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At least 397 records · Page 22

BOREAS TF-11 Decomposition Data over the SSA-Fen

The BOREAS TF-11 team collected several data sets in its efforts to fully describe the flux and site characteristics at the SSA-Fen site. This data set contains decomposition rates of a standard substrate (wheat straw) across treatments. The measurements were conducted in 1994 as part of a 2 x 2 factorial experiment in which we added carbon (300 g/sq m as wheat straw) and nitrogen (6 g/sq m as urea) to four replicate locations in the vicinity of the TF-11 tower. The data are stored in tabular ASCII files.

Valentine, David W.↗

Making a Water Data System Responsive to Information Needs of Decision Makers

Evidence-based environmental management requires data that are sufficient, accessible, useful and used. A mismatch between data, data systems, and data needs for decision making can result in inefficient and inequitable capital investments, resource allocations, environmental protection, hazard mitigation, and quality of life. In this paper, we examine the relationship between data and decision making in environmental management, with a focus on water management. We focus on the concept of decision-driven data systems —data systems that incorporate an assessment of decision-makers' data needs into their design. The aim of the research was to examine the process of translating data into effective decision making by engaging stakeholders in the development of a water data system. Using California's legislative mandate for state agencies to integrate existing water and other environmental data as a case study, we developed and applied a participatory approach to inform data-system design and identify unmet data needs. Using workshops and focused stakeholder meetings, we developed 20 diverse use cases to assess data sources, availability, characteristics, gaps, and other attributes of data used for representative decisions. Federal and state agencies made up about 90% of the data sources, and could readily adapt to a federated data system, our recommended model for the state. The remaining 10% of more-specialized data, central to important decisions across multiple use cases, would require additional investment or incentives to achieve data consistency, interoperability, and compatibility with a federated system. Based on this assessment, we propose a typology of different types of data limitations and gaps described by stakeholders. We also propose technical, governance, and stakeholder engagement evaluation criteria to guide planning and building environmental data systems. Data-system governance involving both producers and users of data was seen as essential to achieving workable standards, stable funding, convenient data availability, resilience to institutional change, and long-term buy-in by stakeholders. Our work provides a replicable lesson for using decision-maker and stakeholder engagement to shape the design of an environmental data system, and inform a technical design that addresses both user and producer needs.

Cantor, Alida↗

The Transition of Satellite Observations Assimilated in GEOS to JEDI

In order to incorporate the Joint Effort for Data assimilation Integration (JEDI) in the Goddard Earth Observing System (GEOS), which is used for weather, climate, and air quality forecasts and producing reanalysis datasets, it is necessary to validate the observing system in JEDI. NASA’s Global Modeling and Assimilation Office (GMAO), with the Joint Center for Satellite Data Assimilation (JCSDA), is developing the Unified Forward Operator (UFO) and adding all the necessary features to replicate existing capability. Various satellite and conventional observations are assimilated by the Gridpoint Statistical Interpolation (GSI)–based GEOS atmospheric data assimilations system. GMAO has been adding, validating, and updating procedures including the GEOS all-sky microwave radiance assimilation framework to assimilate those observation in UFO. Robust tests are conducted to ensure correct configurations of observational data bias correction (BC), quality control (QC), and observation error in UFO and good agreements between UFO and GSI results. Our work on satellite observations is reported in this presentation.

Jianjun Jin↗

Functional characterization of Autographa californica multiple nucleopolyhedrovirus gp16 (ac130)

To investigate the function of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) gp16, multiple gp16-knockout and repair mutants were constructed and characterized. No obvious difference in productivity of budded virus, DNA synthesis, late gene expression and morphogenesis was observed between gp16-knockout and repair viruses, but gp16 deletion resulted in six hours of lengthening in ST{sub 50} to the third instar Spodoptera exigua larvae in bioassays. GP16 was fractionated mainly in the light membrane fraction, by subcellular fractionation. A GP16-EGFP fusion protein was predominantly localized close around the nuclear membrane in infected cells, being coincident with formation of the vesicles associated with the nuclear membrane, which hosted nucleocapsids released from the nucleus. These data suggest that gp16 is not required for viral replication, but may be involved in membrane trafficking associated with the envelopment/de-envelopment of budded viruses when they cross over the nuclear membrane and pass through cytoplasm. - Highlights: • gp16 knockout and repair mutants of AcMNPV were constructed and characterized. • AcMNPV gp16 is not essential to virus replication. • Deletion of gp16 resulted in time lengthening to kill S. exigua larvae. • GP16 was localized close around the nuclear membrane of infected cells. • GP16 was fractionated in the light membrane fraction in subcellular fractionation.

60 APPLIED LIFE SCIENCES↗

Automated nuclear cloud feature extraction from film

Chemical, biological, radiological, nuclear, and explosives incidents require rapid detection and characterization for appropriate response. For a nuclear detonation, visible-light cameras may be used to locate the cloud and characterize fallout deposition when coupled with numerical models. Films from the United States’ nuclear testing era compose the only sizeable collection of imagery depicting high-yield detonations. These films offer unique insights into characteristics of flows involving scales that are difficult to replicate experimentally, and they are a valuable source of data for the validation of models for nuclear fallout transport, either as part of emergency response or forensic activities. In this work, we implement modern computer vision and machine learning techniques to identify and track the cloud automatically and subsequently determine the time dependence of some of its features. We trained a ResNet-18 image classifier on hundreds of images to categorize nuclear cloud morphology. Each category or cloud regime is determined by early cloud evolution and is associated to constitutive properties of the flow, such as distribution of vorticity. Next, we identified keypoint features using the KAZE algorithm and tracked these keypoints in the images, allowing us to determine the dimensions and velocities of the cloud across film frames. These measurements converted to real-world units provide valuable experimental data that can be used in the development and validation of nuclear cloud models. We compared the results of this method against manual cloud rise measurements from two different films. In one, our automated method accelerated the feature extraction process without sacrificing measurement accuracy.

Khristy, Joel [ORNL] (ORCID:0000000209963060)↗

Uncertainty quantification of fireball features extracted from nuclear test films using computer vision

Films from the US’s historic nuclear testing era comprise the only extensive collection of imagery depicting high-yield detonations. These films offer unique insights into the characteristics of flows occurring on scales that are difficult to replicate experimentally, and they are a valuable source of data for the validation of models used to describe nuclear detonations. In recent work, we implemented modern computer vision and machine learning techniques to extract features of the fireball following nuclear detonation. With a training dataset of fireball films, we fine-tuned a You Only Look Once 11 (YOLO11) model to detect and track the fireball. Applied to a video, the outer bounding box produced in each frame by YOLO11 is used as an input prompt to Meta’s Segment Anything Model 2 (SAM2), which is shown to accurately predict the boundary of the fireball over time with high resolution. These state-of-the-art computer vision foundation models exhibit impressive visual accuracy in their results but lack an output of values that robustly quantify uncertainty in scientific applications. In this paper, we develop procedures for uncertainty quantification of extracted fireball features. We outline the application of a parallel attention mechanism to calculate uncertainty ranges that complement and better pose model validation data. This higher quality fireball validation data may serve to improve prognostic models describing nuclear detonations in support of nuclear forensic and emergency response activities.

Khristy, Joel [ORNL] (ORCID:0000000209963060)↗

ESGF Future Architecture Report (V.1.1)

This document reports the findings of the Earth System Grid Federation Future Architecture Face-to-Face Meeting held in the UK 5-7 November 2019, attended by technical representatives from the ESGF partner organisations. ESGF is an International federated archive that provides access to Earth science data. It is fundamentally a distributed file management system with its main function being data dissemination through the provision of services for efficient replication and search. It has been in operation for over ten years and has undergone continuous improvements and enhancements over this time span. The Future Architecture is a major review of the software system including a fundamental reassessment of its requirements with a view to develop a new overall system architecture. This has been initiated in the light of challenges around the maintenance of the existing software legacy and a changing technology landscape and practices in the communities it serves. The work is being carried out under the oversight of the ESGF Executive Committee1,2 and is coordinated activity between ESGF and the European IS-ENES3 project.

54 ENVIRONMENTAL SCIENCES↗

Early Lab scientists had questions, Plastic Man gave them answers

He was a willing subject in countless scientific experiments, a superstar of health physics, as well as a favorite photo prop -- and not just around Halloween time. He was Plastic Man. Beginning in the mid-1950s, the Lab (then called Los Alamos Scientific Laboratory) often relied on several life-sized synthetic test subjects to avoid experimenting on people. In the early days of the Laboratory, not much was known about how different radioisotopes interacted with the human body and how much it absorbed from different radiation sources. Answering queries like these is where Plastic Man came in. For example, during the 1950s and 1960s, the Lab was tasked with developing nuclear rockets for space exploration under the Rover Program. One of the concerns was how astronauts might be affected when exposed to radiation from these rocket engines. So, the Lab’s health group set up an experiment in which Plastic Man was placed in close proximity to an experimental Rover nuclear rocket engine. Running experiments like this using Plastic Man kept humans safer. How life-like was he? There were actually two variations of Plastic Man. Both had hard plastic exteriors, but one of the models encased a real human skeleton. They also had movable joints and simulated organs, such as a liver, a spleen, kidneys, lungs and a thyroid. Although Plastic Man in its entirety was used in experiments, much of the data collected were from research conducted inside on these replicated organs. In time, technology advanced and Plastic Man was able to retire from the Lab. He found a new home in 1964 as a display at the Laboratory’s science museum, and is sometimes displayed today in the Bradbury Science Museum in downtown Los Alamos.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Prototype Biology-Based Radiation Risk Module Project

Biological effects of space radiation and risk mitigation are strategic knowledge gaps for the Evolvable Mars Campaign. The current epidemiology-based NASA Space Cancer Risk (NSCR) model contains large uncertainties (HAT #6.5a) due to lack of information on the radiobiology of galactic cosmic rays (GCR) and lack of human data. The use of experimental models that most accurately replicate the response of human tissues is critical for precision in risk projections. Our proposed study will compare DNA damage, histological, and cell kinetic parameters after irradiation in normal 2D human cells versus 3D tissue models, and it will use a multi-scale computational model (CHASTE) to investigate various biological processes that may contribute to carcinogenesis, including radiation-induced cellular signaling pathways. This cross-disciplinary work, with biological validation of an evolvable mathematical computational model, will help reduce uncertainties within NSCR and aid risk mitigation for radiation-induced carcinogenesis.

Terrier, Douglas↗

Can We Practically Bring Physics-based Modeling Into Operational Analytics Tools?

We present that analytics software is increasingly used to improve and maintain operational efficiency in commercial buildings. Energy managers, owners, and operators are using a diversity of commercial offerings often referred to as Energy Information Systems, Fault Detection and Diagnostic (FDD) systems, or more broadly Energy Management and Information Systems, to cost-effectively enable savings on the order of ten to twenty percent. Most of these systems use data from meters and sensors, with rule-based and/or data-driven models to characterize system and building behavior. In contrast, physics-based modeling uses first-principles and engineering models (e.g., efficiency curves) to characterize system and building behavior. Historically, these physics-based approaches have been used in the design phase of the building life cycle or in retrofit analyses. Researchers have begun exploring the benefits of integrating physics-based models with operational data analytics tools, bridging the gap between design and operations. In this paper, we detail the development and operator use of a software tool that uses hybrid data-driven and physics-based approaches to cooling plant FDD and optimization. Specifically, we describe the system architecture, models, and FDD and optimization algorithms; advantages and disadvantages with respect to purely data-driven approaches; and practical implications for scaling and replicating these techniques. Finally, we conclude with an evaluation of the future potential for such tools and future research opportunities.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Improved Neutron Lifetime Measurement with UCN$\tau$

In this work, we report an improved measurement of the free neutron lifetime $\tau_n$ using the UCN$\tau$ apparatus at the Los Alamos Neutron Science Center. We count a total of approximately 38×10 6 surviving ultracold neutrons (UCNs) after storing in UCN$\tau$’s magnetogravitational trap over two data acquisition campaigns in 2017 and 2018. We extract $\tau$ n from three blinded, independent analyses by both pairing long and short storage time runs to find a set of replicate $\tau$ n measurements and by performing a global likelihood fit to all data while self-consistently incorporating the β-decay lifetime. Both techniques achieve consistent results and find a value $\tau$ n =877.75±0.28 stat +0.22/–0.16 syst s. With this sensitivity, neutron lifetime experiments now directly address the impact of recent refinements in our understanding of the standard model for neutron decay.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Omics-Lethal Human Viruses, West Nile Experiment WDC011

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus (WNVMT) and mutant (WNVE218A) virus infection. Sample data was obtained from primary mouse myeloid dendritic cells for mRNA expression analysis. See Experiment WDC010 (GSE74628) for corresponding independent biological replicate study. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, West Nile Experiment WGCN002

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus infectious clone (WNV-NY99 clone 382) and mutant (WNVE218A) virus infection. Sample data was obtained from mouse granule cell neurons for mRNA and miRNA expression analysis. See Experiment WGCN003 for corresponding independent biological replicate study. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-Lethal Human Viruses, West Nile Experiment WGCN003

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus infectious clone (WNV-NY99 clone 382) and mutant (WNVE218A) virus infection. Sample data was obtained from mouse granule cell neurons for mRNA and miRNA expression analysis. See Experiment WGCN002 for corresponding independent biological replicate study. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗

BOREAS TF-11 CO2 and CH4 Concentration Data from the SSA-Fen

The BOREAS TF-11 team collected several data sets in its efforts to fully describe the flux and site characteristics at the SSA-Fen site. This data set contains temperature, pH, and concentration profiles of methane and carbon dioxide within the surface 50 cm of peat. The measurements were conducted as part of a 2 x 2 factorial experiment in which we added carbon (300 g/sq m as wheat straw) and nitro-gen (6 g/sq m as urea) to four replicate locations in the vicinity of the TF-11 tower. The data set covers the period from the first week of June 1994 through the second week of September 1994. The data are stored in tabular ASCII files.

Hall, Forrest G.↗

Inventory of forest and rangeland and detection of forest stress

The author has identified the following significant results. Seventy-two ground sensors were interfaced with three DCP'S at the Black Hills test site. Unfortunately, the transmitters had to be returned for modification and forestry sensed data is not available. The DCP's did operate properly from the Berkeley laboratory and data were recovered from the Goldstone and Alaska stations via Goddard. Replicated training sets and test sets have been selected from all three test site areas in preparation for the receipt of ERTS imagery and digital tapes. From 600 and 800 points have been selected at each site location and UTM coordinates determined. Templates are being made of these sets. As of September 1, ERTS-generated data had not been received and no statements can be made regarding quality or suitability for forest and range experiments. Aerial photography (scale 1:32,000) of the Manitou (226 C) and Black Hills (226 A) sites was taken with CIR in June. Various scales (1:2,000; 1:10,000; 1:20,000; and 1:40,000) of 70 mm photographs were obtained at Manitou with normal color, CIR, and panchromatic in August.

Heller, R. C.↗

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation. From these assessments we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61-93% of the time. When comparing across different instruments and quantitative technologies, differential genes were reproduced by other data sets from 67-99% of the time. Projecting gene differences to biological pathways and networks increased the similarities. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.

Environmental Molecular Sciences Laboratory↗

BOREAS TF-11 Biomass Data over the SSA-Fen

The BOREAS TF-11 team collected several data sets in its efforts to fully describe the flux and site characteristics at the SSA-Fen site. This data set contains plant cover, standing crop of plant biomass, and estimated net primary productivity at each chamber site at the end of the 1994 field season. The measurements were conducted as part of a 2 x 2 factorial experiment in which we added carbon (300 g/sq m as wheat straw) and nitrogen (6 g/sq m as urea) to four replicate locations in the vicinity of the TF-11 tower. The data are stored in tabular ASCII files.

Valentine, David W.↗