Many real-world complex networks arise as a result of a competition between growth and rewiring processes. Usually the initial part of the evolution is dominated by growth while the later one rather by rewiring. The initial growth allows the network to reach a certain size while rewiring to optimize its function and topology. As a model example we consider tree networks which first grow in a stochastic process of node attachment and then age in a stochastic process of local topology changes. The ageing is implemented as a Markov process that preserves the node-degree distribution. We quantify differences between the initial and aged network topologies and study the dynamics of the evolution. We implement two versions of the ageing dynamics. One is based on reshuffling of leaves and the other on reshuffling of branches. The latter one generates much faster ageing due to nonlocal nature of changes.
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http://dx.doi.org/10.1103/PhysRevE.102.042302 | DOI Listing |
BMC Plant Biol
January 2025
Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77845, USA.
Background: Virus infection and herbivory can alter the expression of stress-responsive genes in plants. This study employed high-throughput transcriptomic and alternative splicing analysis to understand the separate and combined impacts on host gene expression in Arabidopsis thaliana by Myzus persicae (green peach aphid), and turnip mosaic virus (TuMV).
Results: By investigating changes in transcript abundance, the data shows that aphids feeding on virus infected plants intensify the number of differentially expressed stress responsive genes compared to challenge by individual stressors.
Sci Rep
January 2025
Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
We develop an algorithm that finds the consensus among many different clustering solutions of a graph. We formulate the problem as a median set partitioning problem and propose a greedy optimization technique. Unlike other approaches that find median set partitions, our algorithm takes graph structure into account and finds a comparable quality solution much faster than the other approaches.
View Article and Find Full Text PDFNat Commun
January 2025
School of Computer Science, Sichuan University, Chengdu, Sichuan, China.
To overcome the computational barriers of analyzing large-scale single-cell sequencing data, we introduce MetaQ, a metacell algorithm that scales to arbitrarily large datasets with linear runtime and constant memory usage. Inspired by cellular development, MetaQ conceptualizes each metacell as a collective ancestor of biologically similar cells. By quantizing cells into a discrete codebook, where each entry represents a metacell capable of reconstructing the original cells it quantizes, MetaQ identifies homogeneous cell subsets for efficient and accurate metacell inference.
View Article and Find Full Text PDFNat Commun
January 2025
PSI Center for Life Sciences, Villigen PSI, Switzerland.
Microtubule plus-end tracking proteins (+TIPs) participate in nearly all microtubule-based cellular processes and have recently been proposed to function as liquid condensates. However, their formation and internal organization remain poorly understood. Here, we have study the phase separation of Bik1, a CLIP-170 family member and key +TIP involved in budding yeast cell division.
View Article and Find Full Text PDFDiscov Oncol
January 2025
Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University Shanghai, Caolang Highway 2901#, Jinshan District, Shanghai, People's Republic of China.
Background: Lung adenocarcinoma (LUAD) is a leading form of non-small cell lung cancer characterized by a complex tumor microenvironment (TME) that influences disease progression and therapeutic response. Tumor-associated macrophages (TAMs) within the TME promote tumorigenesis and evasion of immune surveillance, though their heterogeneity poses challenges in understanding their roles and therapeutic targeting. Additionally, traditional Chinese medicine (TCM) offers potential anti-cancer agents that could modulate the immune landscape.
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