Given a general physical network and measurements of node dynamics, methods are proposed for reconstructing the network topology. We focus on networks whose connections are sparse and where data are limited. Under these conditions, common in many biological networks, constrained optimization techniques based on the L1 vector norm are found to be superior for inference of the network connections.
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http://dx.doi.org/10.1103/PhysRevE.77.026103 | DOI Listing |
In this study, we performed a comparative analysis based on a total of 255 spider mitogenomes and four outgroups, of which the mitogenomes of 39 species were assembled de novo, to explore the phylogenetic relationships and the adaptive evolution of mitogenomes. Results showed that had the longest mitochondrial length and the most pronounced codon preference to be UUA, followed by CCU. Codon usage frequencies were similar between families and codon usage in the mitogenome of spiders was mainly influenced by natural selection pressures rather than G/C mutation bias.
View Article and Find Full Text PDFMol Phylogenet Evol
January 2025
Laboratory of Diagnosis and Integrated Management of Plant Bio-Aggressors. University of Parakou, BP123 Parakou, Borgou, Benin.
Multigene, genus-wide phylogenetic studies have uncovered the limited taxonomic resolution power of commonly used gene markers, particularly of rRNA genes, to discriminate closely related species of the nematode genus Heterorhabditis. In addition, conflicting tree topologies are often obtained using the different gene markers, which limits our understanding of the phylo- and co-phylogenetic relationships and biogeography of the entomopathogenic nematode genus Heterorhabditis. Here we carried out phylogenomic reconstructions using whole nuclear and mitochondrial genomes, and whole ribosomal operon sequences, as well as multiple phylogenetic reconstructions using various single nuclear and mitochondrial genes.
View Article and Find Full Text PDFBiol Imaging
November 2024
Biological Image Analysis Unit, Institut Pasteur, Université Paris Cité, Paris, France.
We develop a novel method for image segmentation of 3D confocal microscopy images of emerging hematopoietic stem cells. The method is based on the theory of persistent homology and uses an optimal threshold to select the most persistent cycles in the persistence diagram. This enables the segmentation of the image's most contrasted and representative shapes.
View Article and Find Full Text PDFInsects
November 2024
College of Plant Protection, Hebei Agricultural University, Baoding 071001, China.
Ithonidae (moth lacewings) are an enigmatic, small family of the insect order Neuroptera (lacewings). Its phylogenetic position within Neuroptera and internal subfamily relationships remain unresolved. In this study, the complete mitochondrial genome (mitogenome) of Tillyard, 1916 representing the first mitogenome of Ithoninae, as well as the complete mitogenome of Liu, Li and Yang, 2018, were newly reported.
View Article and Find Full Text PDFBioengineering (Basel)
December 2024
Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford OX3 7DQ, UK.
Cardiovascular diseases (CVDs) are the most common health threats worldwide. 2D X-ray invasive coronary angiography (ICA) remains the most widely adopted imaging modality for CVD assessment during real-time cardiac interventions. However, it is often difficult for the cardiologists to interpret the 3D geometry of coronary vessels based on 2D planes.
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