K-core robustness in ecological and financial networks

Nucleation phenomena and extreme vulnerability of spatial k-core systems

K-core percolation is a fundamental dynamical process in complex networks with applications that span numerous real-world systems. Earlier studies focus primarily on random networks without spatial constraints and reveal intriguing mixed-order transitions. However, real-world systems, ranging from transportation and communication networks to complex brain networks, are not random but are spatially embedded. Here, we study k-core percolation on two-dimensional spatially embedded networks and show that, in contrast to regular percolation, the length of connections can control the transition type, leading to four different types of phase transitions associated with interesting phenomena and a rich phase diagram. A key finding is the existence of a metastable phase where microscopic localized damage, independent of system size, can cause a macroscopic phase transition, a result which cannot be achieved in traditional percolation. In this case, local failures spontaneously propagate the damage radially until the system collapses, a phenomenon analogous to the nucleation process.

Network models of protein phosphorylation, acetylation, and ubiquitination connect metabolic and cell signaling pathways in lung cancer

We analyzed large-scale post-translational modification (PTM) data to outline cell signaling pathways affected by tyrosine kinase inhibitors (TKIs) in ten lung cancer cell lines. Tyrosine phosphorylated, lysine ubiquitinated, and lysine acetylated proteins were concomitantly identified using sequential enrichment of post translational modification (SEPTM) proteomics. Machine learning was used to identify PTM clusters that represent functional modules that respond to TKIs. To model lung cancer signaling at the protein level, PTM clusters were used to create a co-cluster correlation network (CCCN) and select protein-protein interactions (PPIs) from a large network of curated PPIs to create a cluster-filtered network (CFN). Next, we constructed a Pathway Crosstalk Network (PCN) by connecting pathways from NCATS BioPlanet whose member proteins have PTMs that co-cluster. Interrogating the CCCN, CFN, and PCN individually and in combination yields insights into the response of lung cancer cells to TKIs. We highlight examples where cell signaling pathways involving EGFR and ALK exhibit crosstalk with BioPlanet pathways: Transmembrane transport of small molecules; and Glycolysis and gluconeogenesis. These data identify known and previously unappreciated connections between receptor tyrosine kinase (RTK) signal transduction and oncogenic metabolic reprogramming in lung cancer. Comparison to a CFN generated from a previous multi-PTM analysis of lung cancer cell lines reveals a common core of PPIs involving heat shock/chaperone proteins, metabolic enzymes, cytoskeletal components, and RNA-binding proteins. Elucidation of points of crosstalk among signaling pathways employing different PTMs reveals new potential drug targets and candidates for synergistic attack through combination drug therapy.

Exploring the mobility in the Madrid Community

Displacements within urban spaces have attracted particular interest among researchers. We examine the journeys that happen in the Madrid Community considering 24 travel typologies and 1390 administrative areas. From an origin-destination (OD) matrix, four classes of major flows are characterised through coarse-graining: hotspot-non-hotspots, non-hotspot-hotspots, hotspots-hotspots, non-hotspot-non-hotspot. In order to make comparisons between them with respect to spatial and temporal patterns, several statistical tests are performed. The spatial activity as well as transition probabilities between administrative zones are also analysed. The mobility network's topology is examined (some parameters such as maximal connected components, average degree, betweenness, and assortativity as well as the k-cores are checked). A model describing the formation of links between zones (existence of at least one trip between them) is constructed based on certain measures of affinity between areas.

A robust core architecture of functional brain networks supports topological resilience and cognitive performance in middle- and old-aged adults

Aging is associated with gradual changes in cognition, yet some individuals exhibit protection against age-related cognitive decline. The topological characteristics of brain networks that promote protection against cognitive decline in aging are unknown. Here, we investigated whether the robustness and resilience of brain networks, queried via the delineation of the brain's core network structure, relate to age and cognitive performance in a cross-sectional dataset of healthy middle- and old-aged adults (n = 478, ages 40 to 90 y). First, we decomposed each subject's functional brain network using k-shell decomposition and found that age was negatively associated with robust core network structures. Next, we perturbed these networks, via attack simulations, and found that resilience of core brain network nodes also declined in relationship to age. We then partitioned our dataset into middle- (ages 40 to 65 y, n = 300) and old- (ages 65 to 90 y, n = 178) aged subjects and observed that older individuals had less robust core connectivity and resilience. Following these analyses, we found that episodic memory was positively related to robust connectivity and core resilience, particularly within the default node, limbic, and frontoparietal control networks. Importantly, we found that age-related differences in episodic memory were positively related to core resilience, which indicates a potential role for core resilience in protection against cognitive decline. Together, these findings suggest that robust core connectivity and resilience of brain networks could facilitate high cognitive performance in aging.

Monolingual and bilingual language networks in healthy subjects using functional MRI and graph theory

Bilingualism requires control of multiple language systems, and may lead to architectural differences in language networks obtained from clinical fMRI tasks. Emerging connectivity metrics such as k-core may capture these differences, highlighting crucial network components based on resiliency. We investigated the influence of bilingualism on clinical fMRI language tasks and characterized bilingual networks using connectivity metrics to provide a patient care benchmark. Sixteen right-handed subjects (mean age 42-years; nine males) without neurological history were included: eight native English-speaking monolinguals and eight native Spanish-speaking (L1) bilinguals with acquired English (L2). All subjects underwent fMRI with gold-standard clinical language tasks. Starting from active clusters on fMRI, we inferred the persistent functional network across subjects and ran centrality measures to characterize differences. Our results demonstrated a persistent network "core" consisting of Broca's area, the pre-supplementary motor area, and the premotor area. K-core analysis showed that Wernicke's area was engaged by the "core" with weaker connection in L2 than L1.

Network analysis of population flow among major cities and its influence on COVID-19 transmission in China

Large-scale and diffuse population flow amplifies the localized COVID-19 outbreak into a widespread pandemic. Network analysis provides a new methodology to uncover the topology and evolution of the population flow and understand its influence on the early dynamics of COVID-19 transmission. In this paper, we simulated 42 transmission scenarios to show the distribution of the COVID-19 outbreak across China. We predicted some original (Guangzhou, Shanghai, Shenzhen) had higher total aggregate population outflows than Wuhan, indicating larger spread scopes and faster growth rates of COVID-19 outbreak. We built an importation risk model to identify some major cities (Dongguan and Foshan) with the highest total importation risk values and the highest standard deviations, indicating the core transmission chains (Dongguan-Shenzhen, Foshan-Guangzhou). We built the population flow networks to analyze their Spatio-temporal characteristics and identify the influential sub-groups and spreaders. By removing different influential spreaders, we identified Guangzhou can most influence the network's topological characteristics, and some major cities' degree centrality was significantly decreased. Our findings quantified the effectiveness of travel restrictions on delaying the epidemic growth and limiting the spread scope of COVID-19 in China, which helped better derive the geographical COVID-19 transmission related to population flow networks' structural features.