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nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares.
Bioinformatics
January 2025
Department of Pathology and Department of Immunobiology, Yale School of Medicine.
Summary: With the increased reliance on multi-omics data for bulk and single cell analyses, the availability of robust approaches to perform unsupervised learning for clustering, visualization, and feature selection is imperative. We introduce nipalsMCIA, an implementation of multiple co-inertia analysis (MCIA) for joint dimensionality reduction that solves the objective function using an extension to Non-linear Iterative Partial Least Squares (NIPALS). We applied nipalsMCIA to both bulk and single cell datasets and observed significant speed-up over other implementations for data with a large sample size and/or feature dimension.
View Article and Find Full Text PDFLow impact of Zostera marina meadows on sediment and water microbiota under brackish conditions.
Environ Microbiome
January 2025
Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), 18119, Rostock, Germany.
Background: Zostera marina is an important ecosystem engineer influencing shallow water environments and possibly shaping the microbiota in surrounding sediments and water. Z. marina is typically found in marine systems, but it can also proliferate under brackish conditions.
View Article and Find Full Text PDFEthnobotany of vascular plants use, conservation and management practice in the homegardens by the people of Dawuro in Southwestern Ethiopia.
J Ethnobiol Ethnomed
January 2025
Department of Biology, College of Natural and Computational Science, Arba Minch University, Arba Minch, Ethiopia.
Background: Homegardens (HGs) are well-time-honored traditional land use systems in small plots of land with purposely designed intricate structure and a mixture of planted vascular plants (VPs) for different purposes. Hence, the present study was initiated to investigate the ethnobotanical information of vascular plants of homegardens and their use, conservation and management practice by the people of Dawuro in southwestern Ethiopia.
Methods: A total of 162 farmer informants were selected and interviewed within a distance of < 2 km, 2-4 km and > 4 km between the natural forest and homegardens, and 0.
A multilevel social network approach to studying multiple disease-prevention behaviors.
Sci Rep
January 2025
Indian Institute of Public Health Shillong, Shillong, Meghalaya, India.
The effective prevention of many infectious and non-infectious diseases relies on people concurrently adopting multiple prevention behaviors. Individual characteristics, opinion leaders, and social networks have been found to explain why people take up specific prevention behaviors. However, it remains challenging to understand how these factors shape multiple interdependent behaviors.
View Article and Find Full Text PDFCRISPR-Hybrid: A CRISPR-Mediated Intracellular Directed Evolution Platform for RNA Aptamers.
Nat Commun
January 2025
Department of Chemistry, Boston College, Chestnut Hill, MA, USA.
Recent advances in gene editing and precise regulation of gene expression based on CRISPR technologies have provided powerful tools for the understanding and manipulation of gene functions. Fusing RNA aptamers to the sgRNA of CRISPR can recruit cognate RNA-binding protein (RBP) effectors to target genomic sites, and the expression of sgRNA containing different RNA aptamers permit simultaneous multiplexed and multifunctional gene regulations. Here, we report an intracellular directed evolution platform for RNA aptamers against intracellularly expressed RBPs.
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