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As the number and variety of assembled genomes continues to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA-based mapping tools help to address this challenge, but they are only able to transfer annotation between closely-related species. Here we introduce LiftOn, a homology-based software tool that integrates DNA and protein alignments to enhance the accuracy of genome-scale annotation and to allow mapping between relatively distant species.
View Article and Find Full Text PDFMetagenomics, particularly genome-resolved metagenomics, has significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies due to the lack of comprehensive reference genome databases and robust bioinformatics tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass although a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology.
View Article and Find Full Text PDFSource-tracing of industrial and municipal wastewater effluent in river water via fluorescence fingerprinting.
Sci Total Environ
December 2024
Institute for Water Quality and Resource Management, TU Wien, Karlsplatz 13/226, 1040 Vienna, Austria.
Fluorescence fingerprinting is a technique to uniquely characterize water samples based on their distinct composition of dissolved organic matter (DOM) measured via 3D fluorescence spectroscopy. It is an effective tool for monitoring the chemical composition of various water systems. This study examines a river affected by several municipal and industrial wastewater treatment plant (WWTP) effluents and aims to source-tracing them via fluorescence fingerprints based on parallel factor analysis (PARAFAC) components.
View Article and Find Full Text PDFUse of an electronic health record training environment with a longitudinal patient case as a teaching tool in an APPE-readiness course.
Curr Pharm Teach Learn
December 2024
Department of Pharmacy Practice, Temple University School of Pharmacy, United States of America. Electronic address:
Background: The integration of Electronic Health Records (EHRs) in healthcare has changed how healthcare is performed, necessitating a comprehensive understanding of these systems among pharmacists. The ability to navigate EHRs is crucial for pharmacy students' success in introductory and advanced pharmacy practice experiences (IPPEs and APPEs). This manuscript describes the development and use of an EHR training environment in an APPE-readiness course.
View Article and Find Full Text PDFA simplified multidimensional scale approach is effective in predicting mortality in hospitalized older adults and highlights the role of nutrition.
Clin Nutr
December 2024
Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy; Geriatric Clinic, Maggiore University Hospital, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), Trieste, Italy; School of Dietetics, University of Trieste - Pordenone branch, Pordenone, Italy.
Background & Aims: Malnutrition and cognitive impairment are among the major contributors to frailty, that significantly increases the risk of mortality of older hospitalized patients. Multidimensional frailty assessment tools, such as the multidimensional prognostic index-MPI, a tool based on a standard comprehensive geriatric assessment (CGA), have proven valuable for predicting adverse outcomes, including mortality of older adults following acute illness but its application in everyday clinical practice is limited. We hypothesized that removing parameters not closely associated with mortality and sorting the patient population according to the presence or not of cognitive impairment with possible integration of common laboratory markers, could provide a simplified approach that could improve practicability in all settings with at least comparable 1-year mortality predictive value.
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