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At least 1,207 records · Page 67

Full Integration of Lipidomics Data into Multi-OMIC Functional Enrichment

Lipids have numerous roles critical to living systems. Many of these vital functions are tightly linked or regulated by proteins. Even though the function of many lipid-related enzymes is known, direct links between most individual lipid species and the enzymes that metabolize them are severely lacking. This missing connection impedes biological progress. A resource that allows users to quickly identify protein-lipid relationships will advance our understanding of lipid homeostasis and metabolic perturbed systems. Databases are readily available for mapping small molecule metabolites (i.e., polar metabolites) and specific oxidized fatty acid lipids (e.g., arachidonic acid derivatives) to proteins/enzymes known to be directly involved in metabolism of these molecules (e.g. SMPDB, Reactome, HMDB, BioCyc). This enables the integration of metabolite and protein (as well as transcript) data when performing functional enrichment and metabolic modeling allowing researchers to rapidly examine metabolic pathways from multiple omics sources. Currently, linking lipidomics data with proteomics data is conducted using a time-intensive, user defined, manual process. Here we propose creating a tool that will link lipidomics and proteomics data and also conduct functional enrichment analysis and visualization allowing for full statistical integration. Using text-mining approaches, we will extract lipid references from uniprot and create a database linking lipid species to enzymes directly related to their metabolism. We will also extract directional annotation, which will allow even greater specificity when linking data types and will help eliminate false positives from functional associations.

59 BASIC BIOLOGICAL SCIENCES↗

Data associated with the manuscript “Radiative impact of record-breaking wildfires from integrated ground-based data” collected in Richland, Washington in September 2020

This data package is associated with the publication “Radiative impact of record-breaking wildfires from integrated ground-based data” submitted to Nature Scientific Reports (Kassianov et al., 2024). Data from ground-based measurements of shortwave and spectrally resolved irradiance and aerosol optical depth (AOD) in the visible and near-infrared spectral ranges were assessed to quantify the radiative impact of the September 2020 wildfires that occurred in the Western United States. Data were collected in September 2020 by several ground-based instruments at the Atmospheric Measurements Laboratory (AML) located in Richland, Washington (46.3451, -119.2792). These data include (1) Aerosol Optical Depth (AOD); (2) spectrally resolved and shortwave (SW) irradiances; (3) backscatter profiles; (4) total sky images; and (5) near-surface ambient air temperatures.The data package consists of five sub-directories: (1) “AML_Ceilometer_”; (2)” AML_CSPHOT_”; (3) “AML_MFRSR_irradiances_”; (4) “AML_SW_irradiances_and_Temp_”; (5) “AML_TSI_images_”; and 6 files stored at the directory level, including the readme, file-level metadata file, and data dictionary. The file-level metadata file (the file ending in “_flmd.csv”) lists all files contained in this data package and descriptions for each. The data dictionary (the file ending in “_dd.csv”) describes each tabular column header’s unit, definition, and structure. Below are descriptions of each sub-directory:“AML_Ceilometer_” includes ceilometer data collected at the AML. These files contain the corresponding narratives of data. Details related to the ceilometer data can be found in Morris (2016). “AML_CSPHOT_” includes ascii files with high-temporal resolution (about 10-15 min) AML CSPHOT data and their daily-averaged counterparts. These two files contain the corresponding narratives of data. Details related to the CSPHOT data can be found in Gregory (2011). “AML_MFRSR_irradiances_” includes ascii files with the AML MFRSR-measured diffuse, normal, and total spectrally resolved irradiance. Details related to the MFRSR data can be found in Hodges and Michalsky (2016) and Koontz et al. (2013). “AML_SW_irradiances_+_Temp_” includes near-surface ambient air temperature and SW irradiances, namely direct normal, diffuse hemispherical, and total hemispheric (global), measured at the AML. These files also incorporate the corresponding narratives of data. Details related to the SW irradiances can be found in Andreas et al. (2018). “AML_TSI_images_” includes Total Sky Images (TSIs) collected at the AML. Details related to the TSI data can be found in Morris (2005).

54 ENVIRONMENTAL SCIENCES↗

The Space Station Data Management System - Avionics that integrate

The Space Station Data Management System (DMS) comprises the networked computers, mass storage, workstations, and instrumentation interfaces required to support onboard systems and payload operations. This paper gives an overview of the current DMS architecture and discusses its role as onboard integrator in four of its major functional areas: (1) data communication; (2) data processing; (3) data administration, storage and retrieval; and (4) data presentation at the human-computer interface.

Whitelaw, Virginia↗

Integrated Task And Data Parallel Programming: Language Design

his research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers '95 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program m. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

Grimshaw, Andrew S.↗

Integrated Task and Data Parallel Programming

This research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers 1995 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

Grimshaw, A. S.↗

The Surface Longwave Downward Fluxes of the NASA GEWEX SRB Release 4.0 IP Products: Validation Against the Surface-Based BSRN and PMEL Observed Data

Since the NASA Global Energy Water Exchanges (GEWEX) Surface Radiation Budget (SRB) project released its 3rd version of products in 2010, the GEWEX Data Assessments Panel (GDAP) has been working on integrating various data products to address issues in the closing of the global energy and water cycles. The 4th version of the SRB products, Rel. 4.0-IP, has integrated data products from the cloud, aerosol, atmosphere, ocean surface, and land surface projects, coordinating within GDAP, to produce a long-term time series of TOA and surface radiative estimates. The Rel. 4-IP shortwave products span 34 years continuously from July 1983 to June 2017 on a quasi-equal-area 1degree longitude by 1degree latitude grid system. The longwave products are for land only from 1983-07 to 1987-12; for both land and ocean from 1988-01 to 2009-12; and ocean only from 2010-01 to 2017-06. The data are provided at 3 hourly, 3-hourly-monthly, daily and monthly means. The ISCCP HXS clouds and radiances are the key cloud input of the current GEWEX SRB algorithms. In addition, the longwave algorithm has also made changes in cloud microphysical property, surface skin temperature input, surface emissivity, atmospheric profile, adding longwave aerosol optical properties, revising cloud overlap procedure, and so on. Details of changes in both inputs and algorithms are documented in a NASA Algorithm Theoretical Basis Document (ATBD). We have validated the surface longwave downward fluxes against the surface-based Baseline Surface Radiation Network (BSRN) and the Pacific Marine Environmental Laboratory (PMEL) buoy data. As of 2020, the BSRN archive has 12,116 site-months of observed records from 73 stations on all seven continents, and as of 2017, PMEL archive has 4389 buoy months of observed records from 64 buoys deployed in the tropics of Pacific, Atlantic and Indian Oceans. This paper presents how the SRB Rel. 4.0-IP surface longwave downward fluxes compare with these surface-based measurements and how the comparison statistics differ from that of Rel. 3.0.

GEWEX SRB↗

Materials Informatics at NASA GRC: Machine Learning Surrogate Modeling, Data Management, and Integrated Toolsets for Establishing/Maintaining the Digital Thread

Integrated Computational Materials Engineering (ICME) has recently received widespread attention due to its promises in reducing dependence on physical testing for engineering design by relying on simulation, reducing both time and cost to market for various applications. ICME however requires validated multiscale material models, which heavily depend on available test data with full material and test pedigree, including material processing, test and measurement equipment, raw data collection, and analysis methodology and results that is findable and usable, along with integrated, efficient toolsets for effectively passing information across various length and time scales across such models. At the NASA Glenn Research Center under the Transformational Tools and Technologies Project, significant recent efforts have been directed towards establishing the required cyberinfrastructure to enable optimized ICME processes and the design of “fit-for-purpose” materials to achieve the goals outlined in the NASA Vision 2040 report. Such efforts include development of multiscale physics-based material models, which can be used to train highly efficient surrogate machine learning models, development of best practices and infrastructure for effective, traceable materials information management, and development of toolsets that integrate with physics-based codes, machine learning models, and an information management system to enable high throughput of materials data collection and analysis, establishment of digital twins and the digital thread, and automation of the ICME design process for material optimization.

Machine Learning↗

Remote Sensing-Driven Hydrodynamic Modeling in Data-Scarce Regions: Integrating ICESat-2, Sentinel-2, SWOT and Re-analysis Models for Coastal Monitoring

Hydrodynamic models in coastal and estuarine systems are typically constrained by sparse bathymetry, boundary, and validation data, especially in regions where field campaigns are costly or impractical. Here we develop and test a fully satellite-driven framework for hydrodynamic modeling in South Africa’s Langebaan Lagoon without using any local in situ measurements. Bathymetry is derived by training multispectral Sentinel-2 reflectance against ICESat-2 ATL24 photon-derived depths using an XGBoost model optimized with Bayesian search. The final satellite-derived bathymetry reproduces independent ATL24 points with RMSE = 0.45 m and R 2 = 0.97. This bathymetry was used in a depth-averaged Delft3D Flexible Mesh model driven at the open boundary by TPXO tidal harmonics and by ERA5 winds. We validate modeled water surface elevation against 16 SWOT low-rate (250 m, unsmoothed) passes in 2023. SWOT–model comparisons yield an overall RMSE of 0.11 m and R 2 = 0.61, with typical point differences <0.10 m (∼7% of the 1.5 m tidal range), and showed consistent spatial gradients in water level from the offshore boundary, through Saldanha Bay, and into the lagoon. At the offshore boundary, TPXO and SWOT sea surface heights agree closely (R 2 = 0.86). A simple phase adjustment of ∼26,min between TPXO and SWOT lowers the RMSE from 0.18,m to 0.11,m, showing that phase offset accounts for some of the discrepancy, with additional errors likely linked to non-tidal signals. Our results demonstrate that combining passive optical, photon-counting LiDAR, radar interferometry, and global tidal/atmospheric models enables robust, transferrable hydrodynamic modeling in data-scarce coastal systems, offering a cost-effective pathway for monitoring.

ICESat-2↗

Doppler Backscattering Data Analysis and Integrated Modeling with OMFIT

One Modeling Framework for Integrated Tasks (OMFIT) is a widely used software tool in the magnetic fusion research community. OMFIT provides magnetic fusion energy researchers with a framework for the development of special-purpose physics modules. This paper describes an OMFIT physics module pertaining to the Doppler Backscattering (DBS) fusion plasma diagnostic. DBS measures density fluctuations and flow velocity through plasma scattering of electromagnetic waves. The OMFIT DBS module was developed to analyze experimental DBS data and facilitate modeling of DBS systems installed on multiple tokamak devices. The OMFIT DBS module is designed to support several analysis workflows: detailed analysis of experimental data, experimental planning, and theory-based synthetic diagnostic modeling. The DBS module uses integrated modeling by leveraging other OMFIT physics modules to perform tasks related to DBS, e.g. ray/beam–tracing simulations, edge-localized mode–synchronized data analysis, magnetic equilibrium reconstruction, and fitting kinetic profile data. Furthermore, this paper describes several supported workflows and serves a reference for the OMFIT DBS module.

Doppler backscattering↗

Integrated Flush Air Data Sensing System Modeling for Planetary Entry Guidance with Direct Force Control

Flush air data sensing (FADS) systems have been previously used at both Earth and Mars to provide onboard estimates of angle of attack, sideslip angle, and dynamic pressure. However, these FADS data were often not used in an in-the-loop sense to inform the onboard guidance and control systems. A method to integrate FADS-derived density and wind estimates with a numerical predictor-corrector guidance algorithm is presented. The method is demonstrated in a high-fidelity simulation of a human-scale Mars entry vehicle that utilizes a hypersonic inflatable aerodynamic decelerator (HIAD) with direct force control. Effects on guidance commands and state uncertainties both with and without FADS system modeling are presented and discussed.

Lugo, Rafael A.↗

Comparing optical four-flux model results with experimental data obtained by integrating sphere measurements

Four-flux theory is a way to model scattering through multiple layers of a system based on diffuse and collimated properties. When compared with measurement results obtained using an integrating sphere or a goniophotometer, an approximation is often made as the physical instrument cannot separate the collimated component from the diffuse light scattered in the forward direction. This paper tries to clarify the meaning of the word diffuse for the different cases and outlines simple corrections to improve the accuracy when comparing four-flux models and measured data based on sample haze and the geometry of the integrating sphere.

Bilokur, Maryna (ORCID:0000000191839650)↗

Data registration and integration requirements for severe storms research

Severe storms research is characterized by temporal scales ranging from minutes (for thunderstorms and tornadoes) to hours (for hurricanes and extra-tropical cyclones). Spatial scales range from tens to hundreds of kilometers. Sources of observational data include a variety of ground based and satellite systems. Requirements for registration and intercomparison of data from these various sources are examined and the potential for operational forecasting application of techniques resulting from the research is discussed. The sensor characteristics and processing procedures relating to the overlay and integrated analysis of satellite and surface observations for severe storms research are reviewed.

Dalton, J. T.↗

Integration of imagery and cartographic data through a common map base

Several disparate data types are integrated by using control points as the basis for spatially registering the data to a map base. The data are reprojected to match the coordinates of the reference UTM (Universal Transverse Mercator) map projection, as expressed in lines and samples. Control point selection is the most critical aspect of integrating the Thematic Mapper Simulator MSS imagery with the cartographic data. It is noted that control points chosen from the imagery are subject to error from mislocated points, either points that did not correlate well to the reference map or minor pixel offsets because of interactive cursorring errors. Errors are also introduced in map control points when points are improperly located and digitized, leading to inaccurate latitude and longitude coordinates. Nonsystematic aircraft platform variations, such as yawl, pitch, and roll, affect the spatial fidelity of the imagery in comparison with the quadrangles. Features in adjacent flight paths do not always correspond properly owing to the systematic panorama effect and alteration of flightline direction, as well as platform variations.

Clark, J.↗

IMG/M: integrated genome and metagenome comparative data analysis system

The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.jgi.doe.gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal, bacterial, eukaryotic and viral genomes from cultured organisms, (ii) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engineered microbiome samples. Sequence data are generated by DOE's Joint Genome Institute (JGI), submitted by individual scientists, or collected from public sequence data archives. Structural and functional annotation is carried out by JGI's genome and metagenome annotation pipelines. A variety of analytical and visualization tools provide support for examining and comparing IMG/M's datasets. IMG/M allows open access interactive analysis of publicly available datasets, while manual curation, submission and access to private datasets and computationally intensive workspace-based analysis require login/password access to its expert review(ER) companion system (IMG/M ER: https://img.jgi.doe.gov/ mer/). Since the last report published in the 2014 NAR Database Issue, IMG/M's dataset content has tripled in terms of number of datasets and overall protein coding genes, while its analysis tools have been extended to cope with the rapid growth in the number and size of datasets handled by the system.

59 BASIC BIOLOGICAL SCIENCES↗