Virus Variation Resource - improved response to emergent viral outbreaks.

The Virus Variation Resource is a value-added viral sequence data resource hosted by the National Center for Biotechnology Information. The resource is located at http://www.ncbi.nlm.nih.gov/genome/viruses/variation/ and includes modules for seven viral groups: influenza virus, Dengue virus, West Nile virus, Ebolavirus, MERS coronavirus, Rotavirus A and Zika virus Each module is supported by pipelines that scan newly released GenBank records, annotate genes and proteins and parse sample descriptors and then map them to controlled vocabulary. These processes in turn support a purpose-built search interface where users can select sequences based on standardized gene, protein and metadata terms. Once sequences are selected, a suite of tools for downloading data, multi-sequence alignment and tree building supports a variety of user directed activities. This manuscript describes a series of features and functionalities recently added to the Virus Variation Resource.

Channeling of particles and associated anomalous transport in a two-dimensional complex plasma crystal.

Implications of the recently discovered effect of channeling of upstream extra particles for transport phenomena in a two-dimensional plasma crystal are discussed. Upstream particles levitated above the lattice layer and tended to move between the rows of lattice particles. An example of heat transport is considered, where upstream particles act as moving heat sources, which may lead to anomalous heat transport. The average channeling length observed was 15-20 interparticle distances. Other features of the channeling process are also reported.

Collective effects in vortex movements in complex plasmas.

We study the onset and characteristics of vortices in complex (dusty) plasmas using two-dimensional simulations in a setup modeled after the PK-3 Plus laboratory. A small number of microparticles initially self-arranges in a monolayer around the void. As additional particles are introduced, an extended system of vortices develops due to a nonzero curl of the plasma forces. We demonstrate a shear-thinning effect in the vortices. Velocity structure functions and the energy and enstrophy spectra show that vortex flow turbulence is present that is in essence of the "classical" Kolmogorov type.

Virus Variation Resource--recent updates and future directions.

Virus Variation (http://www.ncbi.nlm.nih.gov/genomes/VirusVariation/) is a comprehensive, web-based resource designed to support the retrieval and display of large virus sequence datasets. The resource includes a value added database, a specialized search interface and a suite of sequence data displays. Virus-specific sequence annotation and database loading pipelines produce consistent protein and gene annotation and capture sequence descriptors from sequence records then map these metadata to a controlled vocabulary. The database supports a metadata driven, web-based search interface where sequences can be selected using a variety of biological and clinical criteria. Retrieved sequences can then be downloaded in a variety of formats or analyzed using a suite of tools and displays. Over the past 2 years, the pre-existing influenza and Dengue virus resources have been combined into a single construct and West Nile virus added to the resultant resource. A number of improvements were incorporated into the sequence annotation and database loading pipelines, and the virus-specific search interfaces were updated to support more advanced functions. Several new features have also been added to the sequence download options, and a new multiple sequence alignment viewer has been incorporated into the resource tool set. Together these enhancements should support enhanced usability and the inclusion of new viruses in the future.

Pore design and engineering for filters and membranes.

In filtration, the concept of pore size is not easy to define. In microfiltration, there are numerous advantages in employing a surface filtering membrane, rather than one relying on depth filtration mechanisms from a tortuous pore flow channel. Modern manufacturing techniques provide means to produce surface filtering membranes. For filtration, it is shown that a suitable pore design is an array of long thin slots. An analysis of fluid flow through the slots suggests that a short slot is adequate, but experimental data with suspended material indicates that slot length is important. Using long slots and careful control of the flow through the membrane it is possible to filter deforming particles such as oil drops from water.