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At least 433 records · Page 24

All sources NASA NTRS DOE OSTI

DOE OSTI2020

Evolving data standards for cryo-EM structures

Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration have been twofold: to develop the necessary infrastructure for archiving cryo-EM-derived density maps and models, and to promote development of cryo-EM structure validation standards. We describe how cryo-EM data archiving and validation have been developed and jointly coordinated for the Electron Microscopy Data Bank and Protein Data Bank archives over the past two decades, as well as the impact of evolving technology on data standards. Just as for X-ray crystallography and nuclear magnetic resonance, engaging the scientific community via workshops and challenging activities has played a central role in developing recommendations and requirements for the cryo-EM structure data archives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Study of VUV radiation of hybrid and standard X-pinches on KING electric discharge facility

The radiative characteristics of standard and hybrid X-pinches are studied in VUV range on the small-size KING electric discharge facility (200 kA, 190 ns, 45 kV) for the same initial conditions. In this work, studies were performed for different X-pinch materials. A comparative analysis of the VUV spectra was performed and the output energy of soft x-rays and VUV radiation was measured for standard and hybrid X-pinches.

bright spot↗

DOE OSTI2022

Dispersive interactions between standard and Dirac materials and the role of dimensionality

The van der Waals (vdW) interaction plays a prominent role between neutral objects at separations where short ranged chemical forces are negligible. This type of dispersive coupling is determined by the interplay between geometry and response properties of the materials making up the objects. Here, we investigate the vdW interaction between 1D, 2D, and 3D standard and Dirac materials within the Random Phase Approximation, which takes into account collective excitations originating from the electronic Coulomb potential. A comprehensive understanding of characteristic functionalities and scaling laws are obtained for systems with parabolic energy dispersion (standard materials) and crossing linear bands (Dirac materials). By comparing the quantum mechanical and thermal limits the onset of thermal fluctuations in the vdW interaction is discussed showing that thermal effects are significantly pronounced at smaller scales in reduced dimensions.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Abstract Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Standardizing reverberation-measured Mg II time-lag quasars, by using the radius–luminosity relation, and constraining cosmological model parameters

ABSTRACT We use 78 reverberation-measured Mg II time-lag quasars (QSOs) in the redshift range 0.0033 ≤ z ≤ 1.89 to constrain cosmological parameters in six different cosmological models. The basis of our method is the use of the radius–luminosity or R−L relation to standardize these 78 Mg II QSOs. In each cosmological model, we simultaneously determine R−L relation and cosmological model parameters, thus avoiding the circularity problem. We find that the R−L relation parameter values are independent of the cosmological model used in the analysis, thus, establishing that current Mg II QSOs are standardizable candles. Cosmological constraints obtained using these QSOs are significantly weaker than, but consistent with, those obtained from a joint analysis of baryon acoustic oscillation (BAO) observations and Hubble parameter [H(z)] measurements. So, we also analyse these QSOs in conjunction with the BAO + H(z) data and find cosmological constraints consistent with the standard spatially flat ΛCDM model as well as with mild dark energy dynamics and a little spatial curvature. A larger sample of higher quality reverberation-measured QSOs should have a smaller intrinsic dispersion and so should provide tighter constraints on cosmological parameters.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Aspects of the Domain-Wall Standard Model

Abstract In the “Domain-Wall Standard Model,” all the Standard Model (SM) fields are localized in certain domains in a non-compact 5D space-time. While the SM is realized as a 4D effective theory at low energies, the model involves Kaluza–Klein (KK) modes of the SM particles. In this paper we introduce two simple solvable examples which lead to domain-wall configurations for the SM particles and their KK-modes. Based on the examples, we address a variety of phenomenologies of the Domain-Wall SM, such as the KK-mode gauge boson phenomenology at the Large Hadron Collider (LHC), the effect of the KK-mode SM fermions on Higgs boson phenomenology, and the KK-mode fermion search at the LHC with its decay into a corresponding SM fermion and a Nambu–Goldstone boson associated with a spontaneous breaking of the translational invariance in the 5th dimension. We also propose a simple unified picture of localizing all the SM fields.

Physics↗

DOE OSTI2023

Proposed minimal standards for description of methanogenic archaea

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA–DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.

Microbiology↗

DOE OSTI2026

Searches for CE ν NS and physics beyond the standard model using Skipper-CCDs at CONNIE

The Coherent Neutrino-Nucleus Interaction Experiment (CONNIE) aims to detect the coherent scattering ( CE ν NS ) of reactor antineutrinos off silicon nuclei using thick fully depleted high-resistivity silicon CCDs. Two Skipper-CCD sensors with subelectron readout noise capability were installed at the experiment next to the Angra-2 reactor in 2021, making CONNIE the first experiment to employ Skipper-CCDs for reactor neutrino detection. We report on the performance of the Skipper-CCDs, the new data processing, data quality, and event selection for CE ν NS interactions, which enable CONNIE to reach a record low detection threshold of 15 eV. The data were collected over 300 days in 2021–2022 and correspond to exposures of 14.9 g-days with the reactor-on and 3.5 g-days with the reactor-off. The difference between the reactor-on and off event rates shows no excess and yields upper limits for the neutrino interaction rates, comparable with previous CONNIE limits from standard CCDs and higher exposures. Searches for new neutrino interactions beyond the Standard Model improve the previous CONNIE limit on a simplified model with light vector mediators. A first dark matter (DM) search by diurnal modulation by CONNIE obtains the best limits on the DM-electron scattering cross section by a surface-level experiment. These promising results, obtained using a very small-mass sensor, illustrate the potential of Skipper-CCDs to probe rare neutrino interactions and motivate the plans to increase the detector mass in the near future.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Linear point and sound horizon as purely geometric standard rulers

The baryon acoustic oscillations feature (BAO) imprinted in the clustering correlation function is known to furnish us cosmic distance determinations that are independent of the cosmological-background model and the primordial perturbation parameters. These measurements can be accomplished rigorously by means of the purely geometric BAO methods. To date two different purely geometric BAO approaches have been proposed. The first exploits the linear-point standard ruler. The second, called correlation-function model-fitting, exploits the sound-horizon standard ruler. A key difference between them is that, when estimated from clustering data, the linear point makes use of a cosmological-model-independent procedure to extract the ratio of the ruler to the cosmic distance, while the correlation-function model-fitting relies on a phenomenological cosmological model for the correlation function. Nevertheless the two rulers need to be precisely defined independently of any specific observable (e.g., the BAO). We define the linear point and sound horizon and we fully characterize and compare the two rulers’ cosmological-parameter dependence. We find that they are both geometrical (i.e., independent of the primordial cosmological parameters) within the required accuracy, and that they have the same parameter dependence for a wide range of parameter values. We estimate the rulers’ best-fit values and errors, given the cosmological constraints obtained by the Planck Satellite team from their measurements of the cosmic microwave background temperature and polarization anisotropies. We do this for three different cosmological models encompassed by the purely geometric BAO methods. In each case we find that the relative errors of the two rulers coincide and they are insensitive to the assumed cosmological model. Interestingly both the linear point and the sound horizon shift by 0.5σ when we do not fix the spatial geometry to be flat in Λ CDM. Finally, this points toward a sensitivity of the rulers to different cosmological models when they are estimated from the cosmic microwave background.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

New method for fitting coefficients in standard model effective theory

We present an alternative method for carrying out a principal-component analysis of Wilson coefficients in standard model effective field theory (SMEFT). The method is based on singular-value decomposition (SVD). The SVD method provides information about the sensitivity of experimental observables to physics beyond the standard model that is not accessible in the Fisher-information method. In principle, the SVD method can also have computational advantages over diagonalization of the Fisher information matrix. We demonstrate the SVD method by applying it to the dimension-6 coefficients for the process of top-quark decay to a b quark and a W boson and use this example to illustrate some pitfalls in widely used fitting procedures. We also outline an iterative procedure for applying the SVD method to dimension-8 SMEFT coefficients.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Direct CP violation and the ΔI=1/2 rule in K→ππ decay from the standard model

We present a lattice QCD calculation of the Δ I = 1 / 2 , K → π π decay amplitude A 0 and ϵ ' , the measure of direct C P violation in K → π π decay, improving our 2015 calculation [1] of these quantities. Both calculations were performed with physical kinematics on a 32 3 × 64 lattice with an inverse lattice spacing of a - 1 = 1.3784 ( 68 ) GeV . However, the current calculation includes nearly 4 times the statistics and numerous technical improvements allowing us to more reliably isolate the π π ground state and more accurately relate the lattice operators to those defined in the standard model. We find Re ( A 0 ) = 2.99 ( 0.32 ) ( 0.59 ) × 10 - 7 GeV and Im ( A 0 ) = - 6.98 ( 0.62 ) ( 1.44 ) × 10 - 11 GeV , where the errors are statistical and systematic, respectively. The former agrees well with the experimental result Re ( A 0 ) = 3.3201 ( 18 ) × 10 - 7 GeV . These results for A 0 can be combined with our earlier lattice calculation of A 2 [2] to obtain Re ( ϵ ' / ϵ ) = 21.7 ( 2.6 ) ( 6.2 ) ( 5.0 ) × 10 - 4 , where the third error represents omitted isospin breaking effects, and Re ( A 0 ) / Re ( A 2 ) = 19.9 ( 2.3 ) ( 4.4 ) . The first agrees well with the experimental result of Re ( ϵ ' / ϵ ) = 16.6 ( 2.3 ) × 10 - 4 . A comparison of the second with the observed ratio Re ( A 0 ) / Re ( A 2 ) = 22.45 ( 6 ) , demonstrates the standard model origin of this “ Δ I = 1 / 2 rule” enhancement.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Cosmological forecasts for future galaxy surveys with the linear point standard ruler: Toward consistent BAO analyses far from a fiducial cosmology

The linear point (LP) standard ruler was identified as the basis of a purely geometric method for exploiting the baryon acoustic oscillations (BAO). The LP exploits the BAO feature imprinted in the galaxy two-point correlation function to measure cosmological distances independent of any specific cosmological model. We forecast the expected precision of future and ongoing spectroscopic galaxy surveys to measure distances leveraging the linear point. We investigate the cosmological implications of our forecasted results. We focus in particular on a relevant working example: the detection of the late-time cosmic acceleration independent of other cosmological probes. Further, our findings show that, even within the Λ⁢CDM standard cosmological paradigm, estimated distances need to be reliable over a very wide parameter range in order to realize their maximum utility. This is particularly relevant if we aim to properly characterize cosmological tensions. The LP is a promising candidate approach to achieve this reliability. In contrast, widely employed procedures in BAO analysis estimate distances keeping fixed cosmological parameters to fiducial values close to cosmic-microwave-background constraints in flat-Λ⁢CDM. It is unclear whether they are purely geometric methods. Moreover, they rely on untested extrapolations to explore the parameter space away from those fiducial flat-Λ⁢CDM values. We recommend that all BAO methodologies be validated across the full range of models and parameters over which their results are quoted, first by means of linear predictions and then N -body simulations.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Converting Clinical Pathways to BPM+ Standards: A Case Study in Stable Ischemic Heart Disease

Clinical pathways (CPs) are structured healthcare plans designed to implement evidence-based clinical guidelines, medical algorithms, and protocols. In recent years, a community called BPM+ Health has worked to establish a shareable and computer-consumable representation of CP, leveraging standard notations. These notations, collectively referred to as BPM+, include the Business Process Management and Notation (BPMN), Case Management Model and Notation (CMMN), and Decision Model and Notation (DMN), which aim to support clinical management and standardized communication between different stakeholders. However, the adaptation of these notations for the existing guidelines has largely been left unexplored. This paper introduces procedural steps and criteria considerations to apply components of BPM+ notations to reconstruct a guideline for Stable Ischemic Heart Disease. This paper describes how each of the three different notations is mapped to a medical guideline and discusses the advantages and limitations of representing CPs with BPM+ as compared with paper-based medical guidelines.

Chae, Junghoon↗

DOE OSTI2021

Evolution of the IEEE P7009 Standard: Towards Fail-Safe Design of Autonomous Systems

Autonomous systems are complex, diverse, and likely be used in environments that change unpredictably. We must develop mechanisms to cope with failures, potentially caused by both the natural stresses of the operating environment and the system's inadequate environmental models. Failures also arise from system component wear. In 2016, the IEEE launched the Global Initiative on Ethics of Autonomous and Intelligent Systems in response to the proliferation of increasingly-autonomous systems. A cornerstone of this initiative is the IEEE P7000 series of projects, which set the standards for the future of ethical intelligent and autonomous technologies. This paper describes the ongoing development of the IEEE P7009 standard on “Fail-Safe Design of Autonomous and Semi-Autonomous Systems”. We provide a collective perspective on the ongoing development of IEEE P7009, and outline the objectives, current approaches, issues under discussion, and two exemplar use cases from different sectors: one high-regulation, the other low-regulation.

Farrell, Marie↗

DOE OSTI2023

Changes Required in the PMU standards

The Phasor Measurement Unit (PMU) is a representational measuring instrument that gives time-stamped measurements of the power system on the assumption that the measurand can be represented as sinusoidal. However, two standards defining the measured quantities unnecessarily corrupt the results and limit the capabilities of the PMU, and are beginning to tax communications systems. This paper examines the two mistakes in the PMU standards, and proposes a solution.

PMU measurement, phase, phasor, measurement theory↗

DOE OSTI2020

Versailles Project on Advanced Materials and Standards interlaboratory study on intensity calibration for x-ray photoelectron spectroscopy instruments using low-density polyethylene

We report the results of a Versailles Project on Advanced Materials and Standards interlaboratory study on the intensity scale calibration of x-ray photoelectron spectrometers using low-density polyethylene (LDPE) as an alternative material to gold, silver, and copper. An improved set of LDPE reference spectra, corrected for different instrument geometries using a quartz-monochromated Al Kα x-ray source, was developed using data provided by participants in this study. Using these new reference spectra, a transmission function was calculated for each dataset that participants provided. When compared to a similar calibration procedure using the NPL reference spectra for gold, the LDPE intensity calibration method achieves an absolute offset of ~3.0% and a systematic deviation of ±6.5% on average across all participants. For spectra recorded at high pass energies (≥90 eV), values of absolute offset and systematic deviation are ~5.8% and ±5.7%, respectively, whereas for spectra collected at lower pass energies (<90 eV), values of absolute offset and systematic deviation are ~4.9% and ±8.8%, respectively; low pass energy spectra perform worse than the global average, in terms of systematic deviations, due to diminished count rates and signal-to-noise ratio. Differences in absolute offset are attributed to the surface roughness of the LDPE induced by sample preparation. We further assess the usability of LDPE as a secondary reference material and comment on its performance in the presence of issues such as variable dark noise, x-ray warm up times, inaccuracy at low count rates, and underlying spectrometer problems. In response to participant feedback and the results of the study, we provide an updated LDPE intensity calibration protocol to address the issues highlighted in the interlaboratory study. Finally, we also comment on the lack of implementation of a consistent and traceable intensity calibration method across the community of x-ray photoelectron spectroscopy (XPS) users and, therefore, propose a route to achieving this with the assistance of instrument manufacturers, metrology laboratories, and experts leading to an international standard for XPS intensity scale calibration.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Binary pseudorandom array test standard optimized for characterization of large field-of-view optical interferometers

Recently, a technique for calibrating the modulation transfer function (MTF) of a broad variety of metrology instrumentation has been demonstrated. This technique is based on test samples structured as one-dimensional binary pseudo-random (BPR) sequences and two-dimensional BPR arrays (BPRAs). The inherent power spectral density of BPR gratings (sequences) and arrays has a deterministic white-noise-like character that allows direct determination of the MTF with uniform sensitivity over the entire spatial frequency range and field-of-view of an instrument. As such, the BPR samples satisfy the characteristics of a test standard: functionality, ease of specification and fabrication, reproducibility, and low sensitivity to manufacturing error. Here we discuss our recent developments directed to the optimization of the sample design, fabrication, application, and data processing procedures, suitable for thorough characterization of large aperture optical interferometers. Compared with the previous coded-aperture based design, the improved, 'highly randomized' BPRA pattern of the new test standard provides better accuracy and reliability of instrument MTF and aberration characterization, and enables operation optimization of large aperture optical interferometers. We describe the pattern generation algorithm and tests to verify the compliance to desired BPRA topography. The data acquisition and analysis procedures for different applications of the technique are also discussed.

Yashchuk, Valeriy V.↗