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Biology subjects

Kane, B.

Publications and source records attributed to Kane, B..

2 recordsLinked to original sources

Weak evidence for change in wind-induced bending moments on raised and thinned Colorado spruce (Picea pungens)

Trees are routinely pruned to mitigate the risk of wind damage, but there are few studies examining changes in wind loads after pruning, especially for large conifers. In this study, ten Colorado spruces (Picea pungens) were monitored before and after a series of pruning treatments. Trees were pruned to raise or thin crowns over a range of severities between 0% and 40%. Wind-induced bending moments were measured using two calibrated displacement probes installed orthogonally on the lower stem of each tree. Using a hierarchical Bayesian model, the relationship between maximum wind speeds and bending moments was quantified, consistent with theoretical and empirical expectations, as a non-linear power law. Random intercepts for model coefficients were used to account for individual variability in aerodynamic behavior among experimental trees, and predictions were made using the median response marginalized over the observed trees. The modeled relationship between wind speeds and bending moments was physically reasonable and like existing measurements with scaling exponents below two. Despite considerable variation among experimental trees, the aerodynamic behavior of trees, as indicated by model coefficients, was not clearly altered by pruning treatments, and, correspondingly, model predictions of bending moments over the range of observed wind speeds remained similar for all pruning treatments. Ultimately, the study yielded weak evidence for a change in bending moments following conventional pruning treatments for Colorado spruce, and the practical value of pruning to mitigate risk appeared limited for the studied conditions. Highlights- Wind loads were monitored on large Colorado spruce after crown raising and thinning - A hierarchical Bayesian model quantified wind speed and bending moment power laws - Negligible change in bending moments was found for all pruning types and severities - Conventional pruning methods may not mitigate risk for Colorado spruce

biophysics↗

VarStack: a Web Tool for Data Retrieval to Interpret Somatic Variants in Cancer

Background and objectiveAdvances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data in cancer from existing databases. MethodsVarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user-interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer (COSMIC), gnomAD, cBioPortal, ClinVar, OncoKB and UCSC Genome browser. It retrieves the data from these databases and returns back to the user in a fraction of the time it would take to manually navigate each site independently. ResultsUsers submit a variant with gene symbol, peptide change, and coding sequence change. They may select a variety of tumor specific studies in cBioportal to search through in addition to their original query. The results from the databases are presented in tabs. Users can export the results as a CSV file. VarStack also has the batch search feature in which user submits a list of variants and download a CSV file with the data from the databases. With the batch search and data download options users can easily incorporate VarStack into their workflow or tools. VarStack saves time by providing variant data to the user from multiple databases in an easy-to-export and interpretable format. AvailabilityVarStack is freely available under https://varstack.brown.edu.

bioinformatics↗