Community structure in social and biological networks

A weighted prior tensor train decomposition method for community detection in multi-layer networks

Community detection in multi-layer networks stands as a prominent subject within network analysis research. However, the majority of existing techniques for identifying communities encounter two primary constraints: they lack suitability for high-dimensional data within multi-layer networks and fail to fully leverage additional auxiliary information among communities to enhance detection accuracy. To address these limitations, a novel approach named weighted prior tensor training decomposition (WPTTD) is proposed for multi-layer network community detection. Specifically, the WPTTD method harnesses the tensor feature optimization techniques to effectively manage high-dimensional data in multi-layer networks. Additionally, it employs a weighted flattened network to construct prior information for each dimension of the multi-layer network, thereby continuously exploring inter-community connections. To preserve the cohesive structure of communities and to harness comprehensive information within the multi-layer network for more effective community detection, the common community manifold learning (CCML) is integrated into the WPTTD framework for enhancing the performance. Experimental evaluations conducted on both artificial and real-world networks have verified that this algorithm outperforms several mainstream multi-layer network community detection algorithms.

Conformational dynamics and ribosomal interactions of Bacillus subtilis Obg in various nucleotide-bound states: Insights from molecular dynamics simulation

Obg, a GTPase, binds to the premature 50S ribosomal subunit and facilitates recruitment of rproteins and rRNA processing to form the mature 50S subunit. This binding depends on nucleotide-induced conformational changes (GDP/GTP). However, the mechanism by which Obg undergoes conformational changes to associate with the premature 50S subunit is unknown. Therefore, 1000 ns molecular dynamics simulations were conducted to investigate this mechanism. Visualization of the simulated trajectory showed that in GDP and GTP-bound states, the C-domain moved towards the SwI region, while in GTP-Mg2+ and ppGpp-bound states, the C-domain shifted towards the N-tails. Further, positioning these conformations of Obg on the 50S subunit suggests possible mechanisms by which the GTP-Mg2+ bound state is responsible for recruiting rprotein, as well as the impact of the absence of Mg2+ in the GTP-bound state. Furthermore, the study provides insights into the conformational changes that may lead to the dissociation of the GDP-bound state from the 50S subunit and explores the potential role of the ppGpp-bound state in inhibiting 70S ribosome formation. Additionally, RMSF and community network analyses reveal how internal dynamics and intricate connections within Obg affect C-domain motion.

Vasectomy Discussions in South Korea: Central Themes and Public Interest on Question-and-Answer Social Platforms

PURPOSE

The purpose of this paper is to explore public perceptions and key issues related to vasectomy in South Korea. In particular, this paper seeks to analyze how vasectomy is discussed on question-and-answer (Q&A) social platforms including NAVER Jisik iN (knowledge exchange service between NAVER users) and to identify topics that capture public interest.

METHODS

In this study, based on data collected on NAVER Jisik iN from July 2019 to July 2024 with the keyword 'vasectomy,' this paper performs a co-occurrence matrix analysis on the Q&A data to identify key terms related to the topic. By applying connection centrality and community detection techniques, this paper visualizes and examines the network graph to uncover relationships between words and identify the primary topics of discussion.

RESULTS

The co-occurrence matrix analysis reveals that keywords such as 'surgery,' 'vasectomy,' and 'contraception' play a central role in discussions about vasectomies. Both the Q&A data highlight the vasectomy procedure and contraceptive effectiveness as primary topics of discussion. The visualization graphs intuitively display the centrality and strength of connections between these keywords, as well as the interrelatedness of topics through distinct community groups.

CONCLUSION

The analysis shows that the questions primarily focused on the surgical procedure, while the answers were more concerned with contraceptive effectiveness and physiological aspects. These results suggest that the public's interest in vasectomy is closely linked to its effectiveness, potential side effects, and related social issues.

Network community detection via neural embeddings

Recent advances in machine learning research have produced powerful neural graph embedding methods, which learn useful, low-dimensional vector representations of network data. These neural methods for graph embedding excel in graph machine learning tasks and are now widely adopted. However, how and why these methods work-particularly how network structure gets encoded in the embedding-remain largely unexplained. Here, we show that node2vec-shallow, linear neural network-encodes communities into separable clusters better than random partitioning down to the information-theoretic detectability limit for the stochastic block models. We show that this is due to the equivalence between the embedding learned by node2vec and the spectral embedding via the eigenvectors of the symmetric normalized Laplacian matrix. Numerical simulations demonstrate that node2vec is capable of learning communities on sparse graphs generated by the stochastic blockmodel, as well as on sparse degree-heterogeneous networks. Our results highlight the features of graph neural networks that enable them to separate communities in the embedding space.

Synergistic Integration of Local and Global Information for Critical Edge Identification

Identifying critical edges in complex networks is a fundamental challenge in the study of complex networks. Traditional approaches tend to rely solely on either global information or local information. However, this dependence on a single information source fails to capture the multi-layered complexity of critical edges, often resulting in incomplete or inaccurate identification. Therefore, it is essential to develop a method that integrates multiple sources of information to enhance critical edge identification and provide a deeper understanding and optimization of the structure and function of complex networks. In this paper, we introduce a Global-Local Hybrid Centrality method which integrates a second-order neighborhood index, a first-order neighborhood index, and an edge betweenness index, thus combining both local and global perspectives. We further employ the edge percolation process to evaluate the significance of edges in maintaining network connectivity. Experimental results on various real-world complex network datasets demonstrate that the proposed method significantly improves the accuracy of critical edge identification, providing theoretical and methodological support for the analysis and optimization of complex networks.

Overlapping community detection in weighted networks via hierarchical clustering

In real-world networks, community structures often appear as tightly connected clusters of nodes, with recent studies suggesting a hierarchical organization where larger groups subdivide into smaller ones across different levels. This hierarchical structure is particularly complex in trade networks, where actors typically belong to multiple communities due to diverse business relationships and contracts. To address this complexity, we present a novel algorithm for detecting hierarchical structures of overlapping communities in weighted networks, focusing on the interdependency between internal and external quality metrics for evaluating the detected communities. The proposed Graph Hierarchical Agglomerative Clustering (GHAC) approach utilizes maximal cliques as the basis units for hierarchical clustering. The algorithm measures dissimilarities between clusters using the minimal closed trail distance (CT-distance) and the size of maximal cliques within overlaps, capturing the density and connectivity of nodes. Through extensive experiments on synthetic networks with known ground truth, we demonstrate that the adjusted Silhouette index is the most reliable internal metric for determining the optimal cut in the dendrogram. Experimental results indicate that the GHAC method is competitive with widely used community detection techniques, particularly in networks with highly overlapping communities. The method effectively reveals the hierarchical structure of communities in weighted networks, as demonstrated by its application to the OECD weighted trade network, which describes the balanced trade value of bilateral trade relations.

Selecting genes for analysis using historically contingent progress: from RNA changes to protein-protein interactions

Progress in biology has generated numerous lists of genes that share some property. But advancing from these lists of genes to understanding their roles is slow and unsystematic. Here we use RNA silencing in C. elegans to illustrate an approach for prioritizing genes for detailed study given limited resources. The partially subjective relationships between genes forged by both deduced functional relatedness and biased progress in the field was captured as mutual information and used to cluster genes that were frequently identified yet remain understudied. Some proteins encoded by these understudied genes are predicted to physically interact with known regulators of RNA silencing, suggesting feedback regulation. Predicted interactions with proteins that act in other processes and the clustering of studied genes among the most frequently perturbed suggest regulatory links connecting RNA silencing to other processes like the cell cycle and asymmetric cell division. Thus, among the gene products altered when a process is perturbed could be regulators of that process acting to restore homeostasis, which provides a way to use RNA sequencing to identify candidate protein-protein interactions. Together, the analysis of perturbed transcripts and potential interactions of the proteins they encode could help prioritize candidate regulators of any process.

Characterizing the progression from mild cognitive impairment to dementia: a network analysis of longitudinal clinical visits

BACKGROUND

With the recent surge in the utilization of electronic health records for cognitive decline, the research community has turned its attention to conducting fine-grained analyses of dementia onset using advanced techniques. Previous works have mostly focused on machine learning-based prediction of dementia, lacking the analysis of dementia progression and its associations with risk factors over time. The black box nature of machine learning models has also raised concerns regarding their uncertainty and safety in decision making, particularly in sensitive domains like healthcare.

OBJECTIVE

We aimed to characterize the progression of health conditions, such as chronic diseases and neuropsychiatric symptoms, of the participants in Mayo Clinic Study of Aging (MCSA) from initial mild cognitive impairment (MCI) diagnosis to dementia onset through network analysis.

METHODS

We used the data from the MCSA, a prospective population-based cohort study of cognitive aging, and examined the changing association among variables (i.e., participants' health conditions) from the first visit of MCI diagnosis to the visit of dementia onset using network analysis. The number of participants for this study are 97 with the number of visits ranging from 2 visits (30 months) to 7 visits (105 months). We identified the network communities among variables from three-fold collection of instances: (i) the first MCI diagnosis, (ii) progression to dementia, and (iii) dementia diagnosis. We determine the variables that play a significant role in the dementia onset, aiming to identify and prioritize specific variables that prominently contribute towards developing dementia. In addition, we explore the sex-specific impact of variables in relation to dementia, aiming to investigate potential differences in the influence of certain variables on dementia onset between males and females.

RESULTS

We found correlation among certain variables, such as neuropsychiatric symptoms and chronic conditions, throughout the progression from MCI to dementia. Our findings, based on patterns and changing variables within specific communities, reveal notable insights about the time-lapse before dementia sets in, and the significance of progression of correlated variables contributing towards dementia onset. We also observed more changes due to certain variables, such as cognitive and functional scores, in the network communities for the people who progressed to dementia compared to those who does not. Most changes for sex-specific analysis are observed in clinical dementia rating and functional activities questionnaire during MCI onset are followed by chronic diseases, and then by NPI-Q scores.

CONCLUSIONS

Network analysis has shown promising potential to capture significant longitudinal changes in health conditions, spanning from the MCI diagnosis to dementia progression. It can serve as a valuable analytic approach for monitoring the health status of individuals in cognitive impairment assessment. Furthermore, our findings indicate a notable sex difference in the impact of specific health conditions on the progression of dementia.

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.

A Cross-Entropy Approach to the Domination Problem and Its Variants

The domination problem and three of its variants (total domination, 2-domination, and secure domination) are considered. These problems have various real-world applications, including error correction codes, ad hoc routing for wireless networks, and social network analysis, among others. However, each of them is NP-hard to solve to provable optimality, making fast heuristics for these problems desirable. There are a wealth of highly developed heuristics and approximation algorithms for the domination problem; however, such heuristics are much less common for variants of the domination problem. We redress this gap in the literature by proposing a novel implementation of the cross-entropy method that can be applied to any sensible variant of domination. We present results from experiments that demonstrate that this approach can produce good results in an efficient manner even for larger graphs and that it works roughly as well for any of the domination variants considered.

Salt-bridge mediated conformational dynamics in the figure-of-eight knotted ketol acid reductoisomerase (KARI)

The utility of knotted proteins in biological activities has been ambiguous since their discovery. From their evolutionary significance to their functionality in stabilizing the native protein structure, a unilateral conclusion hasn't been achieved yet. While most studies have been performed to understand the stabilizing effect of the knotted fold on the protein chain, more ideas are yet to emerge regarding the interactions in stabilizing the knot. Using classical molecular dynamics (MD) simulations, we have explored the dynamics of the figure-of-eight knotted domain present in ketol acid reductoisomerase (KARI). Our main focus was on the presence of a salt bridge network evident within the knotted region and its role in shaping the conformational dynamics of the knotted chain. Through the potential of mean forces (PMFs) calculation, we have also marked the specific salt bridges that are pivotal in stabilizing the knotted structure. The correlated motions have been further monitored with the help of principal component analysis (PCA) and dynamic cross-correlation maps (DCCM). Furthermore, mutation of the specific salt bridges led to a change in their conformational stability, vindicating their importance.

Structure matters: Assessing the statistical significance of network topologies

Network analysis has found widespread utility in many research areas. However, assessing the statistical significance of observed relationships within networks remains a complex challenge. Traditional node permutation tests are often insufficient in capturing the effect of changing network topology by creating reliable null distributions. We propose two randomization alternatives to address this gap: random rewiring and controlled rewiring. These methods incorporate changes in the network topology through edge swaps. However, controlled rewiring allows for more nuanced alterations of the original network than random rewiring. In this sense, this paper introduces a novel evaluation tool, the Expanded Quadratic Assignment Procedure (EQAP), designed to calculate a specific p-value and interpret statistical tests with enhanced precision. The combination of EQAP and controlled rewiring provides a robust network comparison and statistical analysis framework. The methodology is exemplified through two real-world examples: the analysis of an organizational network structure, illustrated by the Enron-Email dataset, and a social network case, represented by the UK Faculty friendship network. The utility of these statistical tests is underscored by their capacity to safeguard researchers against Type I errors when exploring network metrics dependent on intricate topologies.

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.

Shortest path counting in complex networks based on powers of the adjacency matrix

Complex networks describe a broad range of systems in nature and society. As a fundamental concept of graph theory, the path connecting nodes and edges plays a crucial role in network science, where the computation of shortest path lengths and numbers has garnered substantial focus. It is well known that powers of the adjacency matrix can calculate the number of walks, specifying their corresponding lengths. However, developing methodologies to quantify both the number and length of shortest paths through the adjacency matrix remains a challenge. Here, we extend powers of the adjacency matrix from walks to shortest paths. We address the all-pairs shortest path count problem and propose a fast algorithm based on powers of the adjacency matrix that counts both the number and the length of all shortest paths. Numerous experiments on synthetic and real-world networks demonstrate that our algorithm is significantly faster than the classical algorithms across various network types and sizes. Moreover, we verified that the time complexity of our proposed algorithm significantly surpasses that of the current state-of-the-art algorithms. The superior property of the algorithm allows for rapid calculation of all shortest paths within large-scale networks, offering significant potential applications in traffic flow optimization and social network analysis.

Antifragility of stochastic transport on networks with damage

A system is called antifragile when damage acts as a constructive element improving the performance of a global function. In this paper, we analyze the emergence of antifragility in the movement of random walkers on networks with modular structures or communities. The random walker hops considering the capacity of transport of each link, whereas the links are susceptible to random damage that accumulates over time. We show that in networks with communities and high modularity, the localization of damage in specific groups of nodes leads to a global antifragile response of the system improving the capacity of stochastic transport to more easily reach the nodes of a network. Our findings give evidence of the mechanisms behind antifragile response in complex systems and pave the way for their quantitative exploration in different fields.

Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair

Nucleotide excision repair (NER) is vital for genome integrity. Yet, our understanding of the complex NER protein machinery remains incomplete. Combining cryo-EM and XL-MS data with AlphaFold2 predictions, we build an integrative model of the NER pre-incision complex(PInC). Here TFIIH serves as a molecular ruler, defining the DNA bubble size and precisely positioning the XPG and XPF nucleases for incision. Using simulations and graph theoretical analyses, we unveil PInC's assembly, global motions, and partitioning into dynamic communities. Remarkably, XPG caps XPD's DNA-binding groove and bridges both junctions of the DNA bubble, suggesting a novel coordination mechanism of PInC's dual incision. XPA rigging interlaces XPF/ERCC1 with RPA, XPD, XPB, and 5' ssDNA, exposing XPA's crucial role in licensing the XPF/ERCC1 incision. Mapping disease mutations onto our models reveals clustering into distinct mechanistic classes, elucidating xeroderma pigmentosum and Cockayne syndrome disease etiology.

Cognitive modelling of concepts in the mental lexicon with multilayer networks: Insights, advancements, and future challenges

The mental lexicon is a complex cognitive system representing information about the words/concepts that one knows. Over decades psychological experiments have shown that conceptual associations across multiple, interactive cognitive levels can greatly influence word acquisition, storage, and processing. How can semantic, phonological, syntactic, and other types of conceptual associations be mapped within a coherent mathematical framework to study how the mental lexicon works? Here we review cognitive multilayer networks as a promising quantitative and interpretative framework for investigating the mental lexicon. Cognitive multilayer networks can map multiple types of information at once, thus capturing how different layers of associations might co-exist within the mental lexicon and influence cognitive processing. This review starts with a gentle introduction to the structure and formalism of multilayer networks. We then discuss quantitative mechanisms of psychological phenomena that could not be observed in single-layer networks and were only unveiled by combining multiple layers of the lexicon: (i) multiplex viability highlights language kernels and facilitative effects of knowledge processing in healthy and clinical populations; (ii) multilayer community detection enables contextual meaning reconstruction depending on psycholinguistic features; (iii) layer analysis can mediate latent interactions of mediation, suppression, and facilitation for lexical access. By outlining novel quantitative perspectives where multilayer networks can shed light on cognitive knowledge representations, including in next-generation brain/mind models, we discuss key limitations and promising directions for cutting-edge future research.

Blockchain in clinical trials: Bibliometric and network studies of applications, challenges, and future prospects based on data analytics

This study conducts a comprehensive analysis on the usage of the blockchain technology in clinical trials, based on a curated corpus of 107 scientific articles from the year 2016 through the first quarter of 2024. Utilizing a methodological framework that integrates bibliometric analysis, network analysis, thematic mapping, and latent Dirichlet allocation, the study explores the terrain and prospective developments within this usage based on data analytics. Through a meticulous examination of the analyzed articles, the present study identifies seven key thematic areas, highlighting the diverse applications and interdisciplinary nature of blockchain in clinical trials. Our findings reveal blockchain capability to enhance data management, participant consent processes, as well as overall trial transparency, efficiency, and security. Additionally, the investigation discloses the emerging synergy between blockchain and advanced technologies, such as artificial intelligence and federated learning, proposing innovative directions for improving clinical research methodologies. Our study underscores the collaborative efforts in dealing with the complexities of integrating blockchain into the areas of clinical trials and healthcare, delineating the transformative potential of blockchain technology in revolutionizing these areas by addressing challenges and promoting practices of efficient, secure, and transparent research. The delineated themes and networks of collaboration provide a blueprint for future inquiry, showing the importance of empirical research to narrow the gap between theoretical promise and practical implementation.

Emergency communication networks on Twitter during Hurricane Irma: information flow, influential actors, and top messages

This study combined network analysis with message-level content analysis to investigate patterns of information flow and to examine messages widely distributed on social media during Hurricane Irma of 2017. The results show that while organisational users and media professionals dominated the top 100 information sources, individual citizens played a critical role in information dissemination. Public agencies should increase their retweeting activities and share the information posted by other trustworthy sources; doing so will contribute to the timely exchange of vital information during a disaster. This study also identified the active involvement of nonprofit organisations as information brokers during the post-event stage, indicating the potential for emergency management organisations to integrate their communication efforts into those of nonprofit entities. These findings will inform emergency management practices regarding implementation of communication plans and policies, facilitate the embracement of new partner organisations, and help with establishing and sustaining effective communication ties with a wide range of stakeholders.

Deciphering Internal Regulatory Patterns within the p53 Core Tetramer: Insights from Community Network Analysis

Gene therapy is one of the most effective strategies for cancer treatment. The p53 protein, commonly known as the "guardian of the genome", plays a critical role in gene activation and tumor suppression. Tetramerization of the p53 core domain is an essential allosteric process that supports its suppression functions. This letter presents a framework to analyze the structure, function, and dynamic connectivity of the p53 tetramer, using community network analysis based on all-atom molecular dynamics simulations. The communities within the p53 monomer exhibit distinct functional roles, while interactions between molecules establish a symmetrical network structure. We identified direct evidence of single, double, and multiple pathway regulations within the p53 tetramer and crucial residue pairs involved in these connections. Our study provides a comprehensive framework to understand the community network of the p53 tetramer, offering new insights into the stable formation of the p53 core tetramer.

A control measure for epidemic spread based on the susceptible-infectious-susceptible (SIS) model

When an epidemic occurs in a network, finding the important links and cutting them off is an effective measure for preventing the spread of the epidemic. Traditional methods that remove important links easily lead to a disconnected network, inevitably incurring high costs arising from quarantining individuals or communities in a real-world network. In this study, we combine the clustering coefficient and the eigenvector to identify the important links using the susceptible-infectious-susceptible (SIS) model. The results show that our approach can improve the epidemic threshold while maintaining the connectivity of the network to control the spread of the epidemic. Experiments on multiple real-world and synthetic networks of varying sizes, demonstrate the effectiveness and scalability of our approach.

Global effects of land-use intensity and exotic plants on the structure and phylogenetic signal of plant-herbivore networks

Interactions between plants and herbivorous insects are often phylogenetically structured, with closely related insect species using similar sets of species or lineages of plants, while phylogenetically closer plants tend to share high proportions of their herbivore insect species. Notably, these phylogenetic constraints in plant-herbivore interactions tend to be more pronounced among internal plant-feeding herbivores (i.e., endophages) than among external feeders (i.e., exophages). In the context of growing human-induced habitat conversion and the global proliferation of exotic species, it is crucial to understand how ecological networks respond to land-use intensification and the increasing presence of exotic plants. In this study, we analyzed plant-herbivore network data from various locations of the World to ascertain the degree to which land-use intensity and the prevalence of exotic plants induce predictable changes in their network topology - measured by levels of nestedness and modularity - and phylogenetic structures. Additionally, we investigated whether the intimacy of plant-herbivore interactions, contrasting endophagous with exophagous networks, modulate changes in network structure. Our findings reveal that most plant-herbivore networks are characterized by significant phylogenetic and topological structures. However, neither these structures did not show consistent changes in response to increased levels of land-use intensify. On the other hand, for the networks composed of endophagous herbivores, the level of nestedness was higher in the presence of a high proportion of exotic plants. Additionally, for networks of exophagous herbivores, we observed an increase in the phylogenetic structure of interactions due to exotic host dominance. These results underscore the differential impacts of exotic species and land-use intensity on the phylogenetic and topological structures of plant-herbivore networks.

Predicting Mutation-Induced Allosteric Changes in Structures and Conformational Ensembles of the ABL Kinase Using AlphaFold2 Adaptations with Alanine Sequence Scanning

Despite the success of AlphaFold2 approaches in predicting single protein structures, these methods showed intrinsic limitations in predicting multiple functional conformations of allosteric proteins and have been challenged to accurately capture the effects of single point mutations that induced significant structural changes. We examined several implementations of AlphaFold2 methods to predict conformational ensembles for state-switching mutants of the ABL kinase. The results revealed that a combination of randomized alanine sequence masking with shallow multiple sequence alignment subsampling can significantly expand the conformational diversity of the predicted structural ensembles and capture shifts in populations of the active and inactive ABL states. Consistent with the NMR experiments, the predicted conformational ensembles for M309L/L320I and M309L/H415P ABL mutants that perturb the regulatory spine networks featured the increased population of the fully closed inactive state. The proposed adaptation of AlphaFold can reproduce the experimentally observed mutation-induced redistributions in the relative populations of the active and inactive ABL states and capture the effects of regulatory mutations on allosteric structural rearrangements of the kinase domain. The ensemble-based network analysis complemented AlphaFold predictions by revealing allosteric hotspots that correspond to state-switching mutational sites which may explain the global effect of regulatory mutations on structural changes between the ABL states. This study suggested that attention-based learning of long-range dependencies between sequence positions in homologous folds and deciphering patterns of allosteric interactions may further augment the predictive abilities of AlphaFold methods for modeling of alternative protein sates, conformational ensembles and mutation-induced structural transformations.

Norm Emergence through Conflict-Blocking Interactions in Industrial Internet of Things Environments

Norms have been effectively utilized to facilitate smooth interactions among agents. Norms are usually the global data that agents cannot directly access in complex environments; instead, norms can only be indirectly accessed by agents via maintaining their own beliefs about norms. Establishing norms using decentralized interaction-based methods has attracted much attention. However, the current methods overlook Industrial Internet of Things (IIoT) environments. In IIoT, there is a prevalent feature called "conflict-blocking", where agents' conflicting action strategies can block an interaction from being completed or even cause danger. To facilitate norm emergence in IIoT, we propose a framework to support agent decisions in conflict-blocking interactions. The framework aids in achieving system scalability by integrating the fusion of agent beliefs about norms. We prove that the proposed framework guarantees norm emergence. We also theoretically and experimentally analyze the time required for norm emergence under the influence of various factors, such as the number of agents. A vehicle movement simulator is also developed to vividly illustrate the process of norm emergence.

Stable individual differences from dynamic patterns of function: brain network flexibility predicts openness/intellect, intelligence, and psychoticism

A growing understanding of the nature of brain function has led to increased interest in interpreting the properties of large-scale brain networks. Methodological advances in network neuroscience provide means to decompose these networks into smaller functional communities and measure how they reconfigure over time as an index of their dynamic and flexible properties. Recent evidence has identified associations between flexibility and a variety of traits pertaining to complex cognition including creativity and working memory. The present study used measures of dynamic resting-state functional connectivity in data from the Human Connectome Project (n = 994) to test associations with Openness/Intellect, general intelligence, and psychoticism, three traits that involve flexible cognition. Using a machine-learning cross-validation approach, we identified reliable associations of intelligence with cohesive flexibility of parcels in large communities across the cortex, of psychoticism with disjoint flexibility, and of Openness/Intellect with overall flexibility among parcels in smaller communities. These findings are reasonably consistent with previous theories of the neural correlates of these traits and help to expand on previous associations of behavior with dynamic functional connectivity, in the context of broad personality dimensions.

Tipping points in epithelial-mesenchymal lineages from single-cell transcriptomics data

Understanding cell fate decision-making during complex biological processes is an open challenge that is now aided by high-resolution single-cell sequencing technologies. Specifically, it remains challenging to identify and characterize transition states corresponding to "tipping points" whereby cells commit to new cell states. Here, we present a computational method that takes advantage of single-cell transcriptomics data to infer the stability and gene regulatory networks (GRNs) along cell lineages. Our method uses the unspliced and spliced counts from single-cell RNA sequencing data and cell ordering along lineage trajectories to train an RNA splicing multivariate model, from which cell-state stability along the lineage is inferred based on spectral analysis of the model's Jacobian matrix. Moreover, the model infers the RNA cross-species interactions resulting in GRNs and their variation along the cell lineage. When applied to epithelial-mesenchymal transition in ovarian and lung cancer-derived cell lines, our model predicts a saddle-node transition between the epithelial and mesenchymal states passing through an unstable, intermediate cell state. Furthermore, we show that the underlying GRN controlling epithelial-mesenchymal transition rearranges during the transition, resulting in denser and less modular networks in the intermediate state. Overall, our method represents a flexible tool to study cell lineages with a combination of theory-driven modeling and single-cell transcriptomics data.

Fractal information dissemination and clustering evolution on social hypernetwork

The complexity of systems stems from the richness of the group interactions among their units. Classical networks exhibit identified limits in the study of complex systems, where links connect pairs of nodes, inability to comprehensively describe higher-order interactions in networks. Higher-order networks can enhance modeling capacities of group interaction networks and help understand and predict network dynamical behavior. This paper constructs a social hypernetwork with a group structure by analyzing a community overlapping structure and a network iterative relationship, and the overlapping relationship between communities is logically separated. Considering the different group behavior pattern and attention focus, we defined the group cognitive disparity, group credibility, group cohesion index, hyperedge strength to study the relationship between information dissemination and network evolution. This study shows that groups can alter the connected network through information propagation, and users in social networks tend to form highly connected groups or communities in information dissemination. Propagation networks with high clustering coefficients promote the fractal information dissemination, which in itself drives the fractal evolution of groups within the network. This study emphasizes the significant role of "key groups" with overlapping structures among communities in group network propagation. Real cases provide evidence for the clustering phenomenon and fractal evolution of networks.

The mutual and dynamic role of TSPO and ligands in their binding process: An example with PK-11195

Translocator protein (TSPO) is an 18 kDa transmembrane protein, localized primarily on the outer mitochondrial membrane. It has been found to be involved in various physiological processes and pathophysiological conditions. Though studies on its structure have been performed only recently, there is little information on the nature of dynamics and doubts about some structures referenced in the literature, especially the NMR structure of mouse TSPO. In the present work, we thoroughly study the dynamics of mouse TSPO protein by means of atomistic molecular dynamics simulations, in presence as well as in absence of the diagnostic ligand PKA. We considered two starting structures: the NMR structure and a homology model (HM) generated on the basis of X-ray structures from bacterial TSPO. We examine the conformational landscape in both the modes for both starting points, in presence and absence of the ligand, in order to measure its impact for both structures. The analysis highlights high flexibility of the protein globally, but NMR simulations show a surprisingly flexibility even in the presence of the ligand. Interestingly, this is not the case for HM calculations, to the point that the ligand seems not so stable as in the NMR system and an unbinding event process is partially sampled. All those results tend to show that the NMR structure of mTSPO seems not deficient but is just in another portion of the global conformation space of TSPO.

Networked dynamic systems with higher-order interactions: stability versus complexity

The stability of complex systems is profoundly affected by underlying structures, which are often modeled as networks where nodes indicate system components and edges indicate pairwise interactions between nodes. However, such networks cannot encode the overall complexity of networked systems with higher-order interactions among more than two nodes. Set structures provide a natural description of pairwise and higher-order interactions where nodes are grouped into multiple sets based on their shared traits. Here we derive the stability criteria for networked systems with higher-order interactions by employing set structures. In particular, we provide a simple rule showing that the higher-order interactions play a double-sided role in community stability-networked systems with set structures are stabilized if the expected number of common sets for any two nodes is less than one. Moreover, although previous knowledge suggests that more interactions (i.e. complexity) destabilize networked systems, we report that, with higher-order interactions, networked systems can be stabilized by forming more local sets. Our findings are robust with respect to degree heterogeneous structures, diverse equilibrium states and interaction types.

Detectability of hierarchical communities in networks

We study the problem of recovering a planted hierarchy of partitions in a network. The detectability of a single planted partition has previously been analyzed in detail and a phase transition has been identified below which the partition cannot be detected. Here we show that, in the hierarchical setting, there exist additional phases in which the presence of multiple consistent partitions can either help or hinder detection. Accordingly, the detectability limit for nonhierarchical partitions typically provides insufficient information about the detectability of the complete hierarchical structure, as we highlight with several constructive examples.

Prediction of inhibitor development in previously untreated and minimally treated children with severe and moderately severe hemophilia A using a machine-learning network

BACKGROUND

Prediction of inhibitor development in patients with hemophilia A (HA) remains a challenge.

OBJECTIVES

To construct a predictive model for inhibitor development in HA using a network of clinical variables and biomarkers based on the individual similarity network.

METHODS

Previously untreated and minimally treated children with severe/moderately severe HA, participants of the HEMFIL Cohort Study, were followed up until reaching 75 exposure days (EDs) without inhibitor (INH-) or upon inhibitor development (INH+). Clinical data and biological samples were collected before the start of factor (F)VIII replacement (T0). A predictive model (HemfilNET) was built to compare the networks and potential global topological differences between INH- and INH+ at T0, considering the network robustness. For validation, the "leave-one-out" cross-validation technique was employed. Accuracy, precision, recall, and F1-score were used as evaluation metrics for the machine-learning model.

RESULTS

We included 95 children with HA (CHA), of whom 31 (33%) developed inhibitors. The algorithm, featuring 37 variables, identified distinct patterns of networks at T0 for INH+ and INH-. The accuracy of the model was 74.2% for CHA INH+ and 98.4% for INH-. By focusing the analysis on CHA with high-risk F8 mutations for inhibitor development, the accuracy in identifying CHA INH+ increased to 82.1%.

CONCLUSION

Our machine-learning algorithm demonstrated an overall accuracy of 90.5% for predicting inhibitor development in CHA, which further improved when restricting the analysis to CHA with a high-risk F8 genotype. However, our model requires validation in other cohorts. Yet, missing data for some variables hindered more precise predictions.

Drug Repurposing for COVID-19 by Constructing a Comorbidity Network with Central Nervous System Disorders

In the post-COVID-19 era, treatment options for potential SARS-CoV-2 outbreaks remain limited. An increased incidence of central nervous system (CNS) disorders has been observed in long-term COVID-19 patients. Understanding the shared molecular mechanisms between these conditions may provide new insights for developing effective therapies. This study developed an integrative drug-repurposing framework for COVID-19, leveraging comorbidity data with CNS disorders, network-based modular analysis, and dynamic perturbation analysis to identify potential drug targets and candidates against SARS-CoV-2. We constructed a comorbidity network based on the literature and data collection, including COVID-19-related proteins and genes associated with Alzheimer's disease, Parkinson's disease, multiple sclerosis, and autism spectrum disorder. Functional module detection and annotation identified a module primarily involved in protein synthesis as a key target module, utilizing connectivity map drug perturbation data. Through the construction of a weighted drug-target network and dynamic network-based drug-repurposing analysis, ubiquitin-carboxy-terminal hydrolase L1 emerged as a potential drug target. Molecular dynamics simulations suggested pregnenolone and BRD-K87426499 as two drug candidates for COVID-19. This study introduces a dynamic-perturbation-network-based drug-repurposing approach to identify COVID-19 drug targets and candidates by incorporating the comorbidity conditions of CNS disorders.

Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation

BACKGROUND

Increasing evidence suggests that a substantial proportion of disease-associated mutations occur in enhancers, regions of non-coding DNA essential to gene regulation. Understanding the structures and mechanisms of the regulatory programs this variation affects can shed light on the apparatuses of human diseases.

RESULTS

We collect epigenetic and gene expression datasets from seven early time points during neural differentiation. Focusing on this model system, we construct networks of enhancer-promoter interactions, each at an individual stage of neural induction. These networks serve as the base for a rich series of analyses, through which we demonstrate their temporal dynamics and enrichment for various disease-associated variants. We apply the Girvan-Newman clustering algorithm to these networks to reveal biologically relevant substructures of regulation. Additionally, we demonstrate methods to validate predicted enhancer-promoter interactions using transcription factor overexpression and massively parallel reporter assays.

CONCLUSIONS

Our findings suggest a generalizable framework for exploring gene regulatory programs and their dynamics across developmental processes; this includes a comprehensive approach to studying the effects of disease-associated variation on transcriptional networks. The techniques applied to our networks have been published alongside our findings as a computational tool, E-P-INAnalyzer. Our procedure can be utilized across different cellular contexts and disorders.

Biomarker Selection for Adaptive Systems

Biomarkers enable objective monitoring of a given cell or state in a biological system and are widely used in research, biomanufacturing, and clinical practice. However, identifying appropriate biomarkers that are both robustly measurable and capture a state accurately remains challenging. We present a framework for biomarker identification based upon observability guided sensor selection. Our methods, Dynamic Sensor Selection (DSS) and Structure-Guided Sensor Selection (SGSS), utilize temporal models and experimental data, offering a template for applying observability theory to data from biological systems. Unlike conventional methods that assume well-known, fixed dynamics, DSS adaptively select biomarkers or sensors that maximize observability while accounting for the time-varying nature of biological systems. Additionally, SGSS incorporates structural information and diverse data to identify sensors which are resilient against inaccuracies in our model of the underlying system. We validate our approaches by performing estimation on high dimensional systems derived from temporal gene expression data from partial observations. Our algorithms reliably identify known biomarkers and uncover new ones within our datasets. Additionally, integrating chromosome conformation and gene expression data addresses noise and uncertainty, enhancing the reliability of our biomarker selection approach for the genome.

SmartGD: A GAN-Based Graph Drawing Framework for Diverse Aesthetic Goals

While a multitude of studies have been conducted on graph drawing, many existing methods only focus on optimizing a single aesthetic aspect of graph layouts, which can lead to sub-optimal results. There are a few existing methods that have attempted to develop a flexible solution for optimizing different aesthetic aspects measured by different aesthetic criteria. Furthermore, thanks to the significant advance in deep learning techniques, several deep learning-based layout methods were proposed recently. These methods have demonstrated the advantages of deep learning approaches for graph drawing. However, none of these existing methods can be directly applied to optimizing non-differentiable criteria without special accommodation. In this work, we propose a novel Generative Adversarial Network (GAN) based deep learning framework for graph drawing, called SmartGD, which can optimize different quantitative aesthetic goals, regardless of their differentiability. To demonstrate the effectiveness and efficiency of SmartGD, we conducted experiments on minimizing stress, minimizing edge crossing, maximizing crossing angle, maximizing shape-based metrics, and a combination of multiple aesthetics. Compared with several popular graph drawing algorithms, the experimental results show that SmartGD achieves good performance both quantitatively and qualitatively.

Detection of minimal extended driver nodes in energetic costs reduction

Structures of complex networks are fundamental to system dynamics, where node state and connectivity patterns determine the cost of a control system, a key aspect in unraveling complexity. However, minimizing the energy required to control a system with the fewest input nodes remains an open problem. This study investigates the relationship between the structure of closed-connected function modules and control energy. We discovered that small structural adjustments, such as adding a few extended driver nodes, can significantly reduce control energy. Thus, we propose MInimal extended driver nodes in Energetic costs Reduction (MIER). Next, we transform the detection of MIER into a multi-objective optimization problem and choose an NSGA-II algorithm to solve it. Compared with the baseline methods, NSGA-II can approximate the optimal solution to the greatest extent. Through experiments using synthetic and real data, we validate that MIER can exponentially decrease control energy. Furthermore, random perturbation tests confirm the stability of MIER. Subsequently, we applied MIER to three representative scenarios: regulation of differential expression genes affected by cancer mutations in the human protein-protein interaction network, trade relations among developed countries in the world trade network, and regulation of body-wall muscle cells by motor neurons in Caenorhabditis elegans nervous network. The results reveal that the involvement of MIER significantly reduces control energy required for these original modules from a topological perspective. Additionally, MIER nodes enhance functionality, supplement key nodes, and uncover potential mechanisms. Overall, our work provides practical computational tools for understanding and presenting control strategies in biological, social, and neural systems.

The rules of multiplayer cooperation in networks of communities

Community organisation permeates both social and biological complex systems. To study its interplay with behaviour emergence, we model mobile structured populations with multiplayer interactions. We derive general analytical methods for evolutionary dynamics under high home fidelity when populations self-organise into networks of asymptotically isolated communities. In this limit, community organisation dominates over the network structure and emerging behaviour is independent of network topology. We obtain the rules of multiplayer cooperation in networks of communities for different types of social dilemmas. The success of cooperation is a result of the benefits shared among communal cooperators outperforming the benefits reaped by defectors in mixed communities. Under weak selection, cooperation can evolve and be stable for any size (Q) and number (M) of communities if the reward-to-cost ratio (V/K) of public goods is higher than a critical value. Community organisation is a solid mechanism for sustaining the evolution of cooperation under public goods dilemmas, particularly when populations are organised into a higher number of smaller communities. Contrary to public goods dilemmas relating to production, the multiplayer Hawk-Dove (HD) dilemma is a commons dilemma focusing on the fair consumption of preexisting resources. This game yields mixed results but tends to favour cooperation under larger communities, highlighting that the two types of social dilemmas might lead to solid differences in the behaviour adopted under community structure.

A call for caution when using network methods to study multimorbidity: an illustration using data from the Canadian Longitudinal Study on Aging

OBJECTIVES

To examine the impact of two key choices when conducting a network analysis (clustering methods and measure of association) on the number and type of multimorbidity clusters.

STUDY DESIGN AND SETTING

Using cross-sectional self-reported data on 24 diseases from 30,097 community-living adults aged 45-85 from the Canadian Longitudinal Study on Aging, we conducted network analyses using 5 clustering methods and 11 association measures commonly used in multimorbidity studies. We compared the similarity among clusters using the adjusted Rand index (ARI); an ARI of 0 is equivalent to the diseases being randomly assigned to clusters, and 1 indicates perfect agreement. We compared the network analysis results to disease clusters independently identified by two clinicians.

RESULTS

Results differed greatly across combinations of association measures and cluster algorithms. The number of clusters identified ranged from 1 to 24, with a low similarity of conditions within clusters. Compared to clinician-derived clusters, ARIs ranged from -0.02 to 0.24, indicating little similarity.

CONCLUSION

These analyses demonstrate the need for a systematic evaluation of the performance of network analysis methods on binary clustered data like diseases. Moreover, in individual older adults, diseases may not cluster predictably, highlighting the need for a personalized approach to their care.

Iterative embedding and reweighting of complex networks reveals community structure

Graph embeddings learn the structure of networks and represent it in low-dimensional vector spaces. Community structure is one of the features that are recognized and reproduced by embeddings. We show that an iterative procedure, in which a graph is repeatedly embedded and its links are reweighted based on the geometric proximity between the nodes, reinforces intra-community links and weakens inter-community links, making the clusters of the initial network more visible and more easily detectable. The geometric separation between the communities can become so strong that even a very simple parsing of the links may recover the communities as isolated components with surprisingly high precision. Furthermore, when used as a pre-processing step, our embedding and reweighting procedure can improve the performance of traditional community detection algorithms.

Intervention effect of targeted workplace closures may be approximated by single-layered networks in an individual-based model of COVID-19 control

Individual-based models of infectious disease dynamics commonly use network structures to represent human interactions. Network structures can vary in complexity, from single-layered with homogeneous mixing to multi-layered with clustering and layer-specific contact weights. Here we assessed policy-relevant consequences of network choice by simulating different network structures within an established individual-based model of SARS-CoV-2 dynamics. We determined the clustering coefficient of each network structure and compared this to several epidemiological outcomes, such as cumulative and peak infections. High-clustered networks estimate fewer cumulative infections and peak infections than less-clustered networks when transmission probabilities are equal. However, by altering transmission probabilities, we find that high-clustered networks can essentially recover the dynamics of low-clustered networks. We further assessed the effect of workplace closures as a layer-targeted intervention on epidemiological outcomes and found in this scenario a single-layered network provides a sufficient approximation of intervention effect relative to a multi-layered network when layer-specific contact weightings are equal. Overall, network structure choice within models should consider the knowledge of contact weights in different environments and pathogen mode of transmission to avoid over- or under-estimating disease burden and impact of interventions.

Oncogenic R248W mutation induced conformational perturbation of the p53 core domain and the structural protection by proteomimetic amyloid inhibitor ADH-6

The involvement of p53 aggregation in cancer pathogenesis emphasizes the importance of unraveling the mechanisms underlying mutation-induced p53 destabilization. And understanding how small molecule inhibitors prevent the conversion of p53 into aggregation-primed conformations is pivotal for the development of therapeutics targeting p53-aggregation-associated cancers. A recent experimental study highlights the efficacy of the proteomimetic amyloid inhibitor ADH-6 in stabilizing R248W p53 and inhibiting its aggregation in cancer cells by interacting with the p53 core domain (p53C). However, it remains mostly unclear how R248W mutation induces destabilization of p53C and how ADH-6 stabilizes this p53C mutant and inhibits its aggregation. Herein, we conducted all-atom molecular dynamics simulations of R248W p53C in the absence and presence of ADH-6, as well as that of wild-type (WT) p53C. Our simulations reveal that the R248W mutation results in a shift of helix H2 and β-hairpin S2-S2' towards the mutation site, leading to the destruction of their neighboring β-sheet structure. This further facilitates the formation of a cavity in the hydrophobic core, and reduces the stability of the β-sandwich. Importantly, two crucial aggregation-prone regions (APRs) S9 and S10 are disturbed and more exposed to solvent in R248W p53C, which is conducive to p53C aggregation. Intriguingly, ADH-6 dynamically binds to the mutation site and multiple destabilized regions in R248W p53C, partially inhibiting the shift of helix H2 and β-hairpin S2-S2', thus preventing the disruption of the β-sheets and the formation of the cavity. ADH-6 also reduces the solvent exposure of APRs S9 and S10, which disfavors the aggregation of R248W p53C. Moreover, ADH-6 can preserve the WT-like dynamical network of R248W p53C. Our study elucidates the mechanisms underlying the oncogenic R248W mutation induced p53C destabilization and the structural protection of p53C by ADH-6.

Identifying highly connected sites for risk-based surveillance and control of cucurbit downy mildew in the eastern United States

Objective

Surveillance is critical for the rapid implementation of control measures for diseases caused by aerially dispersed plant pathogens, but such programs can be resource-intensive, especially for epidemics caused by long-distance dispersed pathogens. The current cucurbit downy mildew platform for monitoring, predicting and communicating the risk of disease spread in the United States is expensive to maintain. In this study, we focused on identifying sites critical for surveillance and treatment in an attempt to reduce disease monitoring costs and determine where control may be applied to mitigate the risk of disease spread.

Methods

Static networks were constructed based on the distance between fields, while dynamic networks were constructed based on the distance between fields and wind speed and direction, using disease data collected from 2008 to 2016. Three strategies were used to identify highly connected field sites. First, the probability of pathogen transmission between nodes and the probability of node infection were modeled over a discrete weekly time step within an epidemic year. Second, nodes identified as important were selectively removed from networks and the probability of node infection was recalculated in each epidemic year. Third, the recurring patterns of node infection were analyzed across epidemic years.

Results

Static networks exhibited scale-free properties where the node degree followed a power-law distribution. Betweenness centrality was the most useful metric for identifying important nodes within the networks that were associated with disease transmission and prediction. Based on betweenness centrality, field sites in Maryland, North Carolina, Ohio, South Carolina and Virginia were the most central in the disease network across epidemic years. Removing field sites identified as important limited the predicted risk of disease spread based on the dynamic network model.

Conclusions

Combining the dynamic network model and centrality metrics facilitated the identification of highly connected fields in the southeastern United States and the mid-Atlantic region. These highly connected sites may be used to inform surveillance and strategies for controlling cucurbit downy mildew in the eastern United States.

Memristors with Tunable Volatility for Reconfigurable Neuromorphic Computing

Neuromorphic computing promises an energy-efficient alternative to traditional digital processors in handling data-heavy tasks, primarily driven by the development of both volatile (neuronal) and nonvolatile (synaptic) resistive switches or memristors. However, despite their energy efficiency, memristor-based technologies presently lack functional tunability, thus limiting their competitiveness with arbitrarily programmable (general purpose) digital computers. This work introduces a two-terminal bilayer memristor, which can be tuned among neuronal, synaptic, and hybrid behaviors. The varying behaviors are accessed via facile control over the filament formed within the memristor, enabled by the interplay between the two active ionic species (oxygen vacancies and metal cations). This solution is unlike single-species ion migration employed in most other memristors, which makes their behavior difficult to control. By reconfiguring a single crossbar array of hybrid memristors, two different applications that usually require distinct types of devices are demonstrated - reprogrammable heterogeneous reservoir computing and arbitrary non-Euclidean graph networks. Thus, this work outlines a potential path toward functionally reconfigurable postdigital computers.

Comparative Study and Evaluation of Hybrid Visualizations of Graphs

Hybrid visualizations combine different metaphors into a single network layout, in order to help humans in finding the "right way" of displaying the different portions of the network, especially when it is globally sparse and locally dense. We investigate hybrid visualizations in two complementary directions: (i) On the one hand, we evaluate the effectiveness of different hybrid visualization models through a comparative user study; (ii) On the other hand, we estimate the usefulness of an interactive visualization that integrates all the considered hybrid models together. The results of our study provide some hints about the usefulness of the different hybrid visualizations for specific tasks of analysis and indicates that integrating different hybrid models into a single visualization may offer a valuable tool of analysis.

Congruence between co-occurrence and trait-based networks is scale-dependent: a case study with flea parasites of small mammalian hosts

We applied a novel framework based on network theory and a concept of modularity that estimates congruence between trait-based ( = functional) co-occurrence networks, thus allowing the inference of co-occurrence patterns and the determination of the predominant mechanism of community assembly. The aim was to investigate the relationships between species co-occurrence and trait similarity in flea communities at various scales (compound communities: across regions within a biogeographic realm or across sampling sites within a geographic region; component communities: across sampling sites within a geographic region; and infracommunities: within a sampling site). We found that compound communities within biogeographic realms were assembled via environmental or host-associated filtering. In contrast, functional and spatial/host-associated co-occurrence networks, at the scale of regional compound communities, mostly indicated either stochastic processes or the lack of dominance of any deterministic process. Analyses of congruence between functional and either spatial (for component communities) or host-associated (for infracommunities) co-occurrence networks demonstrated that assembly rules in these communities varied among host species. In component communities, stochastic processes prevailed, whereas environmental filtering was indicated in 4 and limiting similarity/competition in 9 of 31 communities. Limiting similarity/competition processes dominated in infracommunities, followed by stochastic mechanisms. We conclude that assembly processes in parasite communities are scale-dependent, with different mechanisms acting at different scales.

Microbial co-occurrence network demonstrates spatial and climatic trends for global soil diversity

Despite recent research efforts to explore the co-occurrence patterns of diverse microbes within soil microbial communities, a substantial knowledge-gap persists regarding global climate influences on soil microbiota behaviour. Comprehending co-occurrence patterns within distinct geoclimatic groups is pivotal for unravelling the ecological structure of microbial communities, that are crucial for preserving ecosystem functions and services. Our study addresses this gap by examining global climatic patterns of microbial diversity. Using data from the Earth Microbiome Project, we analyse a meta-community co-occurrence network for bacterial communities. This method unveils substantial shifts in topological features, highlighting regional and climatic trends. Arid, Polar, and Tropical zones show lower diversity but maintain denser networks, whereas Temperate and Cold zones display higher diversity alongside more modular networks. Furthermore, it identifies significant co-occurrence patterns across diverse climatic regions. Central taxa associated with different climates are pinpointed, highlighting climate's pivotal role in community structure. In conclusion, our study identifies significant correlations between microbial interactions in diverse climatic regions, contributing valuable insights into the intricate dynamics of soil microbiota.

Prolactin blood concentration relies on the scalability of the TIDA neurons' network efficiency in vivo

Our understanding and management of reproductive health and related disorders such as infertility, menstrual irregularities, and pituitary disorders depend on understanding the intricate sex-specific mechanisms governing prolactin secretion. Using ex vivo experiments in acute slices, in parallel with in vivo calcium imaging (GRIN lens technology), we found that dopamine neurons inhibiting PRL secretion (TIDA), organize as functional networks both in and ex vivo. We defined an index of efficiency of networking (Ieff) using the duration of calcium events and the ability to form plastic economic networks. It determined TIDA neurons' ability to inhibit PRL secretion in vivo. Ieff variations in both sexes demonstrated TIDA neurons' adaptability to physiological changes. A variation in the number of active neurons contributing to the network explains the sexual dimorphism in basal [PRL]blood secretion patterns. These sex-specific differences in neuronal activity and network organization contribute to the understanding of hormone regulation.

Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis

Polymicrobial infection of the airways is a hallmark of obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic obstructive pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated lung function decline and higher mortality rates. Understanding PEx ecology is challenged by high inter-patient variability in airway microbial community profiles. We analyze bacterial communities in 880 CF sputum samples collected during an observational prospective cohort study and develop microbiome descriptors to model community reorganization prior to and during 18 PEx. We identify two microbial dysbiosis regimes with opposing ecology and dynamics. Pathogen-governed PEx show hierarchical community reorganization and reduced diversity, whereas anaerobic bloom PEx display stochasticity and increased diversity. A simulation of antimicrobial treatment predicts better efficacy for hierarchically organized communities. This link between PEx, microbiome organization, and treatment success advances the development of personalized clinical management in CF and, potentially, other obstructive lung diseases.

Dynamical changes of interaction across functional brain communities during propofol-induced sedation

It is crucial to understand how anesthetics disrupt information transmission within the whole-brain network and its hub structure to gain insight into the network-level mechanisms underlying propofol-induced sedation. However, the influence of propofol on functional integration, segregation, and community structure of whole-brain networks were still unclear. We recruited 12 healthy subjects and acquired resting-state functional magnetic resonance imaging data during 5 different propofol-induced effect-site concentrations (CEs): 0, 0.5, 1.0, 1.5, and 2.0 μg/ml. We constructed whole-brain functional networks for each subject under different conditions and identify community structures. Subsequently, we calculated the global and local topological properties of whole-brain network to investigate the alterations in functional integration and segregation with deepening propofol sedation. Additionally, we assessed the alteration of key nodes within the whole-brain community structure at each effect-site concentrations level. We found that global participation was significantly increased at high effect-site concentrations, which was mediated by bilateral postcentral gyrus. Meanwhile, connector hubs appeared and were located in posterior cingulate cortex and precentral gyrus at high effect-site concentrations. Finally, nodal participation coefficients of connector hubs were closely associated to the level of sedation. These findings provide valuable insights into the relationship between increasing propofol dosage and enhanced functional interaction within the whole-brain networks.

Correlations reveal the hierarchical organization of biological networks with latent variables

Deciphering the functional organization of large biological networks is a major challenge for current mathematical methods. A common approach is to decompose networks into largely independent functional modules, but inferring these modules and their organization from network activity is difficult, given the uncertainties and incompleteness of measurements. Typically, some parts of the overall functional organization, such as intermediate processing steps, are latent. We show that the hidden structure can be determined from the statistical moments of observable network components alone, as long as the functional relevance of the network components lies in their mean values and the mean of each latent variable maps onto a scaled expectation of a binary variable. Whether the function of biological networks permits a hierarchical modularization can be falsified by a correlation-based statistical test that we derive. We apply the test to gene regulatory networks, dendrites of pyramidal neurons, and networks of spiking neurons.