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Biology subjects

Aldridge, C.

Publications and source records attributed to Aldridge, C..

2 recordsLinked to original sources

Estimating greater sage-grouse population sizes within the state of Oregon, USA 2017-2024

We fit an N-mixture model to lek (breeding area) count data to estimate annual population sizes of greater sage-grouse (Centrocercus urophasianus; sage-grouse) within the state of Oregon, USA between 2017-2024. Population estimates were delineated among 24 Priority Areas for Conservation (PACs) and considered additional sources of information including male-to-female sex ratios, lek attendance rates, numbers of unmodeled leks, and the existence of unsampled/unknown leks. In 2024, the state of Oregon was estimated to contain approximately 41,875 sage-grouse (95% credible interval [CRI] = 38,980-54,634), which was down from a high of 50,869 (95% CRI = 41,794-66,238) in 2017. A nadir (low point) was identified during 2019, when the median statewide population estimate was 30,644 birds. A complete population oscillation was not evident during the inferential period based on local maxima that were observed during the start (2017) and stop (2024) years of analysis. In addition to estimating population sizes, we evaluated N-mixture model estimates for precision and accuracy after randomly removing single and repeat counts in 10% increments (relative to total sample size). We estimated an increase in absolute bias of approximately 1.6% for every 10% reduction in effort.

ecology↗

Standardized Nomenclature and Reporting for PacBio HiFi Sequencing and Analysis of rAAV Gene Therapy Vectors

Despite recombinant adeno-associated viruses (rAAVs) being the leading platform for gene therapy, there is a lack of standardized computational analysis methods and reporting to assess the contents of each capsid through long-read sequencing. PacBios highly accurate long-read HiFi sequencing enables comprehensive characterization of AAV genomes but requires bioinformatics expertise for analyzing, interpreting and comparing the results. To address this need and improve the understanding of functional viral payloads, our working group established standardized nomenclature and reporting for long-read sequencing data of rAAV vectors. The working group recommendations cover critical quality attributes (CQAs) related to vector purity (full-length vs. fragmented genomes) and identification of contaminants (host DNA, plasmid DNA). Our data analyses of de novo manufacturing runs by the recommended protocol revealed specificity of full and partially filled capsids and high-resolution characterization of partial/truncated vector species. Finally, we provide an open-source software implementing this standardized AAV analysis and reporting to promote transparency, facilitate data comparability, and improve rAAV vector design and quality control.

bioinformatics↗