Diversity, integration, and variability of intergenerational relationships in old age: New insights from personal network research

Relationships between family members from different generations have long been described as a source of solidarity and support in aging populations and, more recently, as a potential risk factor for COVID-19 contagion. Personal or egocentric network research offers a powerful kit of conceptual and methodological tools to study these relationships, but this has not yet been employed to its full potential in the literature. We investigate the heterogeneity, social integration, and individual correlates of intergenerational relationships in old age analyzing highly granular data on the personal networks of 230 older adults (2747 social ties) from a local survey in one of the areas of the world at the forefront of global aging trends (northern Italy). Using information on different layers in broad egocentric networks and on the structure of connectivity among the social contacts of aging people, we propose multiple conceptualizations and measures of intergenerational connectedness. Results show that intergenerational relationships are strongly integrated, but also highly diverse and variable, in older adults' social networks. Different types of intergenerational ties exist in different network layers, with various relational roles, degrees of tie strength, and patterns of association with individual and tie characteristics. We discuss how new and existing personal network data can be leveraged to consider novel questions and hypotheses about intergenerational relationships in contemporary aging families.

Well-being is associated with cortical thickness network topology of human brain

BACKGROUND

Living a happy and meaningful life is an eternal topic in positive psychology, which is crucial for individuals' physical and mental health as well as social functioning. Well-being can be subdivided into pleasure attainment related hedonic well-being or emotional well-being, and self-actualization related eudaimonic well-being or psychological well-being plus social well-being. Previous studies have mostly focused on human brain morphological and functional mechanisms underlying different dimensions of well-being, but no study explored brain network mechanisms of well-being, especially in terms of topological properties of human brain morphological similarity network.

METHODS

Therefore, in the study, we collected 65 datasets including magnetic resonance imaging (MRI) and well-being data, and constructed human brain morphological network based on morphological distribution similarity of cortical thickness to explore the correlations between topological properties including network efficiency and centrality and different dimensions of well-being.

RESULTS

We found emotional well-being was negatively correlated with betweenness centrality in the visual network but positively correlated with eigenvector centrality in the precentral sulcus, while the total score of well-being was positively correlated with local efficiency in the posterior cingulate cortex of cortical thickness network.

CONCLUSIONS

Our findings demonstrated that different dimensions of well-being corresponded to different cortical hierarchies: hedonic well-being was involved in more preliminary cognitive processing stages including perceptual and attentional information processing, while hedonic and eudaimonic well-being might share common morphological similarity network mechanisms in the subsequent advanced cognitive processing stages.

Network centrality, support organizations, exploratory innovation: Empirical analysis of China's integrated circuit industry

Exploratory innovation is critical to the breakthrough of core technologies in the integrated circuit (IC) industry, and cooperative innovation is a promising form of IC industry development. According to the viewpoint of social network, this paper constructs intercity networks of the IC industry by using a data set of cooperation patents from 2011 to 2020 in China. We uncover the evolution characteristics of the innovation networks, explore the relationship between network centrality and exploratory innovation in a city, and consider universities and development zones, named support organizations, as moderating variables. The results of the social network analysis (SNA) and dynamic panel system generalized method of moments model (System-GMM) are given as follows: Cities are increasingly inclined to collaborate with counterparts over time for innovation, but the overall network scale remains small. Beijing occupies core position in the networks. A cooperative innovation model driven by peripheral cities has been formed as the number of the peripheral cities has gradually increased. The network centrality of a city has a positive effect on its exploratory innovation. Both universities and development zones positively moderate the effect of network centrality on exploratory innovation. Based on the characteristics of the network, our study reveals the importance of taking the internal structure of the network and the node support environment into the same framework, which provides guidance for the innovative development of the world IC industry.

Centrality Analysis of Protein-Protein Interaction Networks Using R

Proteins are structural and functional components of cells. They interact with each other to drive specific cellular functions. The physical and functional protein interactions are an important feature of cellular organization and regulation. Protein interactions are represented as a network or a graph in which proteins are nodes, and interactions between them are edges. Perturbations in the network affecting essential or central proteins can have pathological consequences. Network or graph theory is a branch of mathematics that provides a conceptual framework to decipher topologically important proteins in the network. These concepts are known as centrality measures. This chapter introduces various centrality metrics and provides a stepwise protocol to quantify protein's strategic positions in the network using an R programming language.

From a systems view to spotting a hidden island: A narrative review implicating insula function in alcoholism

Excessive use of alcohol promotes the development of alcohol addiction, but the understanding of how alcohol-induced brain alterations lead to addiction remains limited. To further this understanding, we adopted an unbiased discovery strategy based on the principles of systems medicine. We used functional magnetic resonance imaging data from patients and animal models of alcohol addiction-like behaviors, and developed mathematical models of the 'relapse-prone' network states to identify brain sites and functional networks that can be selectively targeted by therapeutic interventions. Our systems level, non-local, and largely unbiased analyses converged on a few well-defined brain regions, with the insula emerging as one of the most consistent finding across studies. In proof-of-concept experiments we were able to demonstrate that it is possible to guide network dynamics towards increased resilience in animals but an initial translation into a clinical trial targeting the insula failed. Here, in a narrative review, we summarize the key experiments, methodological developments and knowledge gained from this completed round of a discovery cycle moving from identification of 'relapse-prone' network states in humans and animals to target validation and intervention trial. Future concerted efforts are necessary to gain a deeper understanding of insula function a in a state-dependent, circuit-specific and cell population perspective, and to develop the means for insula-directed interventions, before therapeutic targeting of this structure may become possible.

Haemosporidian taxonomic composition, network centrality and partner fidelity between resident and migratory avian hosts

Migration can modify interaction dynamics between parasites and their hosts with migrant hosts able to disperse parasites and impact local community transmission. Thus, studying the relationships among migratory hosts and their parasites is fundamental to elucidate how migration shapes host-parasite interactions. Avian haemosporidians are some of the most prevalent and diverse group of wildlife parasites and are also widely studied as models in ecological and evolutionary research. Here, we contrast partner fidelity, network centrality and parasite taxonomic composition among resident and non-resident avian hosts using presence/absence data on haemosporidians parasitic in South American birds as study model. We ran multilevel Bayesian models to assess the role of migration in determining partner fidelity (i.e., normalized degree) and centrality (i.e., weighted closeness) in host-parasite networks of avian hosts and their respective haemosporidian parasites. In addition, to evaluate parasite taxonomic composition, we performed permutational multivariate analyses of variance to quantify dissimilarity in haemosporidian lineages infecting different host migratory categories. We observed similar partner fidelity and parasite taxonomic composition among resident and migratory hosts. Conversely, we demonstrate that migratory hosts play a more central role in host-parasite networks than residents. However, when evaluating partially and fully migratory hosts separately, we observed that only partially migratory species presented higher network centrality when compared to resident birds. Therefore, migration does not lead to differences in both partner fidelity and parasite taxonomic composition. However, migratory behavior is positively associated with network centrality, indicating migratory hosts play more important roles in shaping host-parasite interactions and influence local transmission.

Protein conformational switch discerned via network centrality properties

Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensemble-informed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.

Prediction of human-Streptococcus pneumoniae protein-protein interactions using logistic regression

Streptococcus pneumoniae is a major cause of mortality in children under five years old. In recent years, the emergence of antibiotic-resistant strains of S. pneumoniae increases the threat level of this pathogen. For that reason, the exploration of S. pneumoniae protein virulence factors should be considered in developing new drugs or vaccines, for instance by the analysis of host-pathogen protein-protein interactions (HP-PPIs). In this research, prediction of protein-protein interactions was performed with a logistic regression model with the number of protein domain occurrences as features. By utilizing HP-PPIs of three different pathogens as training data, the model achieved 57-77 % precision, 64-75 % recall, and 96-98 % specificity. Prediction of human-S. pneumoniae protein-protein interactions using the model yielded 5823 interactions involving thirty S. pneumoniae proteins and 324 human proteins. Pathway enrichment analysis showed that most of the pathways involved in the predicted interactions are immune system pathways. Network topology analysis revealed β-galactosidase (BgaA) as the most central among the S. pneumoniae proteins in the predicted HP-PPI networks, with a degree centrality of 1.0 and a betweenness centrality of 0.451853. Further experimental studies are required to validate the predicted interactions and examine their roles in S. pneumoniae infection.

Distinct impaired patterns of intrinsic functional network centrality in patients with early- and late-onset Alzheimer's disease

Early-onset Alzheimer's disease (EOAD) involves multiple cognitive domains and shows more rapid progression than late-onset Alzheimer's disease (LOAD). However, the difference in pathogenesis between EOAD and LOAD is still unclear. Accordingly, we applied intrinsic network analysis to explore the potential neuropathological mechanism underlying distinct clinical phenotypes. According to the cut-off age of 65, we included 20 EOAD patients, 20 LOAD patients, and 36 age-matched controls (19 young and 17 old controls). We employed resting-state functional MRI and network centrality analysis to explore the local (degree centrality (DC)) and global (eigenvector centrality (EC)) functional integrity. Two-sample t-test analysis was performed, with gray matter volume, age, gender, and education as covariates. Furthermore, we performed a correlation analysis between network metrics and cognition. Compared to young controls, EOAD patients exhibited lower DC in the middle temporal gyrus (MTG), parahippocampal gyrus (PHG), superior temporal gyrus (STG), and lower EC in the MTG, PHG, and postcentral gyrus. In contrast, LOAD patients exhibited lower DC in the STG and anterior cingulum gyrus and higher DC in the middle frontal gyrus compared to old controls. No significant difference in EC was observed in LOAD patients. Furthermore, both DC and EC correlated with cognitive performance. Our study demonstrated divergent functional network impairments in EOAD and LOAD patients. EOAD patients showed more complex network damage involving both local and global centrality properties, while LOAD patients mainly featured local functional connectivity changes. Such centrality impairments are related to poor cognition, especially regarding memory performance.

Predicting high-risk areas for African swine fever spread at the wild-domestic pig interface in Ontario

The probability of disease transmission among livestock premises via spillover from wildlife vectors depends on interacting ecological, demographic, and behavioural variables. Wild pigs (Sus scrofa) act as vectors and reservoirs of many diseases, including African Swine Fever (ASF), a highly lethal and contagious viral disease that affects both wild and domestic swine. Wild pigs play a significant role in the spread of ASF in geographic locations where the disease is present. Planning and preparedness will ensure that swift action can be taken to control ASF if it is introduced into North America. We used a network to predict the highest risk areas for ASF spread in Ontario, Canada given the distribution of wild pig sightings and other risk factors for wild pig presence and movement on the landscape. We used network nodes to represent the presence of domestic pig farms in a defined area, and we weighted network edges by the probability of ASF virus movement between nodes via movement of wild pigs. Our network models predicted that central Ontario has relatively high network closeness, suggesting that this area has a relatively high risk of virus exposure. These highly connected areas tended to also have the highest domestic pig farm density within a node. Central and eastern Ontario had the highest predicted network betweenness, suggesting that these areas are important for controlling virus flow across the province. We detected 10 communities or clusters within the overall network, where nodes were highly connected locally and relatively less connected to the rest of the network. Predicting areas with a high risk of exposure to the ASF virus due to wild pig movement in Ontario will guide managers on where to focus surveillance for ASF in the wild pig population and where to heighten biosecurity within commercial and backyard pig farms, ensuring that managers are prepared to act quickly to limit spread of ASF if the virus is introduced.

Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis

COVID-19 (Coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the pathophysiology of this deadly virus is complex and largely unknown, we employ a network biology-fueled approach and integrate multiomics data pertaining to lung epithelial cells-specific co-expression network and human interactome to generate Calu-3-specific human-SARS-CoV-2 Interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 target central nodes of host-viral network that participate in core functional pathways. Network centrality analyses discover 28 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host modifying responses and cytokine storm. Overall, our network centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into SARS-CoV-2 pathogenicity that may foster effective therapeutic design. Funding: This work was supported by the National Science Foundation (IOS-1557796) to M.S.M., and U54 ES 030246 from NIH/NIEHS to M. A. Conflict of Interest: The authors declare no competing interests. The authors also declare no financial interests.

Ensemble disease gene prediction by clinical sample-based networks

BACKGROUND

Disease gene prediction is a critical and challenging task. Many computational methods have been developed to predict disease genes, which can reduce the money and time used in the experimental validation. Since proteins (products of genes) usually work together to achieve a specific function, biomolecular networks, such as the protein-protein interaction (PPI) network and gene co-expression networks, are widely used to predict disease genes by analyzing the relationships between known disease genes and other genes in the networks. However, existing methods commonly use a universal static PPI network, which ignore the fact that PPIs are dynamic, and PPIs in various patients should also be different.

RESULTS

To address these issues, we develop an ensemble algorithm to predict disease genes from clinical sample-based networks (EdgCSN). The algorithm first constructs single sample-based networks for each case sample of the disease under study. Then, these single sample-based networks are merged to several fused networks based on the clustering results of the samples. After that, logistic models are trained with centrality features extracted from the fused networks, and an ensemble strategy is used to predict the finial probability of each gene being disease-associated. EdgCSN is evaluated on breast cancer (BC), thyroid cancer (TC) and Alzheimer's disease (AD) and obtains AUC values of 0.970, 0.971 and 0.966, respectively, which are much better than the competing algorithms. Subsequent de novo validations also demonstrate the ability of EdgCSN in predicting new disease genes.

CONCLUSIONS

In this study, we propose EdgCSN, which is an ensemble learning algorithm for predicting disease genes with models trained by centrality features extracted from clinical sample-based networks. Results of the leave-one-out cross validation show that our EdgCSN performs much better than the competing algorithms in predicting BC-associated, TC-associated and AD-associated genes. de novo validations also show that EdgCSN is valuable for identifying new disease genes.

Structural connectivity centrality changes mark the path toward Alzheimer's disease

Introduction

The pathophysiological process of Alzheimer's disease is thought to begin years before clinical decline, with evidence suggesting prion-like spreading processes of neurofibrillary tangles and amyloid plaques.

Methods

Using diffusion magnetic resonance imaging data from the Alzheimer's Disease Neuroimaging Initiative database, we first identified relevant features for dementia diagnosis. We then created dynamic models with the Nathan Kline Institute-Rockland Sample database to estimate the earliest detectable stage associated with dementia in the simulated disease progression.

Results

A classifier based on centrality measures provides informative predictions. Strength and closeness centralities are the most discriminative features, which are associated with the medial temporal lobe and subcortical regions, together with posterior and occipital brain regions. Our model simulations suggest that changes associated with dementia begin to manifest structurally at early stages.

Discussion

Our analyses suggest that diffusion magnetic resonance imaging–based centrality measures can offer a tool for early disease detection before clinical dementia onset.

A network approach to quantifying radiotherapy effect on cancer: Radiosensitive gene group centrality

Radiotherapy plays a vital role in cancer treatment, for which accurate prognosis is important for guiding sequential treatment and improving the curative effect for patients. An issue of great significance in radiotherapy is to assess tumor radiosensitivity for devising the optimal treatment strategy. Previous studies focused on gene expression in cells closely associated with radiosensitivity, but factors such as the response of a cancer patient to irradiation and the patient survival time are largely ignored. For clinical cancer treatment, a specific pre-treatment indicator taking into account cancer cell type and patient radiosensitivity is of great value but it has been missing. Here, we propose an effective indicator for radiosensitivity: radiosensitive gene group centrality (RSGGC), which characterizes the importance of the group of genes that are radiosensitive in the whole gene correlation network. We demonstrate, using both clinical patient data and experimental cancer cell lines, which RSGGC can provide a quantitative estimate of the effect of radiotherapy, with factors such as the patient survival time and the survived fraction of cancer cell lines under radiotherapy fully taken into account. Our main finding is that, for patients with a higher RSGGC score before radiotherapy, cancer treatment tends to be more effective. The RSGGC can have significant applications in clinical prognosis, serving as a key measure to classifying radiosensitive and radioresistant patients.

Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes

BACKGROUND

Identification of driver genes related to certain types of cancer is an important research topic. Several systems biology approaches have been suggested, in particular for the identification of breast cancer (BRCA) related genes. Such approaches usually rely on differential gene expression and/or mutational landscape data. In some cases interaction network data is also integrated to identify cancer-related modules computationally.

RESULTS

We provide a framework for the comparative graph-theoretical analysis of networks integrating the relevant gene expression, mutations, and potein-protein interaction network data. The comparisons involve a graph-theoretical analysis of normal and tumor network pairs across all instances of a given set of breast cancer samples. The network measures under consideration are based on appropriate formulations of various centrality measures: betweenness, clustering coefficients, degree centrality, random walk distances, graph-theoretical distances, and Jaccard index centrality.

CONCLUSIONS

Among all the studied centrality-based graph-theoretical properties, we show that a betweenness-based measure differentiates BRCA genes across all normal versus tumor network pairs, than the rest of the popular centrality-based measures. The AUROC and AUPR values of the gene lists ordered with respect to the measures under study as compared to NCBI BioSystems pathway and the COSMIC database of cancer genes are the largest with the betweenness-based differentiation, followed by the measure based on degree centrality. In order to test the robustness of the suggested measures in prioritizing cancer genes, we further tested the two most promising measures, those based on betweenness and degree centralities, on randomly rewired networks. We show that both measures are quite resilient to noise in the input interaction network. We also compared the same measures against a state-of-the-art alternative disease gene prioritization method, MUFFFINN. We show that both our graph-theoretical measures outperform MUFFINN prioritizations in terms of ROC and precions/recall analysis. Finally, we filter the ordered list of the best measure, the betweenness-based differentiation, via a maximum-weight independent set formulation and investigate the top 50 genes in regards to literature verification. We show that almost all genes in the list are verified by the breast cancer literature and three genes are presented as novel genes that may potentialy be BRCA-related but missing in literature.

MIDAS: Mining differentially activated subpaths of KEGG pathways from multi-class RNA-seq data

Pathway based analysis of high throughput transcriptome data is a widely used approach to investigate biological mechanisms. Since a pathway consists of multiple functions, the recent approach is to determine condition specific sub-pathways or subpaths. However, there are several challenges. First, few existing methods utilize explicit gene expression information from RNA-seq. More importantly, subpath activity is usually an average of statistical scores, e.g., correlations, of edges in a candidate subpath, which fails to reflect gene expression quantity information. In addition, none of existing methods can handle multiple phenotypes. To address these technical problems, we designed and implemented an algorithm, MIDAS, that determines condition specific subpaths, each of which has different activities across multiple phenotypes. MIDAS utilizes gene expression quantity information fully and the network centrality information to determine condition specific subpaths. To test performance of our tool, we used TCGA breast cancer RNA-seq gene expression profiles with five molecular subtypes. 36 differentially activate subpaths were determined. The utility of our method, MIDAS, was demonstrated in four ways. All 36 subpaths are well supported by the literature information. Subsequently, we showed that these subpaths had a good discriminant power for five cancer subtype classification and also had a prognostic power in terms of survival analysis. Finally, in a performance comparison of MIDAS to a recent subpath prediction method, PATHOME, our method identified more subpaths and much more genes that are well supported by the literature information.

AVAILABILITY

http://biohealth.snu.ac.kr/software/MIDAS/.

Genome-wide profiling of 24 hr diel rhythmicity in the water flea, Daphnia pulex: network analysis reveals rhythmic gene expression and enhances functional gene annotation

Background

Marine and freshwater zooplankton exhibit daily rhythmic patterns of behavior and physiology which may be regulated directly by the light:dark (LD) cycle and/or a molecular circadian clock. One of the best-studied zooplankton taxa, the freshwater crustacean Daphnia, has a 24 h diel vertical migration (DVM) behavior whereby the organism travels up and down through the water column daily. DVM plays a critical role in resource tracking and the behavioral avoidance of predators and damaging ultraviolet radiation. However, there is little information at the transcriptional level linking the expression patterns of genes to the rhythmic physiology/behavior of Daphnia.

Results

Here we analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 44 h time period under a 12:12 LD cycle (diel) conditions using a cosine-fitting algorithm. We used a comprehensive network modeling and analysis approach to identify novel co-regulated rhythmic genes that have similar network topological properties and functional annotations as rhythmic genes identified by the cosine-fitting analyses. Furthermore, we used the network approach to predict with high accuracy novel gene-function associations, thus enhancing current functional annotations available for genes in this ecologically relevant model species. Our results reveal that genes in many functional groupings exhibit 24 h rhythms in their expression patterns under diel conditions. We highlight the rhythmic expression of immunity, oxidative detoxification, and sensory process genes. We discuss differences in the chronobiology of D. pulex from other well-characterized terrestrial arthropods.

Conclusions

This research adds to a growing body of literature suggesting the genetic mechanisms governing rhythmicity in crustaceans may be divergent from other arthropod lineages including insects. Lastly, these results highlight the power of using a network analysis approach to identify differential gene expression and provide novel functional annotation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2998-2) contains supplementary material, which is available to authorized users.

Group structure predicts variation in proximity relationships between male-female and male-infant pairs of mountain gorillas (Gorilla beringei beringei)

Relationships between conspecifics are influenced by both ecological factors and the social organization they live in. Systematic variation of both--consistent with predictions derived from socioecology models--is well documented, but there is considerable variation within species and populations that is poorly understood. The mountain gorilla (Gorilla beringei) is unusual because, despite possessing morphology associated with male contest competition (e.g., extreme sexual dimorphism), they are regularly observed in both single-male and multimale groups. Both male-female and male-infant bonds are strong because males provide protection against infanticide and/or predation. Risk of these threats varies with social structure, which may influence the strength of social relationships among group members (including females and offspring, if females with lower infant mortality risk are less protective of infants). Here, we investigate the relationship between group structure and the strength of proximity relationships between males and females, males and infants, and females and offspring. Data come from 10 social groups containing 1-7 adult males, monitored by the Dian Fossey Gorilla Fund's Karisoke Research Center in Volcanoes National Park, Rwanda. After controlling for group size and infant age, association strength was similar for male-female pairs across group types with both dominant and nondominant males, but male-infant relationships were strongest in single-male groups where paternity certainty was high and animals had fewer social partners to choose from. The male:female and male:infant ratios better predicted both male-female and male-infant associations than the absolute number of males, females, or infants did. The fewer the number of males per female or infant, the more both pair types associated. Dominant males in groups containing fewer males had higher eigenvector centrality (a measure of importance in a social network) than dominant males in groups with more males. Results indicate that nondominant males are an important influence on relationships between dominant males and females/infants despite their peripheral social positions, and that relationships between males and infants must be considered an important foundation of gorilla social structure.