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At least 325 records · Page 18

Speeding genomic island discovery through systematic design of reference database composition

Background Genomic islands (GIs) are mobile genetic elements that integrate site-specifically into bacterial chromosomes, bearing genes that affect phenotypes such as pathogenicity and metabolism. GIs typically occur sporadically among related bacterial strains, enabling comparative genomic approaches to GI identification. For a candidate GI in a query genome, the number of reference genomes with a precise deletion of the GI serves as a support value for the GI. Our comparative software for GI identification was slowed by our original use of large reference genome databases (DBs). Here we explore smaller species-focused DBs. Results With increasing DB size, recovery of our reliable prophage GI calls reached a plateau, while recovery of less reliable GI calls (FPs) increased rapidly as DB sizes exceeded ~500 genomes; i.e., overlarge DBs can increase FP rates. Paradoxically, relative to prophages, FPs were both more frequently supported only by genomes outside the species and more frequently supported only by genomes inside the species; this may be due to their generally lower support values. Setting a DB size limit for our SMA ll R anked T ailored (SMART) DB design speeded runtime ~65-fold. Strictly intra-species DBs would tend to lower yields of prophages for small species (with few genomes available); simulations with large species showed that this could be partially overcome by reaching outside the species to closely related taxa, without an FP burden. Employing such taxonomic outreach in DB design generated redundancy in the DB set; as few as 2984 DBs were needed to cover all 47894 prokaryotic species. Conclusions Runtime decreased dramatically with SMART DB design, with only minor losses of prophages. We also describe potential utility in other comparative genomics projects.

59 BASIC BIOLOGICAL SCIENCES↗

Model simulations of Plum Island Ecosystems LTER low marsh site using ELM-PFLOTRAN

Model simulations using the E3SM Land Model (ELM) coupled to the PFLOTRAN reactive transport model via the Alquimia interface. The simulations were conducted for a tidal salt marsh at the Plum Island Ecosystems LTER near Rowley, Massachusetts, USA. Model simulations were forced using site-specific tidal cycles and salinity, and the simulations used a biogeochemical reaction network including aerobic decomposition, sulfate reduction, iron reduction, and methanogenesis. Model outputs include simulated carbon stocks, carbon dioxide and methane fluxes, and porewater concentrations of key solutes related to sulfur, iron, and carbon cycling. The model simulations included a saline simulation (with tidal sulfate inputs), a fresh simulation (with low salinity and low sulfate inputs), and a saline simulation with lower vegetation productivity to represent the effect of salinity on vegetation. These simulations were conducted to demonstrate that a new model framework incorporating subsurface redox and biogeochemical interactions into a land surface model could reproduce measured surface greenhouse gas fluxes and biogeochemical dynamics in tidal marsh ecosystems, and to test whether including redox interactions in a land surface model would allow the model to resolve contrasts in biogeochemical cycling and greenhouse gas production between saline and freshwater wetlands.The data package includes gzipped tar archives (which can be expanded using standard tar and gzip utilities) of model outputs from three model configurations: saline subsurface and reduced vegetation productivity related to salinity; saline subsurface with vegetation productivity not reduced; and freshwater. Also included are code for the modified E3SM model, Alquimia interface, and PFLOTRAN reactive transport simulator in gzipped tar format; plain text parameter and configuration files; python code files for visualizing model output and defining model configurations; and model output, tide and salinity forcing, and configuration files in netCDF format. See the README.md file in the data package for a detailed description of all files contained in the package. All files are in netCDF (.nc), gzipped tar archive (.tar.gz or .tgz), or text (all other files).Updated: May 13, 2024. Model output, E3SM code, PFLOTRAN input files, and python codes for visualizing results were updated to reflect changes made for the manuscript revision. The updated archive reflects the code and model output from the final accepted manuscript. Changes included updated reaction parameters reflecting improved parameterization and additional comparisons with field measurements. E3SM code changes included better support for multiple grid cells and improved flow and transport parameterization.

54 ENVIRONMENTAL SCIENCES↗

Aerial Data and Processed Models of Port Arthur Coastal Neighborhood and Pleasure Island Golf Course, June 2024

Our Co-design team is from the University of Texas, working on a Department of Energy-funded project focused on the Beaumont-Port Arthur area. As part of this project, we will be developing climate-resilient design solutions for areas of the region. More on www.caee.utexas.edu.We captured aerial photos in the Port Arthur Coastal Neighborhood Community and the Golf Course on Pleasure Island, Texas, in June 2024.Aerial photos taken were through DroneDeploy autonomous flight, and models were processed through the DroneDeploy engine as well. All aerial photos are in .JPG format and contained in zipped files for each area.The processed data package includes 3D models, geospatial data, mappings, and point clouds. Please be aware that DTM, Elevation toolbox, Point cloud, and Orthomosaic use EPSG: 6588. And 3D Model uses EPSG: 3857.For using these data:- The Adobe Suite gives you great software to open .Tif files.- You can use LASUtility (Windows), ESRI ArcGIS Pro (Windows), or Blaze3D (Windows, Linux) to open a LAS file and view the data it contains.- Open an .OBJ file with a large number of free and commercial applications. Some examples include Microsoft 3D Builder, Apple Preview, Blender, and Autodesk.- You may use ArcGIS, Merkaartor, Blender (with the Google Earth Importer plug-in), Global Mapper, and Marble to open .KML files.- The .tfw world file is a text file used to georeference the GeoTIFF raster images, like the orthomosaic and the DSM. You need suitable software like ArcView to open a .TFW file.This dataset provides researchers with sufficient geometric data and the status quo of the land surface at the locations mentioned above. This dataset could streamline researchers' decision-making processes and enhance the design as well.

2D mapping↗

Real-time kinematic (RTK) Drone-collected Data and Processed Models of Port Arthur Coastal Neighborhood and Pleasure Island Golf Course, June 2024

The Southeast Texas Urban Integrated field lab’s Co-design team captured aerial photos in the Port Arthur Coastal Neighborhood Community and the Golf Course on Pleasure Island, Texas, in June 2024. Aerial photos taken were through autonomous flight, and models were processed through the DroneDeploy engine. All aerial photos are in .JPG format and contained in zipped files for each area. The processed data package includes 3D models, geospatial data, mappings, and point clouds. Please be aware that DTM, Elevation toolbox, Point Cloud, and Orthomosaic use EPSG: 6588. And 3D Model uses EPSG: 3857.For using these data:- The Adobe Suite gives you great software to open .Tif files.- You can use LASUtility (Windows), ESRI ArcGIS Pro (Windows), or Blaze3D (Windows, Linux) to open a LAS file and view the data it contains.- Open an .OBJ file with a large number of free and commercial applications. Some examples include Microsoft 3D Builder, Apple Preview, Blender, and Autodesk.- You may use ArcGIS, Merkaartor, Blender (with the Google Earth Importer plug-in), Global Mapper, and Marble to open .KML files.- The .tfw world file is a text file used to georeference the GeoTIFF raster images, like the orthomosaic and the DSM. You need suitable software like ArcView to open a .TFW file.This dataset provides researchers with sufficient geometric data and the status quo of the land surface at the locations mentioned above. This dataset will support researchers' decision-making processes under uncertainties.

2D mapping↗

ELM model simulations of Plum Island Ecosystems LTER low marsh site 2018-2020

Model simulations using the Department of Energy's Energy Exascale Earth System Model (E3SM) land model (ELM) with improved capabilities to represent vegetation response to salinity and inundation. The simulations were conducted for a tidal salt marsh at Plum Island Ecosystems Long Term Ecological Research (LTER) site near Rowley, Massachusetts, USA; the site is a low marsh dominated by Spartina alterniflora. The model was forced with site-specific meteorology, salinity and tidal cycles from 2018-2020. Four sets of model simulations are included and described below:1. Parameterization of the salinity response function. These simulations tested different combinations of values for optimal salinity and salinity tolerance.2. Model evaluation. This comparison conducted simulations using the default model, the salinity function only, the submergence function only, and both the salinity and submergence functions. 3. Salinity scenarios. These simulations used the 2018 salinity input data varied by -5 to +10 ppt salinity.4. Water level scenarios. These simulations used the tide height varied by -10 to +50 cm. These simulations were used to demonstrate how the salinity and submergence functions better represent carbon uptake by tidal salt marshes.The data package includes netCDF files used as forcing files for tide height and salinity, one for each year 2018-2020 at observed salinity concentrations, and an additional three forcing files in which salinity concentrations were varied 5 ppt lower, 5 ppt higher, and 10 ppt higher than the measured 2018 time series. Also included are python scripts for creating forcing files, plain text parameter and command files for running simulations, model outputs in netCDF format, and python scripts for visualizing outputs. Code for the modified E3SM model is archived in Sulman et al 2023 at doi:10.15485/1991625. More detail about files is provided in the README.md file.

54 ENVIRONMENTAL SCIENCES↗

AmeriFlux US-NYk NYSM - Staten Island

This is the AmeriFlux version of the carbon flux data for the site US-NYk NYSM - Staten Island. Site Description - Located in an urban setting. It is on a rooftop. Obstructions within 100m include tall buildings. The soil type is N/A - Rooftop. This site is a part of the New York State Mesonet Flux Network, one of multiple subnetworks (e.g. Profiler, Snow) operated by the New York State Mesonet. It also operates as a NYC Profiler site and a Standard meteorological site.

Miller, Scott [University at Albany]↗

Crossing transition in the EIC HSR with a resonance island jump scheme

The Resonance Island Jump (RIJ) scheme for transition crossing in the Hadron Storage Ring of the Electron-Ion Collider is radically new, and untested. Beam experiments in RHIC will be necessary if it becomes necessary to consider the RIJ scheme as a serious alternative to upgrading the first order linear jump scheme currently implemented in RHIC. This paper outlines the theoretical foundations of the RIJ scheme, and considers how a beam experiment in RHIC could be performed.

Accelerator Physics↗

Microgrid Design Toolkit (MDT) Simple Use Case Example for Islanded Mode Optimization (Software v1.3)

This simple Microgrid Design Toolkit (MDT) use case will provide you an example of a basic microgrid design. It will introduce basic principles of using the MDT islanded mode optimization by modifying a baseline microgrid design and performing an analysis of the results. Please reference the MDT User Guide (SAND2020-4550) for detailed instructions on how to use the tool.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Fission to Fusion: An Island Goes Missing

Hollywood actor Reed Hadley walked the decks of the USS Estes with the practiced ease characteristic of his profession. Stopping periodically to relight his pipe, Hadley narrated an AEC film depicting the final hours and minutes leading up to the detonation of Mike, the world’s first thermonuclear bomb. Hadley’s smooth camera presence contrasted sharply with those of the scientists and technicians he interviewed, particularly Alvin Graves, who came across wooden and condescending. Just after Hadley put on his dark goggles to prevent flash blindness, Mike exploded with a force of 10.4 megatons, completely vaporizing the entire ground zero island of Elugelab. The film made one thing clear – Los Alamos scientists could build a thermonuclear bomb, but they could not act.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Techno-Economic Analysis of Product Diversification Options for Sustainability of the Monticello and Prairie Island Nuclear Power Plants

The objective of this work was to perform techno-economic analysis (TEA) of hybrid options that could be integrated with light water reactor (LWR) nuclear power plants (NPPs) in order to improve the viability and sustainability of existing LWRs through product diversification by utilizing nuclear energy not only to produce grid electricity but to also produce carbon free products such as hydrogen, ammonia or synthetic fuels. Much of the analysis herein could be generally applied to any LWR (high temperature steam electrolysis- HTSE design), but hydrogen demand and the optimization of the HTSE was completed with specific collaboration and data from Xcel Energy’s Prairie Island and Monticello nuclear generating stations and the surrounding market and logistics potential in the greater Minneapolis region. Xcel Energy has set aggressive goals with regards to decarbonization, including an 80% reduction in CO 2 emissions from 2005 levels, by 2030 and 100% carbon free by 2050. Other TEAs regarding hydrogen production with nuclear energy have been completed in collaboration with other utility companies previously. Besides being the first TEA in this regard specific to Xcel Energy and the surrounding markets and logistics, this TEA adds to the previously completed TEAs by providing the most up to date and state of the art analysis and optimization of the hydrogen production plant integrated with nuclear power (NPP-HTSE).

08 HYDROGEN↗

Providencia Island High-Level Power System Capacity Expansion Analyses [Slides]

Results of a high level cost-benefit analysis using HOMER Pro software are presented for Providencia Island, Colombia. The analysis focuses on integrating solar photovoltaics (PV) and a battery energy storage system (BESS) into an existing diesel-only remote power system. The analysis uses fuel costs and discount rates provided by the stakeholders and NREL-derived capital cost estimates.

14 SOLAR ENERGY↗

Resonance Island Jump theory for the HSR

The Resonance Island Jump (RIJ) scheme for transition crossing in HSR (or the CERN SPS [1, 2]) is radically new, and untested. Beam experiments in RHIC will be necessary if the RIJ scheme is to be considered as a serious alternative to upgrading the first order linear jump scheme currently implemented in RHIC [3]. This note outlines the planning and the theoretical foundations that are necessary for such a beam experiment, perhaps to be performed in 2024.

43 PARTICLE ACCELERATORS↗