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NASA NTRSDate not supplied

NASA Life Sciences Portal (NLSP): Supporting Scientific Transparency and Reproducibility

NASA’s Life Sciences Ports (NLSP) serves the scientific community by providing curated data from space life science experiment. The Human Research Program (HRP) with the help of NLSP is currently transforming their life sciences data archive systems and processes to improve compliance with the FAIR principles [1]. Some of these improvements will at the same time support the twin pillars of Open Science [2]: transparency of methods and reproducibility of results. Scientific transparency is marked by the easily intelligible communication of what has been investigated: what were the procedures for collecting sample and the characteristics of samples collected? what kinds of measurements were made, what were the environmental conditions of the measurements? What were the analysis techniques of the collected data? Reproducibility of the results and findings from the investigation requires a high level of transparency for all but the simplest investigations; the slightest deviation in communicating and replicating complex experimental procedures or data analyses can often yield quite different data and even findings, thwarting their validation. One of the ways the NLSP is aiming to improve the communication of scientific information is through the use of ontology-driven metadata. Ontologies are powerful, graph-based knowledge representation structures, which can be leveraged to increase data interoperability, the area of the FAIR principles in which many data systems most lack compliance. Over the past decade, there has been a concerted effort in the biomedical community to develop modular and narrowly focused domain and application-specific ontologies in a common, open-source framework, the Open Biological and Biomedical Ontology (OBO) Foundry [3]. The open sharing and modular nature of this effort promises huge increases in harmonized data sharing for systems that leverage these models. Which is in line with the FAIR Data Principles of Findability, Accessibility, Interoperability, and Reuse for scientific data management and stewardship. 1. Wilkinson, M.D., et al., The FAIR Guiding Principles for scientific data management and stewardship. Sci Data, 2016. 3: p. 160018. 2. National Academies of Sciences, E. and Medicine, Open Science by Design: Realizing a Vision for 21st Century Research. 2018, Washington, DC: The National Academies Press. 232. 3. Smith, B., et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 2007. 25(11): p. 1251-5.

Life Sciences data↗

NASA NTRSDate not supplied

NASA Life Sciences Portal (NLSP): Supporting Scientific Transparency and Reproducibility

Life Sciences data↗

DOE OSTI2022

Molecular Characterization of Water-Soluble Brown Carbon Chromophores in Snowpack from Northern Xinjiang, China

This study reports molecular-level characterization of brown carbon (BrC) attributed to water-soluble organic carbon in six snowpack samples collected from northern Xinjiang, China. Here, the molecular composition and light-absorbing properties of BrC chromophores were unraveled by application of high-performance liquid chromatography (HPLC) coupled to a photodiode array (PDA) detector and high-resolution mass spectrometry. The chromophores were classified into five major types, that is, (1) phenolic/lignin-derived compounds, (2) flavonoids, (3) nitroaromatics, (4) oxygenated aromatics, and (5) other chromophores. Identified chromophores account for ~23–64% of the total light absorption measured by the PDA detector in the wavelength range of 300–370 nm. In the representative samples from urban and remote areas, oxygenated aromatics and nitroaromatics dominate the absorption in the wavelengths below and above 320 nm, respectively. The highly polluted urban sample shows the most complex HPLC-PDA chromatogram, and more other chromophores contribute to the bulk absorption. Phenolic/ lignin-derived compounds are the most light-absorbing species in the soil-influenced sample. Chromophores in two remote samples exhibit ultraviolet–visible features distinct from other samples, which are attributed to flavonoids. Identification of individual chromophores and quantitative analysis of their optical properties are helpful for elucidating the roles of BrC in snow radiative balance and photochemistry.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1995

Systolic Processor Array For Recognition Of Spectra

Spectral signatures of materials detected and identified quickly. Spectral Analysis Systolic Processor Array (SPA2) relatively inexpensive and satisfies need to analyze large, complex volume of multispectral data generated by imaging spectrometers to extract desired information: computational performance needed to do this in real time exceeds that of current supercomputers. Locates highly similar segments or contiguous subsegments in two different spectra at time. Compares sampled spectra from instruments with data base of spectral signatures of known materials. Computes and reports scores that express degrees of similarity between sampled and data-base spectra.

Chow, Edward T.↗

NASA NTRS2007

Bayesian Analysis of the Cosmic Microwave Background

There is a wealth of cosmological information encoded in the spatial power spectrum of temperature anisotropies of the cosmic microwave background! Experiments designed to map the microwave sky are returning a flood of data (time streams of instrument response as a beam is swept over the sky) at several different frequencies (from 30 to 900 GHz), all with different resolutions and noise properties. The resulting analysis challenge is to estimate, and quantify our uncertainty in, the spatial power spectrum of the cosmic microwave background given the complexities of "missing data", foreground emission, and complicated instrumental noise. Bayesian formulation of this problem allows consistent treatment of many complexities including complicated instrumental noise and foregrounds, and can be numerically implemented with Gibbs sampling. Gibbs sampling has now been validated as an efficient, statistically exact, and practically useful method for low-resolution (as demonstrated on WMAP 1 and 3 year temperature and polarization data). Continuing development for Planck - the goal is to exploit the unique capabilities of Gibbs sampling to directly propagate uncertainties in both foreground and instrument models to total uncertainty in cosmological parameters.

methods - statistical↗

DOE OSTI2022

Protocol for single-cell isolation and genome amplification of environmental microbial eukaryotes for genomic analysis

We describe environmental microbial eukaryotes (EMEs) sample collection, single-cell isolation, lysis, and genome amplification, followed by the rDNA amplification and OTU screening for recovery of high-quality species-specific genomes for de novo assembly. These protocols are part of our pipeline that also includes bioinformatic methods. The pipeline and its application on a wide range of phyla of different sample complexity are described in our complementary paper. In addition, this protocol describes optimized lysis, genome amplification, and OTU screening steps of the pipeline. For complete details on the use and execution of this protocol, please refer to Ciobanu et al. (2021).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Restructuring of Benzimidazole-Based Copper Complexes during Electrochemical CO 2 Reduction

Copper-based molecular catalysts have been widely used for the electrochemical reduction of carbon dioxide (ERCO 2 ). However, establishing a correlation between structure and catalytic performance has been challenging due to the dynamic nature of these materials under ERCO 2 working conditions. Here, we report on the restructuring of the copper complexes [Cu(bzimpy)Cl 2 ] and [Cu(pyrben) 2 (NO 3 )]NO 3 during ERCO 2 in an acidic medium, evidencing its effects on the observed activity, selectivity, and stability. In situ X-ray absorption spectroscopy (XAS) suggested that, at sufficiently negative potentials, the Cu 2+ centers of both complexes are reduced to undercoordinated Cu 0 species. Pb underpotential deposition of post-ERCO 2 samples indicated that such Cu 0 species also present a dominant contribution of the (100) domain, which is in line with the high Faradaic efficiency toward C 2 products (∼45%) shown by both complexes at −1.24 V vs RHE. By combining online electrochemical mass spectrometry, in situ XAS, electron paramagnetic resonance (EPR), and quantitative product analysis, we found that [Cu(bzimpy)Cl 2 ] exhibits a partially reversible restructuring, regenerating the main complex moiety, [Cu(bzimpy)] 2+ , and its geometry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Revealing nano-scale lattice distortions in implanted material with 3D Bragg ptychography

Small ion-irradiation-induced defects can dramatically alter material properties and speed up degradation. Unfortunately, most of the defects irradiation creates are below the visibility limit of state-of-the-art microscopy. As such, our understanding of their impact is largely based on simulations with major unknowns. Here we present an x-ray crystalline microscopy approach, able to image with high sensitivity, nano-scale 3D resolution and extended field of view, the lattice strains and tilts in crystalline materials. Using this enhanced Bragg ptychography tool, we study the damage helium-ion-irradiation produces in tungsten, revealing a series of crystalline details in the 3D sample. Our results lead to the conclusions that few-atom-large ‘invisible’ defects are likely isotropic in orientation and homogeneously distributed. A partially defect-denuded region is observed close to a grain boundary. These findings open up exciting perspectives for the modelling of irradiation damage and the detailed analysis of crystalline properties in complex materials.

42 ENGINEERING↗

DOE OSTI2022

A Multi-Branch Decoder Network Approach to Adaptive Temporal Data Selection and Reconstruction for Big Scientific Simulation Data

A key challenge in scientific simulation is that the simulation outputs often require intensive I/O and storage space to store the results for effective post hoc analysis. This article focuses on a quality-aware adaptive temporal data selection and reconstruction problem where the goal is to adaptively select simulation data samples at certain key timesteps in situ and reconstruct the discarded samples with quality assurance during post hoc analysis. This problem is motivated by the limitation of current solutions that a significant amount of simulation data samples are either discarded or aggregated during the sampling process, leading to inaccurate modeling of the simulated phenomena. Two unique challenges exist: 1) the sampling decisions have to be made in situ and adapted to the dynamics of the complex scientific simulation data; 2) the reconstruction error must be strictly bounded to meet the application requirement. To address the above challenges, we develop DeepSample , an error-controlled convolutional neural network framework, that jointly integrates a set of coherent multi-branch deep decoders to effectively reconstruct the simulation data with rigorous quality assurance. The results on two real-world scientific simulation applications show that DeepSample significantly outperforms other state-of-the-art methods on both sampling efficiency and reconstructed simulation data quality.

Zhang, Yang↗

DOE OSTI2021

Neutron Radiography and Computed Tomography of Biological Systems at the Oak Ridge National Laboratory's High Flux Isotope Reactor

Neutrons have historically been used for a broad range of biological applications employing techniques such as small-angle neutron scattering, neutron spin echo, diffraction, and inelastic scattering. Unlike neutron scattering techniques that obtain information in reciprocal space, attenuation-based neutron imaging measures a signal in real space that is resolved on the order of tens of micrometers. The principle of neutron imaging follows the Beer-Lambert law and is based on the measurement of the bulk neutron attenuation through a sample. Greater attenuation is exhibited by some light elements (most notably, hydrogen), which are major components of biological samples. Contrast agents such as deuterium, gadolinium, or lithium compounds can be used to enhance contrast in a similar fashion as it is done in medical imaging, including techniques such as optical imaging, magnetic resonance imaging, X-ray, and positron emission tomography. For biological systems, neutron radiography and computed tomography have increasingly been used to investigate the complexity of the underground plant root network, its interaction with soils, and the dynamics of water flux in situ. Moreover, efforts to understand contrast details in animal samples, such as soft tissues and bones, have been explored. This manuscript focuses on the advances in neutron bioimaging such as sample preparation, instrumentation, data acquisition strategy, and data analysis using the High Flux Isotope Reactor CG-1D neutron imaging beamline. The aforementioned capabilities will be illustrated using a selection of examples in plant physiology (herbaceous plant/root/soil system) and biomedical applications (rat femur and mouse lung).

Bilheux, Hassina↗

DOE OSTI2019

Successes and Lessons Learned in the Design, Construction and Use of a Tool for Sampling the WR-1 Reactor Core - 1900z

Whiteshell Laboratories, located in Manitoba, Canada, provided research facilities for the Canadian nuclear industry since the early 1960's. The facility was centered on an organically cooled, heavy water moderated nuclear reactor in the world, Whiteshell Reactor 1 (WR-1). WR-1 was safely shut down in 1985, de-fueled and drained, and has been in a safe Storage with Surveillance (Deferred Decommissioning) state until present day. In support of an Environmental Assessment for proposed In Situ Decommissioning of WR-1, detailed characterization information regarding the reactor core components (calandria, calandria tubes, pressure tubes) was necessary to verify inventory estimates and neutron activation models produced circa 1992. The Fuel Channels of WR-1 (pressure tubes) were expected to be the most activated components of the reactor core, and to account for about 60% of the reactor core inventory. The interior surface of the fuel channel is also the most readily accessible surface within the reactor core. As such the decision was made to collect a sample of one of each of 3 Fuel Channel material types (Stainless Steel, Zr-2.5Nb, Ozhenite) for comparison to modelled estimates of neutron activation of various core materials. The expected dose rates from the samples were between 5 and 100 mSv (500-10,000 mrem) on contact based on a 200 mg sample. Sampling the Fuel Channels required verification the Fuel Channel was drained of organic coolant, removal of residual organic coolant from the Fuel Channel wall, removal of material from the interior surface of the Fuel Channel at the centerline of flux (∼25' below the operator position), and extraction of that material from the core. Several options for existing tooling and technologies, including hydraulic scrapers, and horizontal drill technologies, were looked at for their applicability to WR-1. While suitable approaches to higher radiation field sample collection, they were overly complex, costly and time consuming for the configuration at WR-1. In an effort to reduce costs, and to simplify the sampling process, a specialized and simple tool was developed to mechanically scrape a small sample of the interior wall of the Fuel Channels, collect the sample into a vial, and remove the sample from the core for analysis. The tool was designed, constructed, tested and implemented in the field entirely by Canadian Nuclear Laboratories Staff. The tool required no powered components, or electronic guidance or measurements; and was designed and constructed for a fraction of the cost of other commercially available technologies for sample collection within reactor cores. The samples were successfully collected without any injuries, contamination events or equipment failures. The tool remains operational in the event additional sampling is required. This paper provides additional details of the design, construction, testing and use of the tool and the successes and lessons learned during the various stages of design and implementation. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Sustainable Shape Memory Elastomers with Reduced Melt Viscosity and Enhanced Stiffness

Melt reactive processing of lignin with nitrile rubber is a promising approach to synthesizing shape memory materials. The strong intramolecular interactions in lignin macromolecular structures, caused by π–π stacking in aromatic rings and hydrogen bonding, often result in large phase separation or low miscibility with rubbers. In this study, we investigated the chemical and molecular characteristics, as well as the stiffness and complex viscosity, of modified kraft lignin melt-reacted with an acrylonitrile/butadiene copolymer containing 41% acrylonitrile (NBR41). To enhance the macromolecular compatibility of kraft lignin with NBR41, kraft lignin was cross-linked with poly(propylene glycol) diglycidyl ether (PPDE) and trimethylolpropane triglycidyl ether (TTE), both rich in epoxy reactive groups capable of forming chemical bonds with hydroxyl and carboxyl groups. Here, our findings demonstrate that the modification of kraft lignin with PPDE and TTE resulted in significantly increased stiffness of the composites. The elastic modulus of NBR41-Kraft lignin-PPDE and NBR41-Kraft lignin-TTE increased by 82 and 162%, respectively. Both the yield strength and Young’s modulus of these two samples showed dramatic improvements. Specifically, the yield strength and Young’s modulus of NBR41-Kraft lignin-TTE increased nearly 4 and 3-fold, respectively, compared to the control sample. Interestingly, despite significant improvements in mechanical properties, the viscosity of NBR41-Kraft lignin-PPDE was substantially lower than that of the control sample. At 210 °C and an angular frequency of 1 rad/s, the complex viscosity of NBR41-Kraft lignin was approximately 100.25 ± 4.77 kPa·s, while that of NBR41-Kraft lignin-PPDE was significantly lower at 56 ± 0.93 kPa·s. These findings were validated through Fourier transform infrared spectroscopy, scanning electron microscopy, dynamic mechanical analysis, thermal characterization, rheological tests, and quasi-elastic neutron scattering techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Machine-learning-assisted automation of single-crystal neutron diffraction

Neutron scattering is a powerful but expensive technique to study materials and discover new matter. Advanced detector technology has significantly improved the efficiency of neutron experiments, increasing the complexity of neutron data reduction and analysis. Machine learning (ML) brings new directions for neutron diffraction data reduction and experiment operation. Here, this work presents an ML-assisted data reduction and analysis method for precise recognition of Bragg peaks and the corresponding regions of interest; it can then automatically screen and align a measured crystal using the recognized peaks, and subsequently plan and optimize the data collection with user-provided information and uncertainty quantification values of detected peaks. This method shows robust performance in different complex sample environments and enables automated single-crystal neutron diffraction.

47 OTHER INSTRUMENTATION↗

NASA NTRS1986

Multiple instrument coverage analysis

In the Space Station era comprehensive investigations of the physical processes of the earth will rely on observations from several types of space-based instruments. Preliminary studies indicate that, due to projected limitations on spacecraft and launch-vehicle capability, these complementary instrument sets may have to be distributed among several spacecraft. The task of analyzing the coincident coverage areas between instruments operating from multiple spacecraft will be complex. Such factors as the instruments' observing capabilities, orbital parameters, and viewing constraints will have to be considered. To aid in this analysis a computer model is being developed. This model has the capability, among others, to compute the coincident coverage areas between two independently orbiting instruments. This paper describes the model, its capabilities, and several sample applications.

Horvat, G. M.↗

NASA NTRS2015

Geologic Investigations Spurred by Analog Testing at the 7504 Cone-SP Mountain Area of the San Francisco Volcanic Field

The SP Mountain area of the San Francisco Volcanic Field, AZ, has been used as an analog mission development site for NASA since 1998. This area consists of basaltic cinder cones, lava flows and maar craters that have been active since mid-Miocene, with the youngest events occurring within the last 10,000 years. The area has been used because its geologic and topographic resemblance to lunar and Martian terrains provides an ideal venue for testing hardware and science operations practices that might be employed on planetary surfaces, as well as training astronauts in field geology. Analog operations have often led to insights that spurred new scientific investigations. Most recently, an investigation of the 7504 cone was initiated due to perceptions that Apollo-style traverse plans executed during the Desert RATS 2010 mission had characterized the area incorrectly, leading to concerns that the Apollo traverse planning process was scientifically flawed. This investigation revealed a complex history of fissure eruptions of lava and cinders, cinder cone development, a cone-fill-and-spill episode, extensive rheomorphic lava flow initiation and emplacement, and cone sector collapse that led to a final lava flow. This history was not discernible on pre-RATS mission photogeology, although independent analysis of RATS 2010 data and samples develped a "75% complete solution" that validated the pre-RATS mission planning and Apollo traverse planning and execution. The study also pointed out that the development of scientific knowledge with time in a given field area is not linear, but may follow a functional form that rises steeply in the early period of an investigation but flattens out in the later period, asymptotically approaching a theoretical "complete knowledge" point that probably cannot be achieved. This implies that future human missions must be prepared to shift geographic areas of investigation regularly if significant science returns are to be forthcoming.

Eppler, Dean B.↗

DOE OSTI2025

Energy-resolved neutron imaging and diffraction including grain orientation mapping using event camera technology

Time-of-flight neutron diffraction and energy-resolved imaging each provide unique perspectives into material properties. Neutron diffraction is useful for assessing microstructural parameters such as phase composition, texture, and dislocation densities, though it typically provides averaged data over the sampled volume. Energy-resolved imaging, on the other hand, offers both spatial and spectral information by detecting Bragg edges and neutron absorption resonances, which enables detailed mapping of microstructure and isotopic composition. When combined, these techniques have the potential to enrich our understanding of material behavior across different scales, enhancing our understanding of complex materials. Traditionally, these modalities are conducted on separate instruments, which is time-consuming and poses challenges for data integration. Here, we report the integration of the LumaCam, an event-mode energy-resolved neutron imaging camera with the HIPPO time-of-flight diffractometer at LANSCE. This integration enables simultaneous diffraction and imaging across the full spectrum, with analysis optimized for diffraction and Bragg-edge imaging in the thermal range (0.45–10 Å) and resonance imaging in the epithermal range (0.5–3000 eV), facilitating comprehensive multi-modal analysis. We demonstrate its capabilities through case studies, including spatial mapping of grain orientations in a steel sample and accurate thickness estimations for irregular samples including a depleted uranium cylinder and a natural silver-containing mineral specimen. The combined setup enhances real-time sample alignment and provides comprehensive data for crystal structure, texture, and isotopic composition analysis. This approach opens new possibilities for advanced applications in nuclear engineering, archaeology, and materials science.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Capturing Carbonation: Understanding Kinetic Complexities through a New Era of Electron Microscopy

Cryogenic plasma focused ion beam (PFIB) electron microscopy analysis is applied to visualizing ex situ (surface industrial) and in situ (subsurface geologic) carbonation products, to advance understanding of carbonation kinetics. Ex situ carbonation is investigated using NIST fly ash standard #2689 exposed to aqueous sodium bicarbonate solutions for brief periods of time. In situ carbonation pathways are investigated using volcanic flood basalt samples from Schaef et al. (2010) exposed to aqueous CO 2 solutions by them. The fly ash reaction products at room temperature show small amounts of incipient carbonation, with calcite apparently forming via surface nucleation. Reaction products at 75° C show beginning stages of an iron carbonate phase, e.g., siderite or ankerite, common phases in subsurface carbon sequestration environments. This may suggest an alternative to calcite in carbonation low calcium-bearing fly ashes. Flood basalt carbonation reactions show distinct zonation with high calcium and calcium-magnesium bearing zones alternating with high iron-bearing zones. The calcium-magnesium zones are notable with occurrence of localized pore space. Oscillatory zoning in carbonate minerals is distinctly associated with far-from-equilibrium conditions where local chemical environments fluctuate via a coupling of reaction with transport. The high porosity zones may reflect a precursor phase (e.g., aragonite) with higher molar volume that then “ripens” to the high-Mg calcite phase-plus-porosity. These observations reveal that carbonation can proceed with evolving local chemical environments, formation and disappearance of metastable phases, and evolving reactive surface areas. Together this work shows that future application of cryo-PFIB in carbonation studies would provide advanced understanding of kinetic mechanisms for optimizing industrial-scale and commercial-scale applications.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Assessing and benchmarking the fidelity of posterior inference methods for astrophysics data analysis

In this era of large and complex astronomical survey data, interpreting, validating, and comparing inference techniques becomes increasingly difficult. This is particularly critical for emerging inference methods like Simulation-Based Inference (SBI), which offer significant speedup potential and posterior modeling flexibility, especially when deep learning is incorporated. We present a study to assess and compare the performance and uncertainty prediction capability of Bayesian inference algorithms – from traditional MCMC sampling of analytic functions to deep learning-enabled SBI. We focus on testing the capacity of hierarchical inference modeling in those scenarios. Before we extend this study to cosmology, we first use astrophysical simulation data to ensure interpretability. We demonstrate a probabilistic programming implementation of hierarchical and non-hierarchical Bayesian inference using simulations derived from the DeepBench software library, a benchmarking tool developed by our group that generates simple and controllable astrophysical objects from first principles. This study will enable astronomers and physicists to harness the inference potential of these methods with confidence.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗