Dynamic Grid Adaptation Using the MPDATA Scheme

A dynamic grid adaptation (DGA) scheme is developed using various combinations of the multidimensional positive definite advection transport algorithm (MPDATA) to show the applicability of DGA with the MPDATA scheme to solve advection problems. A one-dimensional model is used to show the effects of varying the number of grid points and the parameters that control the grid redistribution scheme, to determine a stability criteria for the scheme and to investigate the effect of several MPDATA options. A two-dimensional model is used to show the applicability of the scheme in multiple dimensions and to illustrate the effects of DGA in combination with MPDATA options. Diffusion errors are reduced by more than 90% using DGA when compared to static, uniformly spaced grid computations. Phase errors are reduced using certain MPDATA options by more than 25%

From Sea to Sea: Canada's Three Oceans of Biodiversity

Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada's three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada's three oceans, this synthesis is intended to serve as a biodiversity baseline for a new program on marine biodiversity, the Canadian Healthy Ocean Network. A major effort needs to be undertaken to establish a complete baseline of Canadian marine biodiversity of all taxonomic groups, especially if we are to understand and conserve this part of Canada's natural heritage

A prenylated dsRNA sensor protects against severe COVID-19

Inherited genetic factors can influence the severity of COVID-19, but the molecular explanation underpinning a genetic association is often unclear. Intracellular antiviral defenses can inhibit the replication of viruses and reduce disease severity. To better understand the antiviral defenses relevant to COVID-19, we used interferon-stimulated gene (ISG) expression screening to reveal that OAS1, through RNase L, potently inhibits SARS-CoV-2. We show that a common splice-acceptor SNP (Rs10774671) governs whether people express prenylated OAS1 isoforms that are membrane-associated and sense specific regions of SARS-CoV-2 RNAs, or only express cytosolic, nonprenylated OAS1 that does not efficiently detect SARS-CoV-2. Importantly, in hospitalized patients, expression of prenylated OAS1 was associated with protection from severe COVID-19, suggesting this antiviral defense is a major component of a protective antiviral response

Large scale urban simulations with FCT

Airborne contaminant transport in cities presents challenging new requirements for CFD. The unsteady flow physics is complicated by very complex geometry, multi-phase particle and droplet effects, radiation, latent and sensible heating effects, and buoyancy effects. Turbulence is one of the most important of these phenomena and yet the overall problem is sufficiently difficult that the turbulence must be included efficiently with an absolute minimum of extra memory and computing time. This paper describes the Monotone Integrated Large Eddy Simulation (MILES) methodology used in NRL's FAST3D-CT simulation model for urban contaminant transport (CT) (see Boris in Comput. Sci. Eng. 4:22--32, 2002 and references therein). We also describe important extensions of the underlying Flux-Corrected Transport (FCT) convection algorithms to further reduce numerical dissipation in narrow channels (streets)