Dynamic Network Analysis Research Articles

Node Centrality Based on Edge Dynamics in a Chaotic Network

This paper introduces a novel node centrality index based on edge dynamics in a complex network: adjacent edge index. Through the analysis of network dynamics and topology, we provide a neat index to qualify node importance, which is calculated by the eigenvector components corresponding to the Fiedler value of the network. Notably, it identifies nodes whose adjacent edge sets play a significant role in network synchronization. The index indicates that not only a node’s degree but also its location should be considered. To demonstrate the effectiveness of the proposed index, consider a double-star network and a Jazz Musicians network in which chaotic Chua’s circuits as nodes are coupled. By factoring in the dynamic information exchange between nodes and their neighbors, this index offers valuable insights for optimizing strategies in engineering areas such as efficient information dissemination.

Impact of climate risk on energy market risk spillover: Evidence from dynamic heterogeneous network analysis

Using meteorological monitoring data from eight climate disasters across the globe, the Climate Policy Uncertainty (CPU) Index, and the financial data of eight energy markets between 2010 and 2020, this study employs the fixed base extreme difference entropy method to construct a Climate Risk Index (CRI) and investigates the impact of climate risk on the risk spillover among energy markets based on dynamic heterogeneous network analysis. The results confirm that the CRI fluctuated periodically and exhibited an upward trend during the sample period. In terms of risk spillover, the oil, geothermal, and fuel cell markets act as risk receivers, whereas the gas, wind, and bioenergy markets functions as risk emitters. Climate risk significantly increases the network complexity between energy markets and the risk spillover of gas, solar, water, and wind markets but decreases the risk spillover of oil, bioenergy, fuel cells, and geothermal markets. Additionally, the fossil fuel market is more sensitive to climate risk than is the renewable energy market.

Distinct gut microbiomes in Thai patients with colorectal polyps.

Colorectal polyps that develop via the conventional adenoma-carcinoma sequence [e.g., tubular adenoma (TA)] often progress to malignancy and are closely associated with changes in the composition of the gut microbiome. There is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway, such as hyperplastic polyps (HP). Exploration of microbiome alterations associated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal carcinogenesis. To investigate gut microbiome signatures, microbial associations, and microbial functions in HP and TA patients. Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps [control group (CT), n = 40], patients with HP (n = 52), and patients with TA (n = 60). Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or TA. Analytical techniques in this study included differential abundance analysis, co-occurrence network analysis, and differential pathway analysis. Colorectal cancer (CRC)-associated bacteria, including Streptococcus gallolyticus (S. gallolyticus), Bacteroides fragilis, and Clostridium symbiosum, were identified as characteristic microbial species in TA patients. Mediterraneibacter gnavus, associated with dysbiosis and gastrointestinal diseases, was significantly differentially abundant in the HP and TA groups. Functional pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively, whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis (e.g., mevalonate); S. gallolyticus was a major contributor. Co-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients, whereas TA patients exhibited co-occurrence of CRC-associated bacteria. Furthermore, the co-occurrence of SCFA-producing bacteria was lower in TA patients than HP patients. This study revealed distinct gut microbiome signatures associated with pathways of colorectal polyp development, providing insights concerning the roles of microbial species, functional pathways, and microbial interactions in colorectal carcinogenesis.

Alterations of resting-state network dynamics in Alzheimer's disease based on leading eigenvector dynamics analysis.

Alzheimer's disease (AD) is a neurodegenerative disease, and mild cognitive impairment (MCI) is considered a transitional stage between healthy aging and dementia. Early detection of MCI can help slow down the progression of AD. At present, there are few studies exploring the characteristics of abnormal dynamic brain activity in AD. This article uses a method called leading eigenvector dynamics analysis (LEiDA) to study resting-state functional magnetic resonance imaging (rs-fMRI) data of AD, MCI, and cognitively normal (CN) participants. By identifying repetitive states of phase coherence, intergroup differences in brain dynamic activity indicators are examined, and the neurobehavioral scales were used to assess the relationship between abnormal dynamic activities and cognitive function. The results showed that in the indicators of occurrence probability and lifetime, the globally synchronized state of the patient group decreased. The activity state of the limbic regions significantly detected the difference between AD and the other two groups. Compared to CN, AD and MCI have varying degrees of increase in default and visual region activity states. In addition, in the analysis related to the cognitive scales, it was found that individuals with poorer cognitive abilities were less active in the globally synchronized state and more active in limbic region activity state and visual region activity state. Taken together, these findings reveal abnormal dynamic activity of resting-state networks in patients with AD and MCI, provide new insights into the dynamic analysis of brain networks, and contribute to a deeper understanding of abnormal spatial dynamic patterns in AD patients.NEW & NOTEWORTHY Alzheimer's disease (AD) is a neurodegenerative disease, but few studies have explored the characteristics of abnormal dynamic brain activity in AD patients. Here, our report reveals the abnormal dynamic activity of the patients' resting-state network, providing new insights into the dynamic analysis of brain networks and helping to gain a deeper understanding of the abnormal spatial dynamic patterns in AD patients.

Dynamic network analysis of electrophysiological task data

Abstract An important approach for studying the human brain is to use functional neuroimaging combined with a task. In electrophysiological data, this often involves a time-frequency analysis, in which recorded brain activity is time-frequency transformed and epoched around task events of interest, followed by trial-averaging of the power. While this simple approach can reveal fast oscillatory dynamics, the brain regions are analysed one at a time. This causes difficulties for interpretation and a debilitating number of multiple comparisons. In addition, it is now recognised that the brain responds to tasks through the coordinated activity of networks of brain areas. As such, techniques that take a whole-brain network perspective are needed. Here, we show how the oscillatory task responses from conventional time-frequency approaches can be represented more parsimoniously at the network level using two state-of-the-art methods: the HMM (Hidden Markov Model) and DyNeMo (Dynamic Network Modes). Both methods reveal frequency-resolved networks of oscillatory activity with millisecond resolution. Comparing DyNeMo, HMM, and traditional oscillatory response analysis, we show DyNeMo can identify task activations/deactivations that the other approaches fail to detect. DyNeMo offers a powerful new method for analysing task data from the perspective of dynamic brain networks.

Mutations in LIFR rewire the JAK/STAT signaling pathway: A study unveiling mechanistic details of Stüve-Wiedemann syndrome

Stüve-Wiedemann syndrome (SWS), a rare autosomal recessive disorder, characterized by diminutive size, curvature of the elongated bones, bent fingers, episodes of heightened body temperature, respiratory distress or periods of breath-holding, and challenges with feeding, especially causes fatality in infants. SWS is an outcome of potential missense mutations in the leukemia inhibitory factor receptor gene reflected as numerous amino acid mutations at protein level. Employing in silico tools and techniques like mutational screening with Pred_MutHTP, I-Mutant2.0, PANTHER.db, PolyPhen, to classify mutations as deleterious/destabilizing, in conjunction with experimental data analysis, P136A and S279P emerged as ‘effect’-causing mutations. Pre-existing knowledge suggests, SWS progression is effectuated conformationally altered and dysfunctional LIFR, unable to bind to LIF and further form the LIF/LIFR/gp130 signalling complex. To gain functional insights into the effect of the said mutations on the wild type protein, an all-atom, explicit, solvent molecular dynamics simulation was performed following docking approaches. Consequently, referring to the RMSD, RMSF, protein dynamic network analysis, energy landscape plots and domain motion analysis, it was revealed that unbound LIFR_WT was more prone to LIF binding as usual whereas the mutants exhibited considerable domain closure to inhibit LIF binding. We conducted binding affinity analysis via MM/GBSA and dissociation constant estimation after LIFR-LIF docking and found the WT_complex to be more stable and compact as a whole when compared to the flexible mutant complexes thus being associated with SWS. Our study offers a route for understanding molecular level implications upon LIFR mutations which opens an avenue for therapeutic interventions.

Integrative network pharmacology, molecular docking, and dynamic simulation analysis of a polyherbal formulation for potential therapeutic impact on prostate cancer

BackgroundProstate cancer (PCa) remains a significant health concern globally, prompting a continual search for novel therapeutic strategies. In this study, we employed a comprehensive approach combining network pharmacology, molecular docking and dynamic simulation to explore the potential impact of a polyherbal formulation on PCa. MethodsUtilizing comprehensive network pharmacology approaches, we elucidated the complex interactions between the bioactive compounds within the polyherbal formulation and key targets associated with PCa progression, highlighting their multitarget mechanisms through integrated protein‒protein interaction and KEGG pathway analyses. Molecular docking simulation studies were performed to predict the binding affinities and modes of interaction between the identified bioactive compounds and their respective protein targets. ResultsComplex connections comprising 486 nodes and 845 edges were found by the compound-target network analysis. Significant interactions were observed, and the average node degree was 4.23. KEGG research revealed that PCa and the PI3K-Akt signalling pathway are implicated in modulating prostate cancer. The Quercetin docking investigations revealed that the binding energies for AR and PIK3R1 were −9 and −9.5 kcal/mol, respectively. Based on the results of the MD simulations, it appears that tiny molecules and proteins have formed stable complexes with low fluctuations. ConclusionIn conclusion, this comprehensive method emphasises the value of network pharmacology in conjunction with molecular docking and dynamic simulation in revealing the anti-PCa therapeutic potential of polyherbal formulations, opening up new possibilities for the creation of efficient anti-cancer medicines.

Extreme risk contagions among fossil energy companies in China: Insights from a multilayer dynamic network analysis

Since the severity and frequency of extreme events have seriously threatened the stability of fossil energy markets, this paper conducts multilayer dynamic network analysis to demonstrate the evolution of the entire market structure during extreme events. Based on the data of 64 Chinese energy firms ranging from March 2018 to February 2023, this paper examines the sectoral discrepancies, and identifies systemically important companies during different crises. The results indicate that the risk transmission mechanisms among fossil energy markets are different induced by the two crises, namely the COVID-19 pandemic and the Russia–Ukraine conflict. Specifically, the COVID-19 has rendered greater influence on the oil and gas industry, while the Russia–Ukraine conflict has brought instability to the coal industry. Additionally, the heterogeneous effects of these events on individual energy firms are identified, and the results suggest that both small and large firms have played prominent roles in risk transmission.

Major Problems in Clinical Psychological Science and How to Address them. Introducing a Multimodal Dynamical Network Approach

Abstract Background Despite impressive dissemination programs of best-practice therapies, clinical psychology faces obstacles in developing more efficacious treatments for mental disorders. In contrast to other medical disciplines, psychotherapy has made only slow progress in improving treatment outcomes. Improvements in the classification of mental disorders could enhance the tailoring of treatments to improve effectiveness. We introduce a multimodal dynamical network approach, to address some of the challenges faced by clinical research. These challenges include the absence of a comprehensive meta-theory, comorbidity, substantial diagnostic heterogeneity, violations of ergodicity assumptions, and a limited understanding of causal processes. Methods Through the application of multimodal dynamical network analysis, we describe how to advance clinical research by addressing central problems in the field. By utilizing dynamic network analysis techniques (e.g., Group Iterative Multiple Model Estimation, multivariate Granger causality), multimodal measurements (i.e., psychological, psychopathological, and neurobiological data), intensive longitudinal data collection (e.g., Ecological Momentary Assessment), and causal inference methods (e.g., GIMME), our approach could improve the comprehension and treatment of mental disorders. Under the umbrella of the systems approach and utilizing e.g., graph theory and control theory, we aim to integrate data from longitudinal, multimodal measurements. Results The multimodal dynamical network approach enables a comprehensive understanding of mental disorders as dynamic networks of interconnected symptoms. It dismantles artificial diagnostic boundaries, facilitating a transdiagnostic view of psychopathology. The integration of longitudinal data and causal inference techniques enhances our ability to identify influential nodes, prioritize interventions, and predict the impact of therapeutic strategies. Conclusion The proposed approach could improve psychological treatment by providing individualized models of psychopathology and by suggesting individual treatment angles.

Network Models of BACE-1 Inhibitors: Exploring Structural and Biochemical Relationships.

This study investigates the clustering patterns of human β-secretase 1 (BACE-1) inhibitors using complex network methodologies based on various distance functions, including Euclidean, Tanimoto, Hamming, and Levenshtein distances. Molecular descriptor vectors such as molecular mass, Merck Molecular Force Field (MMFF) energy, Crippen partition coefficient (ClogP), Crippen molar refractivity (MR), eccentricity, Kappa indices, Synthetic Accessibility Score, Topological Polar Surface Area (TPSA), and 2D/3D autocorrelation entropies are employed to capture the diverse properties of these inhibitors. The Euclidean distance network demonstrates the most reliable clustering results, with strong agreement metrics and minimal information loss, indicating its robustness in capturing essential structural and physicochemical properties. Tanimoto and Hamming distance networks yield valuable clustering outcomes, albeit with moderate performance, while the Levenshtein distance network shows significant discrepancies. The analysis of eigenvector centrality across different networks identifies key inhibitors acting as hubs, which are likely critical in biochemical pathways. Community detection results highlight distinct clustering patterns, with well-defined communities providing insights into the functional and structural groupings of BACE-1 inhibitors. The study also conducts non-parametric tests, revealing significant differences in molecular descriptors, validating the clustering methodology. Despite its limitations, including reliance on specific descriptors and computational complexity, this study offers a comprehensive framework for understanding molecular interactions and guiding therapeutic interventions. Future research could integrate additional descriptors, advanced machine learning techniques, and dynamic network analysis to enhance clustering accuracy and applicability.

Computational analysis of hydrogen bonds network dynamics in the water layers surrounding Aβ(1-42) and Aβ(1-40) peptide dimers

The amyloid-β peptide (Aβ) dimer is involved in the development of Alzheimer’s disease through forming amyloid plaques. Aβ(1-40) and Aβ(1-42) are the most common and poisonous species causing Alzheimer’s disease. They form homogeneous dimers containing two similar peptides and heterogeneous dimers containing different ones. The low molecular weight, fast dynamics, and varying compositions of these dimers make it difficult to study them by conventional experimental methods. Hence, we clarify the effect of the diversity of the Aβ dimers on the structure of the water molecules around the peptides by the molecular dynamics (MD) simulation method in this study. MD simulations of the Aβ(1-40) and Aβ(1-42) monomers are also performed for the comparison. The calculations are repeated in the presence of dimethyl sulfoxide (DMSO). The water molecules positioned at distances of 0.5, 0.75, 1, 1.25, and 1.5 nm from the protein were chosen to investigate the distribution and dynamics of hydrogen bonds in the layers surrounding the peptide. The results show that the heterogeneity of the dimer system increases the percentage of hydrogen (H) atoms not involved in any water-water hydrogen bonds around the peptides in the different layers. While it decreases the percentage of H atoms involved in one and two water-water hydrogen bonds. The DMSO presence reduces the percentage of H atoms involved in two hydrogen bonds in the systems containing a mixture of water and DMSO. The average interaction energy of the dimers demonstrates the enhanced interactions of the two peptides in water in comparison with that in the mixture of water and DMSO. The behavior of the water molecules around the heterogeneous dimer is very similar to that around the Aβ(1-42) homogeneous dimer.

Dynamic impact of the US yield curve on green bonds: Navigating through recent crises

We examine the effect of the US yield curve on the global green bond markets at the forefront of the climate change fight. For this purpose, we compute three components (level, slope, and curvature) of the US yield curve based on daily data of the treasury yields with several maturities from January 2009 to June 2022 and employ country-level S&P green bond indices. Our dynamic network analysis shows that the level component of the yield curve is more influential in transmitting return and volatility shocks to green bonds, while curvature is primarily absorptive. The European, the US, and Hong Kong green bonds are the leading players in shock propagation. Both return- and volatility spillovers are time-varying and remain high during periods of systemically important events, especially COVID-19 and the Russia-Ukraine war, supporting the Global Financial Cycle Hypothesis. The war also changes the net behaviors (transmitter versus receiver) of the components and the indices. Investors and issuers of green bonds are advised to keenly observe the shape of the US yield curve and systemic events for better decision-making regarding investment horizons and contagion risk management.

Spatio-Temporal Graph Hubness Propagation Model for Dynamic Brain Network Classification.

Dynamic brain network has the advantage over static brain network in characterizing the variation pattern of functional brain connectivity, and it has attracted increasing attention in brain disease diagnosis. However, most of the existing dynamic brain networks analysis methods rely on extracting features from independent brain networks divided by sliding windows, making them hard to reveal the high-order dynamic evolution laws of functional brain networks. Additionally, they cannot effectively extract the spatio-temporal topology features in dynamic brain networks. In this paper, we propose to use optimal transport (OT) theory to capture the topology evolution of the dynamic brain networks, and develop a multi-channel spatio-temporal graph convolutional network that collaboratively extracts the temporal and spatial features from the evolution networks. Specifically, we first adaptively evaluate the graph hubness of brain regions in the brain network of each time window, which comprehensively models information transmission among multiple brain regions. Second, the hubness propagation information across adjacent time windows is captured by optimal transport, describing high-order topology evolution of dynamic brain networks. Moreover, we develop a spatio-temporal graph convolutional network with attention mechanism to collaboratively extract the intrinsic temporal and spatial topology information from the above networks. Finally, the multi-layer perceptron is adopted for classifying the dynamic brain network. The extensive experiment on the collected epilepsy dataset and the public ADNI dataset show that our proposed method not only outperforms several state-of-the-art methods in brain disease diagnosis, but also reveals the key dynamic alterations of brain connectivities between patients and healthy controls.

Assessing the impact of repetitive transcranial magnetic stimulation on effective connectivity in autism spectrum disorder: An initial exploration using TMS-EEG analysis

Initial indications propose that repetitive transcranial magnetic stimulation (rTMS) could mitigate clinical manifestations in patients with autism spectrum disorder (ASD). Nevertheless, the precise mechanisms responsible for these therapeutic and behavioral outcomes remain elusive. We examined alterations in effective connectivity induced by rTMS using concurrent transcranial magnetic stimulation and electroencephalography (TMS-EEG) in children with ASD. TMS-EEG data were acquired from 12 children diagnosed with ASD both before and following rTMS treatment. The rTMS intervention regimen included delivering 5-s trains at a frequency of 15 Hz, with 10-min intervals between trains, targeting the left parietal lobe. This was conducted on each consecutive weekday over 3 weeks, totaling 15 sessions. The dynamic EEG network analysis revealed that following the rTMS intervention, long-range feedback connections within the brains of ASD patients were strengthened (e.g., frontal to parietal regions, frontal to occipital regions, and frontal to posterior temporal regions), and short-range connections were weakened (e.g., between the bilateral occipital regions, and between the occipital and posterior temporal regions). In alignment with alterations in network connectivity, there was a corresponding amelioration in fundamental ASD symptoms, as assessed through clinical scales post-treatment. According to our findings, people with ASD may have increased long-range frontal-posterior feedback connection on application of rTMS to the parietal lobe.

Dynamic dependability analysis of shuffle-exchange networks

Dynamic dependability analysis of shuffle-exchange networks

Energy landscape analysis of brain network dynamics in Alzheimer's disease.

Alzheimer's disease (AD) is a common neurodegenerative dementia, characterized by abnormal dynamic functional connectivity (DFC). Traditional DFC analysis, assuming linear brain dynamics, may neglect the complexity of the brain's nonlinear interactions. Energy landscape analysis offers a holistic, nonlinear perspective to investigate brain network attractor dynamics, which was applied to resting-state fMRI data for AD in this study. This study utilized resting-state fMRI data from 60 individuals, comparing 30 Alzheimer's patients with 30 controls, from the Alzheimer's Disease Neuroimaging Initiative. Energy landscape analysis was applied to the data to characterize the aberrant brain network dynamics of AD patients. The AD group stayed in the co-activation state for less time than the healthy control (HC) group, and a positive correlation was identified between the transition frequency of the co-activation state and behavior performance. Furthermore, the AD group showed a higher occurrence frequency and transition frequency of the cognitive control state and sensory integration state than the HC group. The transition between the two states was positively correlated with behavior performance. The results suggest that the co-activation state could be important to cognitive processing and that the AD group possibly raised cognitive ability by increasing the occurrence and transition between the impaired cognitive control and sensory integration states.

Engineering of Halide Methyltransferase BxHMT through Dynamic Cross-Correlation Network Analysis.

Halide methyltransferases (HMTs) provide an effective way to regenerate S-adenosyl methionine (SAM) from S-adenosyl homocysteine and reactive electrophiles, such as methyl iodide (MeI) and methyl toluene sulfonate (MeOTs). As compared with MeI, the cost-effective unnatural substrate MeOTs can be accessed directly from cheap and abundant alcohols, but shows only limited reactivity in SAM production. In this study, we developed a dynamic cross-correlation network analysis (DCCNA) strategy for quickly identifying hot spots influencing the catalytic efficiency of the enzyme, and applied it to the evolution of HMT from Paraburkholderia xenovorans. Finally, the optimal mutant, M4 (V55T/C125S/L127T/L129P), exhibited remarkable improvement, with a specific activity of 4.08 U/mg towards MeOTs, representing an 82-fold increase as compared to the wild-type (WT) enzyme. Notably, M4 also demonstrated a positive impact on the catalytic ability with other methyl donors. The structural mechanism behind the enhanced enzyme activity was uncovered by molecular dynamics simulations. Our work not only contributes a promising biocatalyst for the regeneration of SAM, but also offers a strategy for efficient enzyme engineering.

Dynamic analysis and hardware implementation of multi-scroll Hopfield neural networks with three different memristor synapses

Dynamic analysis and hardware implementation of multi-scroll Hopfield neural networks with three different memristor synapses

Analysis of Peatland Research Trends Based on BERTopic

Peatlands comprise approximately 3% of the land area worldwide. Peatland exists in most countries, including tropical, subtropical, and boreal regions. Accordingly, peatland has garnered increased research attention as a potential countermeasure against climate change. Therefore, it is necessary to identify and comprise the topics constituting global peatland research. In this study, we applied BERTopic—a topic modeling technique—to analyze relatedness between research topics to classify global peatland research trends, evaluate changes over time, and analyze the relationships between topics. To this end, we searched the keyword “peatland” on ScienceDirect—a global academic publication data platform—and collected the titles and abstracts from 10,158 publications from 1953 to 2022 for dynamic topic modeling and network analysis. Eighty-two peatland research topics were identified, which were combined into 15 main topics. Over time, an increasing trend was observed in topics related to production, management, and fire. In addition, upon analysis of the relationships between topics, three groups centered on fire, peatland value, and carbon were identified. We anticipate that the findings of this study can be expanded to analyze trends in research related to fires in peatlands, regional characteristics of peat soil, prediction of greenhouse gases emission and mitigation due to peatland fires, and prediction of future peatland research topics.

A complex network approach to analyse pre-trained language models for ancient Chinese.

Ancient Chinese is a splendid treasure within Chinese culture. To facilitate its compilation, pre-trained language models for ancient Chinese are developed. After that, researchers are actively exploring the factors contributing to their success. However, previous work did not study how language models organized the elements of ancient Chinese from a holistic perspective. Hence, we adopt complex networks to explore how language models organize the elements in ancient Chinese system. Specifically, we first analyse the characters' and words' co-occurrence networks in ancient Chinese. Then, we study characters' and words' attention networks, generated by attention heads within SikuBERT from two aspects: static and dynamic network analysis. In the static network analysis, we find that (i) most of attention networks exhibit small-world properties and scale-free behaviour, (ii) over 80% of attention networks exhibit high similarity with the corresponding co-occurrence networks, (iii) there exists a noticeable gap between characters' and words' attention networks across layers, while their fluctuations remain relatively consistent, and (iv) the attention networks generated by SikuBERT tend to be sparser compared with those from Chinese BERT. In dynamic network analysis, we find that the sentence segmentation task does not significantly affect network metrics, while the part-of-speech tagging task makes attention networks sparser.