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Premise: Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here.
Methods: Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae.
Results: Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches.
Discussion: The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814182 | PMC |
http://dx.doi.org/10.1002/aps3.11295 | DOI Listing |
Sci Rep
December 2024
Department of Mechatronics, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
Haze can significantly reduce visibility and contrast of images captured outdoors, necessitating the enhancement of images. This degradation in image quality can adversely affect various applications, including autonomous driving, object detection, and surveillance, where poor visibility may lead to navigation errors and obscure crucial details. Existing dehazing techniques face several challenges: spatial methods tend to be computationally heavy, transform methods often fall short in quality, hybrid methods can be intricate and demanding, and deep learning methods require extensive datasets and computational power.
View Article and Find Full Text PDFPLoS Negl Trop Dis
December 2024
CBGP, IRD, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France.
Schistosomiasis is a neglected tropical disease of public health significance. In view of its elimination as a public health problem by 2030, adopting a One Health approach is necessary, considering its multidimensional nature. Animal reservoirs, in particular, pose a significant threat to schistosomiasis control in Africa and beyond.
View Article and Find Full Text PDFJ Chem Theory Comput
December 2024
Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K.
Classical reaction barriers in density-functional theory are considered from the perspective of the density-fixed adiabatic connection. A 'reaction adiabatic-connection integrand', , is introduced, where λ is the electron-electron interaction strength, for which equals the barrier, meaning the barrier can be easily visualized as the area under a plot of vs λ. For five chemical reactions, plots of reference , calculated from Lieb maximizations at the coupled-cluster level of theory, are compared with approximate , calculated from common exchange-correlation functionals using coordinate scaling, for coupled-cluster densities.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA.
Field-theoretic simulations are numerical methods for polymer field theory, which include fluctuation corrections beyond the mean-field level, successfully capturing various mesoscopic phenomena. Most field-theoretic simulations of polymeric fluids use the auxiliary field (AF) theory framework, which employs Hubbard-Stratonovich transformations for the particle-to-field conversion. Nonetheless, the Hubbard-Stratonovich transformation imposes significant limitations on the functional form of the non-bonded potentials.
View Article and Find Full Text PDFACS Meas Sci Au
December 2024
Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States.
This article presents a colorimetric visual biosensor designed for direct application in undiluted biofluids, which holds significant promise for point-of-need applications. Unlike traditional biosensors that struggle with heavily diluted sample matrices, the presented biosensor does not require any instrumentation or trained personnel, making it highly practical. The sensor features an oligonucleotide probe covalently attached to magnetically separable magnetite (FeO) particles.
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