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Thomas, Chris

Publications and source records attributed to Thomas, Chris.

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

59 BASIC BIOLOGICAL SCIENCES↗

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

59 BASIC BIOLOGICAL SCIENCES↗

Engineered Multifunctional Surfaces for Fluid Handling

Designs incorporating variations in capillary geometry and hydrophilic and/or antibacterial surface properties have been developed that are capable of passive gas/liquid separation and passive water flow. These designs can incorporate capillary grooves and/or surfaces arranged to create linear and circumferential capillary geometry at the micro and macro scale, radial fin configurations, micro holes and patterns, and combinations of the above. The antibacterial property of this design inhibits the growth of bacteria or the development of biofilm. The hydrophilic property reduces the water contact angle with a treated substrate such that water spreads into a thin layer atop the treated surface. These antibacterial and hydrophilic properties applied to a thermally conductive surface, combined with capillary geometry, create a novel heat exchanger capable of condensing water from a humid, two-phase water and gas flow onto the treated heat exchanger surfaces, and passively separating the condensed water from the gas flow in a reduced gravity application. The overall process to generate the antibacterial and hydrophilic properties includes multiple steps to generate the two different surface properties, and can be divided into two major steps. Step 1 uses a magnetron-based sputtering technique to implant the silver atoms into the base material. A layer of silver is built up on top of the base material. Completion of this step provides the antibacterial property. Step 2 uses a cold-plasma technique to generate the hydrophilic surface property on top of the silver layer generated in Step 1. Completion of this step provides the hydrophilic property in addition to the antibacterial property. Thermally conductive materials are fabricated and then treated to create the antibacterial and hydrophilic surface properties. The individual parts are assembled to create a condensing heat exchanger with antibacterial and hydrophilic surface properties and capillary geometry, which is capable of passive phase separation in a reduced gravity application. The plasma processes for creating antibacterial and hydrophilic surface properties are suitable for applications where water is present on an exposed surface for an extended time, such that bacteria or biofilms could form, and where there is a need to manage the water on the surface. The processes are also suitable for applications where only the hydrophilic property is needed. In particular, the processes are applicable to condensing heat exchangers (CHXs), which benefit from the antibacterial properties as well as the hydrophilic properties. Water condensing onto the control surfaces of the CHX will provide the moist conditions necessary for the growth of bacteria and the formation of biofilms. The antibacterial properties of the base layer (silver) will mitigate and prevent the growth of bacteria and formation of biofilms that would otherwise reduce the CHX performance. In addition, the hydrophilic properties reduce the water contact angle and prevent water droplets from bridging between control surfaces. Overall, the hydrophilic properties reduce the pressure drop across the CHX.

Thomas, Chris↗