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Estimating the economic consequences of leveraging the novel cobas® HIV-1/HIV-2 Qualitative NAT Test in routine HIV testing.
Clin Infect Dis
January 2025
IQVIA Inc., Falls Church, VA.
Article Synopsis
- The study compared the costs of the current CDC 3-step HIV testing algorithm with a new single-test alternative (cobas) for efficiency in diagnosing HIV.
- A decision-tree model estimated costs and testing needs for 1 million people, revealing significant reductions in total tests and retests required when using the alternative method.
- Findings indicate that the new algorithm could simplify HIV testing processes, cut overall testing numbers, and keep healthcare costs stable, thereby improving patient outcomes.
SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.
Brief Bioinform
November 2024
Department of Biology, University of Padova, Via U.Bassi 58/ B, 35131, Italy.
Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy number alterations (CNAs). However, there remains a gap for a standardized workflow specifically designed for sWGS analysis. To address this need, in this work we present SAMURAI, a bioinformatics pipeline specifically designed for analyzing CNAs from sWGS data in a standardized and reproducible manner.
View Article and Find Full Text PDFA multi-scale cognitive interaction model of instrument operations at the Linac Coherent Light Source.
Rev Sci Instrum
January 2025
Bennu Climate, Inc. and Symbolic Systems Program, Stanford University, Stanford, California 94305, USA.
The Linac Coherent Light Source (LCLS) is the world's first x-ray free electron laser. It is a scientific user facility operated by the SLAC National Accelerator Laboratory, at Stanford, for the U.S.
View Article and Find Full Text PDFExploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.
mSystems
January 2025
Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%.
View Article and Find Full Text PDFTime-varying reproduction number estimation: fusing compartmental models with generalized additive models.
J R Soc Interface
January 2025
Department of Mathematics, The University of Manchester, Manchester, UK.
The reproduction number, the mean number of secondary cases infected by each primary case, gives an indication of the effort required to control the disease. Beyond the well-known reproduction number, there are two natural extensions, namely the and reproduction numbers. As behaviour, population immunity and viral characteristics can change with time, these reproduction numbers can vary over time.
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