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A proposal on bird focal species selection for higher tier risk assessments of plant protection products in the EU.
Integr Environ Assess Manag
January 2025
tier3 solutions GmbH, Leverkusen, Germany.
The revised EFSA 2023 Guidance on the risk assessment of plant protection products for birds and mammals emphasises vulnerability as a relevant criterion for focal species (FS) selection rather than prevalence. The EFSA 2023 Guidance suggests to rank FS candidates for each dietary group according to their expected exposure by estimating a species-specific daily dietary dose (DDD). Species experiencing higher exposure would be ranked as potentially more vulnerable and can be identified as FS candidates.
View Article and Find Full Text PDFmultistrap: boosting phylogenetic analyses with structural information.
Nat Commun
January 2025
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.
In a phylogeny, trustworthy reliability branch support estimates are as important as the tree itself. We show that reliability support values based on bootstrapping can be improved by combining sequence and structural information from proteins. Our approach relies on the systematic comparison of homologous intra-molecular structural distances.
View Article and Find Full Text PDFExplainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics.
Brief Bioinform
November 2024
GENYO, Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada, Avenida de la Ilustración 114, Granada 18016, Spain.
Recent advances in single-cell RNA-Sequencing (scRNA-Seq) technologies have revolutionized our ability to gather molecular insights into different phenotypes at the level of individual cells. The analysis of the resulting data poses significant challenges, and proper statistical methods are required to analyze and extract information from scRNA-Seq datasets. Sample classification based on gene expression data has proven effective and valuable for precision medicine applications.
View Article and Find Full Text PDFFlexible framework of computing binding free energy using the energy representation theory of solution.
J Chem Phys
January 2025
Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
Host-guest binding plays a crucial role in the functionality of various systems, and its efficiency is often quantified using the binding free energy, which represents the free-energy difference between the bound and dissociated states. Here, we propose a methodology to compute the binding free energy based on the energy representation (ER) theory of solution, which enables us to evaluate the free-energy difference between the systems of interest with the molecular dynamics (MD) simulations. Unlike the other free-energy methods, such as the Bennett acceptance ratio (BAR), the ER theory does not require the MD simulations for hypothetical intermediate states connecting the systems of interest, leading to reduced computational costs.
View Article and Find Full Text PDFUnveiling immunity gaps and determining a suitable age for a third dose of the measles-containing vaccine: a strategic approach to accelerating measles elimination.
Lancet Reg Health Southeast Asia
January 2025
Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
Background: In highly measles immunized countries, immunity gaps in adolescents and young adults are a key issue posing an obstacle to measles elimination. This study aims to identify the gaps by estimating the age-stratified probability of seropositivity, and to ascertain a suitable age for the administration of a third dose of a measles-containing vaccine (MCV3) to effectively fill these gaps.
Methods: We retrospectively obtained measles serological results from hospital setting among among individuals aged 13-39 years and developed a serocatalytic dynamic probability model, stratifying seropositivity due to vaccination or natural infection.
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