Engineering topics

Suzuki, Nobuhiro

Publications and source records attributed to Suzuki, Nobuhiro.

3 records

DOE OSTI2025

Virus species names have been standardized; virus names remain unchanged

Virus taxonomy, comprising classification and nomenclature, is regulated by the International Committee on Taxonomy of Viruses (ICTV). Taxon names are standardized to facilitate recognition and communication, with defined suffixes for each rank (e.g., the names of orders, families, and genera end in -virales, -viridae, and -virus, respectively). However, until recently, a standard format for species names was lacking. In 2021, following extensive discussion and community consultation, the ICTV decided to adopt a standardized binomial (Linnaean) format for virus species names, consisting of the genus name followed by a "freeform" species epithet. Previously assigned virus species names that were non-compliant with the binomial format have been fully updated. In contrast to taxon names regulated by the ICTV, the names of viruses, or "common" names, such as yellow fever virus or human immunodeficiency virus, are not under the remit of the ICTV and have not been changed.

Zerbini, F Murilo↗

DOE OSTI2023

Four principles to establish a universal virus taxonomy

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Surface waves affect frontogenesis

Here, this paper provides a detailed analysis of momentum, angular momentum, vorticity, and energy budgets of a submesoscale front undergoing frontogenesis driven by an upper–ocean, submesoscale eddy field in a Large Eddy Simulation (LES). The LES solves the wave–averaged, or Craik–Leibovich, equations in order to account for the Stokes forces that result from interactions between nonbreaking surface waves and currents, and resolves both submesoscale eddies and boundary layer turbulence down to 4.9 m × 4.9 m × 1.25 m grid scales. It is found that submesoscale frontogenesis differs from traditional frontogenesis theory due to four effects: Stokes forces, momentum and kinetic energy transfer from submesoscale eddies to frontal secondary circulations, resolved turbulent stresses, and unbalanced torque. In the energy, momentum, angular momentum, and vorticity budgets for the frontal overturning circulation, the Stokes shear force is a leading–order contributor, typically either the second or third largest source of frontal overturning. These effects violate hydrostatic and thermal wind balances during submesoscale frontogenesis. The effect of the Stokes shear force becomes stronger with increasing alignment of the front and Stokes shear and with a nondimensional scaling. The Stokes shear force and momentum transfer from submesoscale eddies significantly energize the frontal secondary circulation along with the buoyancy.

58 GEOSCIENCES↗