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At least 451 records · Page 25

TU-A-12A-04: Quantitative Texture Features Calculated in Lung Tissue From CT Scans Demonstrate Consistency Between Two Databases From Different Institutions

Purpose: To evaluate the consistency of computed tomography (CT) scan texture features, previously identified as stable in a healthy patient cohort, in esophageal cancer patient CT scans. Methods: 116 patients receiving radiation therapy (median dose: 50.4Gy) for esophageal cancer were retrospectively identified. For each patient, diagnostic-quality pre-therapy (0-183 days) and post-therapy (5-120 days) scans (mean voxel size: 0.8mm×0.8mm×2.5mm) and a treatment planning scan and associated dose map were collected. An average of 501 32x32-pixel ROIs were placed randomly in the lungs of each pre-therapy scan. ROI centers were mapped to corresponding locations in post-therapy and planning scans using the displacement vector field output by demons deformable registration. Only ROIs with mean dose <5Gy were analyzed, as these were expected to contain minimal post-treatment damage. 140 texture features were calculated in pre-therapy and post-therapy scan ROIs and compared using Bland-Altman analysis. For each feature, the mean feature value change and the distance spanned by the 95% limits of agreement were normalized to the mean feature value, yielding normalized range of agreement (nRoA) and normalized bias (nBias). Using Wilcoxon signed rank tests, nRoA and nBias were compared with values computed previously in 27 healthy patient scans (mean voxel size: 0.67mm×0.67mm×1mm) acquired at a different institution. Results: nRoA was significantly (p<0.001) larger in cancer patients than healthy patients. Differences in nBias were not significant (p=0.23). The 20 features identified previously as having nRoA<20% for healthy patients had the lowest nRoA values in the current database, with an average increase of 5.6%. Conclusion: Despite differences in CT scanner type, scan resolution, and patient health status, the same 20 features remained stable (i.e., low variability and bias) in the absence of disease changes for databases from two institutions. Identification of these features is the first step towards quantifying radiation-induced changes between preand post-therapy scans. Supported, in part, by NIH Grant Nos. S10 RR021039, and P30 CA14599, the Virginia and D. K. Ludwig Fund for Cancer Research, Imaging Research Institute, Biological Sciences Division, The University of Chicago, and The Institute for Translational Medicine Pilot Award, The University of Chicago.

60 APPLIED LIFE SCIENCES↗

SU-F-P-10: A Web-Based Radiation Safety Relational Database Module for Regulatory Compliance

Purpose: Maintaining compliance with Radioactive Materials Licenses is inherently a time-consuming task requiring focus and attention to detail. Staff tasked with these responsibilities, such as the Radiation Safety Officer and associated personnel must retain disparate records for eventual placement into one or more annual reports. Entering results and records in a relational database using a web browser as the interface, and storing that data in a cloud-based storage site, removes procedural barriers. The data becomes more adaptable for mining and sharing. Methods: Web-based code was written utilizing the web framework Django, written in Python. Additionally, the application utilizes JavaScript for front-end interaction, SQL, HTML and CSS. Quality assurance code testing is performed in a sequential style, and new code is only added after the successful testing of the previous goals. Separate sections of the module include data entry and analysis for audits, surveys, quality management, and continuous quality improvement. Data elements can be adapted for quarterly and annual reporting, and for immediate notification of user determined alarm settings. Results: Current advances are focusing on user interface issues, and determining the simplest manner by which to teach the user to build query forms. One solution has been to prepare library documents that a user can select or edit in place of creation a new document. Forms are being developed based upon Nuclear Regulatory Commission federal code, and will be expanded to include State Regulations. Conclusion: Establishing a secure website to act as the portal for data entry, storage and manipulation can lead to added efficiencies for a Radiation Safety Program. Access to multiple databases can lead to mining for big data programs, and for determining safety issues before they occur. Overcoming web programming challenges, a category that includes mathematical handling, is providing challenges that are being overcome.

61 RADIATION PROTECTION AND DOSIMETRY↗

Description of Emission Processes in Molecular Gases Based with the HITRAN Database

Methods for calculating the emission characteristics of a molecular gas in vibrational–rotational transitions involving information collected in the HITRAN database have been discussed. It has been shown that a series of vibrational–rotational transitions induced by the absorption of photons by CO{sub 2} molecules lead to the formation of unstable autoionizing states. Algorithms for calculating the partial absorption coefficients and radiation fluxes from the bulk of the molecular gas have been developed involving the HITRAN database. Advantages and disadvantages of this approach for calculating the emission characteristics of molecular gas layers have been discussed. The results have been demonstrated in application to carbon dioxide and methane in the Earth’s atmosphere.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The tundra phenology database: more than two decades of tundra phenology responses to climate change

Observations of changes in phenology have provided some of the strongest signals of the effects of climate change on terrestrial ecosystems. The International Tundra Experiment (ITEX), initiated in the early 1990s, established a common protocol to measure plant phenology in tundra study areas across the globe. Today, this valuable collection of phenology measurements depicts the responses of plants at the colder extremes of our planet to experimental and ambient changes in temperature over the past decades. The database contains 150 434 phenology observations of 278 plant species taken at 28 study areas for periods of 1–26 years. Here we describe the full data set to increase the visibility and use of these data in global analyses and to invite phenology data contributions from underrepresented tundra locations. Portions of this tundra phenology database have been used in three recent syntheses, some data sets are expanded, others are from entirely new study areas, and the entirety of these data are now available at the Polar Data Catalogue (https://doi.org/10.21963/13215).

54 ENVIRONMENTAL SCIENCES↗

GOTTCHA Database, Version 1

One major challenge in the field of shotgun metagenomics is the accurate identification of the organisms present within the community, based on classification of short sequence reads. Though microbial community profiling methods have emerged to attempt to rapidly classify the millions of reads output from contemporary sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling tool with significantly smaller FDR, which is also capable of classifying never-before seen genomes into the appropriate parent taxa.The algorithm is based upon three primary computational phases: (I) genomic decomposition into bit vectors, (II) bit vector intersections to identify shared regions, and (III) bit vector subtractions to remove shared regions and reveal unique, signature regions.In the Decomposition phase, genomic data is first masked to highlight only the valid (non-ambiguous) regions and then decomposed into overlapping 24-mers. The k-mers are sorted along with their start positions, de-replicated, and then prefixed, to minimize data duplication. The prefixes are indexed and an identical data structure is created for the start positions to mimic that of the k-mer data structure.During the Intersection phase -- which is the most computationally intensive phase -- as an all-vs-all comparison is made, the number of comparisons is first reduced by four methods: (a) Prefix restriction, (b) Overlap detection, (c) Overlap restriction, and (d) Result recording. In Prefix restriction, only k-mers of the same prefix are compared. Within that group, potential overlap of k-mer suffixes that would result in a non-empty set intersection are screened for. If such an overlap exists, the region which intersects is first reduced by performing a binary search of the boundary suffixes of the smaller set into the larger set, which defines the limits of the zipper-based intersection process. Rather than recording the actual k-mers of the intersection, another data structure of identical "shape" is created which consists of only bit vectors so that only a 1 or 0 will be stored in the location of the k-mer suffix that was found in the intersection. This reduces the amount of data generated and stored considerably.During the Subtraction phase, relevant intersection bitmasks are first unionized together to form a single bitmask which is then applied over the original genome to reveal only those regions of the genome that are unique. These regions are then exported to disk in FASTA format and used in the application of determining the constituents of an unknown metagenomic community.The DATABASE provided is the result of the algorithm described.

Freitas, Tracey↗

NaTGenPD (National Thermal Generator Performance Database)

The National Thermal Generator Performance Database (NaTGenPD) is a code base used for the processing (extraction, cleaning, filtering, and fitting) and analysis of EPA CEMS data to produce a National Thermal Generator Performance Database.

Buster, Grant↗

Building Performance Database API (BPD API) v2.1

The Building Performance Database (BPD) is the largest publicly-available source of measured energy performance data for buildings in the United States. It contains information about the building's energy use, location, and physical and operational characteristics. The BPD can be used by building owners, operators, architects and engineers to compare a building's energy efficiency against customized peer groups, identify energy efficiency opportunities, and set energy efficiency targets. It can also be used by energy efficiency program implementers and policymakers to analyze energy efficiency features and trends in the building stock. The BPD compiles data from various data sources, converts it into a standard format, cleanses and quality checks the data, and provides users with access to the data in a way that maintains anonymity for data providers. This software is the database and the Application Programming Interface (API). Users can utilize the BPD's data to develop their own applications using the API. Version 2.1 included a major update for multiple years of data and refactoring of code for faster queries.

Mathew, Paul↗

Familial Associations of Prevalence and Cause-Specific Mortality for Thoracic Aortic Disease and Bicuspid Aortic Valve in a Large-Population Database

Thoracic aortic disease and bicuspid aortic valve (BAV) likely have a heritable component, but large population-based studies are lacking. This study characterizes familial associations of thoracic aortic disease and BAV, as well as cardiovascular and aortic-specific mortality, among relatives of these individuals in a large-population database. In this observational case-control study of the Utah Population Database, we identified probands with a diagnosis of BAV, thoracic aortic aneurysm, or thoracic aortic dissection. Age- and sex-matched controls (10:1 ratio) were identified for each proband. First-degree relatives, second-degree relatives, and first cousins of probands and controls were identified through linked genealogical information. Cox proportional hazard models were used to quantify the familial associations for each diagnosis. We used a competing-risk model to determine the risk of cardiovascular-specific and aortic-specific mortality for relatives of probands. The study population included 3,812,588 unique individuals. Familial hazard risk of a concordant diagnosis was elevated in the following populations compared with controls: first-degree relatives of patients with BAV (hazard ratio [HR], 6.88 [95% CI, 5.62–8.43]); first-degree relatives of patients with thoracic aortic aneurysm (HR, 5.09 [95% CI, 3.80–6.82]); and first-degree relatives of patients with thoracic aortic dissection (HR, 4.15 [95% CI, 3.25–5.31]). In addition, the risk of aortic dissection was higher in first-degree relatives of patients with BAV (HR, 3.63 [95% CI, 2.68–4.91]) and in first-degree relatives of patients with thoracic aneurysm (HR, 3.89 [95% CI, 2.93–5.18]) compared with controls. Dissection risk was highest in first-degree relatives of patients who carried a diagnosis of both BAV and aneurysm (HR, 6.13 [95% CI, 2.82–13.33]). First-degree relatives of patients with BAV, thoracic aneurysm, or aortic dissection had a higher risk of aortic-specific mortality (HR, 2.83 [95% CI, 2.44–3.29]) compared with controls. Our results indicate that BAV and thoracic aortic disease carry a significant familial association for concordant disease and aortic dissection. The pattern of familiality is consistent with a genetic cause of disease. Furthermore, we observed higher risk of aortic-specific mortality in relatives of individuals with these diagnoses. In conclusion, this study provides supportive evidence for screening in relatives of patients with BAV, thoracic aneurysm, or dissection.

60 APPLIED LIFE SCIENCES↗

Exposing new taxonomic variation with inflammation — a murine model-specific genome database for gut microbiome researchers

The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally.

59 BASIC BIOLOGICAL SCIENCES↗

ORNL Compiled Mercury Methylator Database

This is a custom reference database compiled by ORNL researchers, containing mercury methylation genes (hgcA and hgcB) from predicted and known mercury methylating microorganisms. The database contains 301 hgcA and 239 hgcB sequences from pure culture and environmental genomes publicly available from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov). The reference packages can be used to assign taxonomic classification to HgcA sequences from cloning, amplicon, or meta-omic datasets.

HG SFA↗

Utility Rate Database

The Utility Rate Database is a free storehouse of rate structure information from utilities in the United States. The database includes rates for utilities based on the authoritative list of U.S. utility companies maintained by the U.S. Department of Energy’s Energy Information Administration.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

International Soil Carbon Network (ISCN) Database v3-1

The ISCN is an international scientific community devoted to the advancement of soil carbon research. The ISCN manages an open-access, community-driven soil carbon database. This is version 3-1 of the ISCN Database, released in December 2015. It gathers 38 separate dataset contributions, totalling 67,112 sites with data from 71,198 soil profiles and 431,324 soil layers. For more information about the ISCN, its scientific community and resources, data policies and partner networks visit: http://iscn.fluxdata.org/.

Nave, Luke↗

NEWTS EPA FGD Effluent Database

Data from the US EPA FGD Database containing FGD effluent data from selected U.S. coal power plants. Original data from: Nguyen, Dan-Tam, Eastern Research Group. Sep 29, 2015. Analytical Database for the Steam Electric Rulemaking - DCN SE05359. https://www.regulations.gov/document/EPA-HQ-OW-2009-0819-5640

FGD Effluent↗

NEWTS USGS Brackish Water Database

Data from the USGS Brackish Water Database on brackish water compositions from across the US. Data has been filtered for high salinity and completeness of data attributes. Data has been transposed and converted for ease of input into aqueous chemistry modeling software including OLI Systems and Geochemist's Workbench. Original data from: Qi, S.L., and Harris, A.C., 2017, Geochemical Database for the Brackish Groundwater Assessment of the United States: U.S. Geological Survey data release, https://doi.org/10.5066/F72F7KK1.

Brackish Groundwater↗

NEWTS USGS Produced Waters Database

Data from the USGS Produced Waters Database on produced water compositions from across the US. Data has been filtered for completeness of data attributes. Data has been transposed and converted for ease of input into aqueous chemistry modeling software including OLI Systems and Geochemist's Workbench. Original data from: Blondes, M. S., Gans, K. D., Engle, M. A., Kharaka, Y. K., Reidy, M. E., Saraswathula, V., Thordsen, J. J., Rowan, E. L., & Morrissey, E. A. (2019). U.S. Geological Survey National Produced Waters Geochemical Database v2.3 [Data set]. U.S. Geological Survey. https://doi.org/10.5066/F7J964W8

Geochemists Workbench↗

NEWTS State-Level Database Dashboard

The National Energy Water Treatment and Speciation (NEWTS) State-Level Database Dashboard enables quick visualization and exploration of energy-related wastewater data collected from state environmental agencies and research projects across the United States. The dashboard features a subset of the NEWTS Integrated Dataset (version 1.0), which was built to provide stakeholders with a unified and standardized database to support wastewater treatment and critical minerals exploration. The full NEWTS Integrated Dataset and citations for the original data resources can be found here: https://edx.netl.doe.gov/dataset/newts-integrated-dataset-version-1-0

abandoned mine drainage↗

Advanced Infrastructure Integrity Modeling (AIIM) Onshore Pipeline Database

The Advanced Infrastructure Integrity Modeling (AIIM) Onshore Pipeline Database is an interoperable spatial resource containing critical environmental, operational, and reported stressors tied to publicly available oil and gas pipeline locations across the contiguous U.S. and Alaska. This database contains two layers: 1. Pipeline point locations (‘pipeline_points’) – More than 500,000 points (at every kilometer along pipelines, and end points) to which more than 350 stress-related variables have been appended. 2. Merged pipelines (‘merged_pipelines’) – The original, publicly available pipeline data (see table below) merged together into one feature class.

Carbon Transport↗

Component Database for the APS Upgrade

The Advanced Photon Source Upgrade (APS-U) project will replace the existing APS storage ring with a multi-bend achromat (MBA) lattice to provide extreme transverse coherence and extreme brightness x-rays to its users. As the time to replace the existing storage ring accelerator is of critical concern, an aggressive one-year removal/installation/testing period is being planned. To aid in the management of the thousands of components to be installed in such a short time, the Component Database (CDB) application is being developed with the purpose to identify, document, track, locate, and organize components in a central database. Three major domains are being addressed: Component definitions (which together make up an exhaustive "Component Catalog"), Designs (groupings of components to create subsystems), and Component Instances (“Inventory”). Relationships between the major domains offer additional "system knowledge" to be captured that will be leveraged with future tools and applications. It is imperative to provide sub-system engineers with a functional application early in the machine design cycle. Topics discussed in this paper include the initial design and deployment of CDB, as well as future development plans.

Veseli, S.↗