, our groupwise registration framework facilitates more accurate alignment of longitudinal infant brain images.

Finding multifaceted communities in multiplex networks

Identifying communities in multilayer networks is crucial for understanding the structural dynamics of complex systems. Traditional community detection algorithms often overlook the presence of overlapping edges within communities, despite the potential significance of such relationships. In this work, we introduce a novel modularity measure designed to uncover communities where nodes share specific multiple facets of connectivity. Our approach leverages a null network, an empirical layer of the multiplex network, not a random network, that can be one of the network layers or a complement graph of that, depending on the objective. By analyzing real-world social networks, we validate the effectiveness of our method in identifying meaningful communities with overlapping edges. The proposed approach offers valuable insights into the structural dynamics of multiplex systems, shedding light on nodes that share similar multifaceted connections.

Family Environmental Risk and Perceived Stress in Adolescent Depressive Symptoms: A Network Analysis

This study, grounded in the Process-Person-Context-Time framework, investigates the complex interplay of family environmental factors and their influence on adolescent depressive symptoms, focusing on the role of 'perceived stress'. Using network analysis, we examined data from 735 junior high students (52.1% female adolescents) from three provinces in China (Jiangsu, Shandong, and Henan), with an average age of 13.81 ± 0.92 years, ranging from 12 to 16 years, exploring the relationships between depressive symptoms, perceived stress, and seven family risk factors. The analysis identified three distinct communities. The incorporation of perceived stress led to its integration into a community that included depressive symptoms, parental restrictive monitoring, and family economic strain. Perceived stress emerged as the strongest predictor of depressive symptoms, surpassing parental restrictive monitoring. Furthermore, it overtook depressive symptoms as the node with the strongest bridging connection within its community. These findings underscore the importance of interventions targeting both family conditions and the internal processing of these stressors by adolescents, especially in challenging family environments, to mitigate the risk of depression and promote resilience.

Repression of developmental transcription factor networks triggers aging-associated gene expression in human glial progenitor cells

Human glial progenitor cells (hGPCs) exhibit diminished expansion competence with age, as well as after recurrent demyelination. Using RNA-sequencing to compare the gene expression of fetal and adult hGPCs, we identify age-related changes in transcription consistent with the repression of genes enabling mitotic expansion, concurrent with the onset of aging-associated transcriptional programs. Adult hGPCs develop a repressive transcription factor network centered on MYC, and regulated by ZNF274, MAX, IKZF3, and E2F6. Individual over-expression of these factors in iPSC-derived hGPCs lead to a loss of proliferative gene expression and an induction of mitotic senescence, replicating the transcriptional changes incurred during glial aging. miRNA profiling identifies the appearance of an adult-selective miRNA signature, imposing further constraints on the expansion competence of aged GPCs. hGPC aging is thus associated with acquisition of a MYC-repressive environment, suggesting that suppression of these repressors of glial expansion may permit the rejuvenation of aged hGPCs.

Network Structure and Clustering Analysis Relating to Individual Symptoms of Problematic Internet Use in a Community Adolescent Population

INTRODUCTION

Problematic internet use (PIU) is a psychopathology that includes multiple symptoms and psychological constructs. Because no studies have considered both network structures and clusters among individual symptoms in the context of PIU in a Korean adolescent population, this study aimed to investigate network structures and clustering in relation to PIU symptoms in adolescents.

METHODS

Overall, 73,238 adolescents were included. PIU severity was assessed using a self-rating scale comprising 20 items and 6 subscales, namely, the Internet Addiction Proneness Scale for Youth-Short Form; KS scale. Network structures and clusters among symptoms were analyzed using a Gaussian graphical model and exploratory graph analysis, respectively. Centrality of strength, closeness, and betweenness scores was also calculated.

RESULTS

Our study identified four clusters: disturbance in adaptive functioning, virtual interpersonal relationships, withdrawal, and tolerance. The symptom of confidence served as a node bridging the cluster of virtual interpersonal relationships and other clusters of withdrawal and disturbances of adaptive function. The symptom of craving served as a bridge between the clusters of withdrawal and tolerance with high betweenness centrality.

CONCLUSION

This study identified network structures and clustering among PIU symptoms in adolescents and revealed that positive experiences derived from online interpersonal relationships were an important mechanism underlying PIU. These are novel insights concerning the interconnection among multiple symptoms and related clustering for the mechanism of adolescent PIU in terms of KS-scale PIU assessment.

Community detection in directed weighted networks using Voronoi partitioning

Community detection is a ubiquitous problem in applied network analysis, however efficient techniques do not yet exist for all types of network data. Directed and weighted networks are an example, where the different information encoded by link weights and the possibly high graph density can cause difficulties for some approaches. Here we present an algorithm based on Voronoi partitioning generalized to deal with directed weighted networks. As an added benefit, this method can directly employ edge weights that represent lengths, in contrast to algorithms that operate with connection strengths, requiring ad-hoc transformations of length data. We demonstrate the method on inter-areal brain connectivity, air transportation networks, and several social networks. We compare the performance with several other well-known algorithms, applying them on a set of randomly generated benchmark networks. The algorithm can handle dense graphs where weights are the main factor determining communities. The hierarchical structure of networks can also be detected, as shown for the brain. Its time efficiency is comparable or even outperforms some of the state-of-the-art algorithms, the part with the highest time-complexity being Dijkstra's shortest paths algorithm ( O ( | E | + | V | log | V | ) ).

Network analysis of anxiety and depressive symptoms during the COVID-19 pandemic in older adults in the United Kingdom

The health crisis caused by COVID-19 in the United Kingdom and the confinement measures that were subsequently implemented had unprecedented effects on the mental health of older adults, leading to the emergence and exacerbation of different comorbid symptoms including depression and anxiety. This study examined and compared depression and anxiety symptom networks in two specific quarantine periods (June-July and November-December) in the older adult population in the United Kingdom. We used the database of the English Longitudinal Study of Aging COVID-19 Substudy, consisting of 5797 participants in the first stage (54% women) and 6512 participants in the second stage (56% women), all over 50 years of age. The symptoms with the highest centrality in both times were: "Nervousness (A1)" and "Inability to relax (A4)" in expected influence and predictability, and "depressed mood (D1"; bridging expected influence). The latter measure along with "Irritability (A6)" overlapped in both depression and anxiety clusters in both networks. In addition, a the cross-lagged panel network model was examined in which a more significant influence on the direction of the symptom "Nervousness (A1)" by the depressive symptoms of "Anhedonia (D6)", "Hopelessness (D7)", and "Sleep problems (D3)" was observed; the latter measure has the highest predictive capability of the network. The results report which symptoms had a higher degree of centrality and transdiagnostic overlap in the cross-sectional networks (invariants) and the cross-lagged panel network model of anxious and depressive symptomatology.

The clinical relevance of subgroups of autistic adults: Stability and predictive value

Autism in adulthood is characterized by heterogeneity, complicating the provision of tailored support. In previous work, we aimed to capture this heterogeneity by determining subgroups of autistic adults that differed in clinical outcomes: cognitive failures, psychological difficulties, and quality of life (QoL). Two subgroups were identified: a "Feelings of Low Grip" subgroup characterized by experiencing a lower sense of mastery and a higher susceptibility to difficulties in daily life, and a "Feelings of High Grip" subgroup characterized by a higher sense of mastery and lower susceptibility to difficulties in daily life. The current pre-registered study involves a longitudinal extension to determine (a) stability and (b) predictive value of the previously identified two subgroups. Subgroups were identified using community detection based on 14 self-report measures related to demographic, psychological, and lifestyle characteristics in two samples (aged 31-86 years) that were analyzed separately: Sample 1 (NAutism = 80) measured 5 years after baseline and Sample 2 (NAutism = 241, NComparison = 211) measured 2 years after baseline. The stability over time was assessed based on (a) the number of subgroups, (b) subgroup profiles, and (c) subgroup membership. Predictive validity was assessed for cognitive failures, psychological difficulties, and QoL. Results indicated that autistic and non-autistic adults formed distinct subgroups. Within both autism samples, the two previously identified autism subgroups were replicated at follow-up. Subgroup profiles were similar for >50% of the variables at two-year follow-up, and 21% at five-year follow-up. Moreover, ≥76% remained in the same subgroup at two-year follow-up, and ≥ 57% after 5 years. Subgroup membership was predictive of external clinical outcomes up to 5 years. Thus, this study demonstrated the stability and predictive value of the autism subgroups, especially for the two-year follow-up. A further focus on their clinical utility might increase the aptness of support, and may provide more insight into the aging process when being autistic.

Coarse graining and criticality in the human connectome

In the face of the stupefying complexity of the human brain, network analysis is a most useful tool that allows one to greatly simplify the problem, typically by approximating the billions of neurons making up the brain by means of a coarse-grained picture with a practicable number of nodes. But even such relatively small and coarse networks, such as the human connectome with its 100-1000 nodes, may present challenges for some computationally demanding analyses that are incapable of handling networks with more than a handful of nodes. With such applications in mind, we set out to study the extent to which dynamical behavior and critical phenomena in the brain may be preserved following a severe coarse-graining procedure. Thus we proceeded to further coarse grain the human connectome by taking a modularity-based approach, the goal being to produce a network of a relatively small number of modules. After finding that the qualitative dynamical behavior of the coarse-grained networks reflected that of the original networks, albeit to a less pronounced extent, we then formulated a hypothesis based on the coarse-grained networks in the context of criticality in the Wilson-Cowan and Ising models, and we verified the hypothesis, which connected a transition value of the former with the critical temperature of the latter, using the original networks. This preservation of dynamical and critical behavior following a severe coarse-graining procedure, in principle, allows for the drawing of similar qualitative conclusions by analyzing much smaller networks, which opens the door for studying the human connectome in contexts typically regarded as computationally intractable, such as Integrated Information Theory and quantum models of the human brain.

Fast-slow traits predict competition network structure and its response to resources and enemies

Plants interact in complex networks but how network structure depends on resources, natural enemies and species resource-use strategy remains poorly understood. Here, we quantified competition networks among 18 plants varying in fast-slow strategy, by testing how increased nutrient availability and reduced foliar pathogens affected intra- and inter-specific interactions. Our results show that nitrogen and pathogens altered several aspects of network structure, often in unexpected ways due to fast and slow growing species responding differently. Nitrogen addition increased competition asymmetry in slow growing networks, as expected, but decreased it in fast growing networks. Pathogen reduction made networks more even and less skewed because pathogens targeted weaker competitors. Surprisingly, pathogens and nitrogen dampened each other's effect. Our results show that plant growth strategy is key to understand how competition respond to resources and enemies, a prediction from classic theories which has rarely been tested by linking functional traits to competition networks.

Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes

MOTIVATION

The functional complexity of biochemical processes is strongly related to the interplay of proteins and their assembly into protein complexes. In recent years, the discovery and characterization of protein complexes have substantially progressed through advances in cryo-electron microscopy, proteomics, and computational structure prediction. This development results in a strong need for computational approaches to analyse the data of large protein complexes for structural and functional characterization. Here, we aim to provide a suitable approach, which processes the growing number of large protein complexes, to obtain biologically meaningful information on the hierarchical organization of the structures of protein complexes.

RESULTS

We modelled the quaternary structure of protein complexes as undirected, labelled graphs called complex graphs. In complex graphs, the vertices represent protein chains and the edges spatial chain-chain contacts. We hypothesized that clusters based on the complex graph correspond to functional biological modules. To compute the clusters, we applied the Leiden clustering algorithm. To evaluate our approach, we chose the human respiratory complex I, which has been extensively investigated and exhibits a known biological module structure experimentally validated. Additionally, we characterized a eukaryotic group II chaperonin TRiC/CCT and the head of the bacteriophage Φ29. The analysis of the protein complexes correlated with experimental findings and indicated known functional, biological modules. Using our approach enables not only to predict functional biological modules in large protein complexes with characteristic features but also to investigate the flexibility of specific regions and coformational changes. The predicted modules can aid in the planning and analysis of experiments.

AVAILABILITY AND IMPLEMENTATION

Jupyter notebooks to reproduce the examples are available on our public GitHub repository: https://github.com/MolBIFFM/PTGLtools/tree/main/PTGLmodulePrediction.

Comparing community detection algorithms in psychometric networks: A Monte Carlo simulation

Identifying the correct number of factors in multivariate data is fundamental to psychological measurement. Factor analysis has a long tradition in the field, but it has been challenged recently by exploratory graph analysis (EGA), an approach based on network psychometrics. EGA first estimates a network and then applies the Walktrap community detection algorithm. Simulation studies have demonstrated that EGA has comparable or better accuracy for recovering the same number of communities as there are factors in the simulated data than factor analytic methods. Despite EGA's effectiveness, there has yet to be an investigation into whether other sparsity induction methods or community detection algorithms could achieve equivalent or better performance. Furthermore, unidimensional structures are fundamental to psychological measurement yet they have been sparsely studied in simulations using community detection algorithms. In the present study, we performed a Monte Carlo simulation using the zero-order correlation matrix, GLASSO, and two variants of a non-regularized partial correlation sparsity induction methods with several community detection algorithms. We examined the performance of these method-algorithm combinations in both continuous and polytomous data across a variety of conditions. The results indicate that the Fast-greedy, Louvain, and Walktrap algorithms paired with the GLASSO method were consistently among the most accurate and least-biased overall.

Community detection with Greedy Modularity disassembly strategy

Community detection recognizes groups of densely connected nodes across networks, one of the fundamental procedures in network analysis. This research boosts the standard but locally optimized Greedy Modularity algorithm for community detection. We introduce innovative exploration techniques that include a variety of node and community disassembly strategies. These strategies include methods like non-triad creating, feeble, random as well as inadequate embeddedness for nodes, as well as low internal edge density, low triad participation ratio, weak, low conductance as well as random tactics for communities. We present a methodology that showcases the improvement in modularity across the wide variety of real-world and synthetic networks over the standard approaches. A detailed comparison against other well-known community detection algorithms further illustrates the better performance of our improved method. This study not only optimizes the process of community detection but also broadens the scope for a more nuanced and effective network analysis that may pave the way for more insights as to the dynamism and structures of its functioning by effectively addressing and overcoming the limitations that are inherently attached with the existing community detection algorithms.

A Network Analysis Approach to Understanding Centrality and Overlap of 21 Dark Triad Items in Adults of 10 Countries

Background

Previous research has suggested that manipulation and callousness are central to Dark Triad traits, but it has not identified which specific manifestations are expressed across various countries.

Objective

This study aimed to identify the core and overlapping manifestations of Dark Triad traits across 10 countries.

Methods

We used the Short Dark Triad (SD3) scale and assessed a sample of 8093 participants (59.7% women, M(age) = 32.68 years). For graphical representation, the spinglass algorithm was applied to understand the cluster distribution among Machiavellianism, psychopathy, and subclinical narcissism traits. Centrality indices were used to identify the most influential items, and the clique-percolation algorithm was employed to detect shared attributes among multiple Dark Triad items.

Results

Straightforward SD3-21 items demonstrated better interpretability as aversive traits within the broader system. Items with higher centrality values were those related to short-term verbal manipulation from the psychopathy domain, clever manipulation, strategic revenge-seeking from Machiavellianism, and narcissistic motivations for connecting with significant individuals. The most predicted items were linked to planned revenge, using information against others from Machiavellianism, short-term psychopathic verbal manipulation, and narcissistic belief of specialness based on external validation. Items like short-term verbal manipulation had overlaps with both psychopathy and narcissism clusters, while clever manipulation overlapped with Machiavellianism and psychopathy.

Conclusion

This cross-cultural study highlights the central role of verbal manipulation within the Dark Triad traits, along with identifying overlapping items among traits measured using straightforward SD3 scale items. In line with our findings, future research that incorporates a wide range of cultural contexts is encouraged to establish the consistency of these findings with the SD3 Scale or alternative measures.

Optimizing parameter search for community detection in time-evolving networks of complex systems

Network representations have been effectively employed to analyze complex systems across various areas and applications, leading to the development of network science as a core tool to study systems with multiple components and complex interactions. There is a growing interest in understanding the temporal dynamics of complex networks to decode the underlying dynamic processes through the temporal changes in network structures. Community detection algorithms, which are specialized clustering algorithms, have been instrumental in studying these temporal changes. They work by grouping nodes into communities based on the structure and intensity of network connections over time, aiming to maximize the modularity of the network partition. However, the performance of these algorithms is highly influenced by the selection of resolution parameters of the modularity function used, which dictate the scale of the represented network, in both size of communities and the temporal resolution of the dynamic structure. The selection of these parameters has often been subjective and reliant on the characteristics of the data used to create the network. Here, we introduce a method to objectively determine the values of the resolution parameters based on the elements of self-organization and scale-invariance. We propose two key approaches: (1) minimization of biases in spatial scale network characterization and (2) maximization of scale-freeness in temporal network reconfigurations. We demonstrate the effectiveness of these approaches using benchmark network structures as well as real-world datasets. To implement our method, we also provide an automated parameter selection software package that can be applied to a wide range of complex systems.

Global renewable energy trade network: patterns and determinants

The renewable energy product trade is critically important to global economic prospects and its rapid development, making it a key issue in international economics of much interest to scholars. Previous studies have paid attention to bilateral trade, yet we still know little about the patterns of renewable energy product trade and its evolution from the whole industry perspective. Based on bilateral trade data, complex network, as well as ERGM and TERGM, we build global renewable energy trade networks (GRETNs) during 2000-2018 and explore the patterns and determinants. The results show that (1) the GRETNs expand during 2000-2018, characterized by a small-world, reciprocity, degree disassortative, and export volume heterogeneity. (2) The GRETNs form four communities, and the community patterns greatly fluctuate over time. (3) Economies in North America, Europe, and Asia play dominant roles, while the USA, Germany, and China are the cores of the GRETNs. (4) Endogenous structure of reciprocity, structural embeddedness, and out-degree popularity are essential parts of the evolving patterns of GRETNs. Most trade relationships are developed between economies located within the same continent, participating in APEC or WTO, or having similar areas. There is heterophily in GDP and per capita income, and Matthew effects in GDP, urbanization, and industrialization rate. Countries that share a common geographic border, language, religion, or currency, being former colonies of the same colonialists, and having signed regional trade agreements are more likely to trade in renewable energy products.

OMICs Signatures Linking Persistent Organic Pollutants to Cardiovascular Disease in the Swedish Mammography Cohort

Cardiovascular disease (CVD) development may be linked to persistent organic pollutants (POPs), including organochlorine compounds (OCs) and perfluoroalkyl and polyfluoroalkyl substances (PFAS). To explore underlying mechanisms, we investigated metabolites, proteins, and genes linking POPs with CVD risk. We used data from a nested case-control study on myocardial infarction (MI) and stroke from the Swedish Mammography Cohort - Clinical (n = 657 subjects). OCs, PFAS, and multiomics (9511 liquid chromatography-mass spectrometry (LC-MS) metabolite features; 248 proteins; 8110 gene variants) were measured in baseline plasma. POP-related omics features were selected using random forest followed by Spearman correlation adjusted for confounders. From these, CVD-related omics features were selected using conditional logistic regression. Finally, 29 (for OCs) and 12 (for PFAS) unique features associated with POPs and CVD. One omics subpattern, driven by lipids and inflammatory proteins, associated with MI (OR = 2.03; 95% CI = 1.47; 2.79), OCs, age, and BMI, and correlated negatively with PFAS. Another subpattern, driven by carnitines, associated with stroke (OR = 1.55; 95% CI = 1.16; 2.09), OCs, and age, but not with PFAS. This may imply that OCs and PFAS associate with different omics patterns with opposite effects on CVD risk, but more research is needed to disentangle potential modifications by other factors.