Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Consensus”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)

Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their construction and maintenance demand substantial resources and necessitate substantial collaboration between domain experts, curators, and ontology experts. We present Dynamic Retrieval Augmented Generation of Ontologies using AI (DRAGON-AI), an ontology generation method employing Large Language Models (LLMs) and Retrieval Augmented Generation (RAG). DRAGON-AI can generate textual and logical ontology components, drawing from existing knowledge in multiple ontologies and unstructured text sources.We assessed performance of DRAGON-AI on de novo term construction across ten diverse ontologies, making use of extensive manual evaluation of results. Our method has high precision for relationship generation, but has slightly lower precision than from logic-based reasoning. Our method is also able to generate definitions deemed acceptable by expert evaluators, but these scored worse than human-authored definitions. Notably, evaluators with the highest level of confidence in a domain were better able to discern flaws in AI-generated definitions. We also demonstrated the ability of DRAGON-AI to incorporate natural language instructions in the form of GitHub issues.These findings suggest DRAGON-AI's potential to substantially aid the manual ontology construction process. However, our results also underscore the importance of having expert curators and ontology editors drive the ontology generation process.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2020

Microbiome definition re-visited: old concepts and new challenges

The field of microbiome research has evolved rapidly over the past few decades, and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term ‘microbiome’. Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and uture outlook. We propose a definition of microbiome based on the compact, clear and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota, and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Fidelity-preserving enhancement of ptychography with foundational text-to-image models

Ptychographic phase retrieval enables high-resolution imaging of complex samples but often suffers from artifacts such as grid pathology and multislice crosstalk, which degrade reconstructed images. We propose a plug-and-play (PnP) framework that integrates physics model-based phase retrieval with text-guided image editing using foundational diffusion models. By employing the alternating direction method of multipliers, our approach ensures consensus between data fidelity and artifact removal subproblems, maintaining physical consistency while enhancing image quality. Artifact removal is achieved using a text-guided diffusion image editing method (LEDITS++) with a pre-trained foundational diffusion model, allowing users to specify artifacts for removal in natural language. Demonstrations on simulated and experimental datasets show significant improvements in artifact suppression and structural fidelity, validated by metrics such as peak signal-to-noise ratio and diffraction pattern consistency. This work highlights the combination of text-guided generative models and model-based phase retrieval algorithms as a transferable and fidelity-preserving method for high-quality diffraction imaging.

image editing↗
DOE OSTI2023

Four principles to establish a universal virus taxonomy

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., “arboviruses”), infecting a certain type of host (e.g., “mycoviruses,” “bacteriophages”) or displaying specific pathogenicity (e.g., “human immunodeficiency viruses”), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Insights from a workplace SARS-CoV-2 specimen collection program, with genomes placed into global sequence phylogeny

In 2020, the Department of Energy established the National Virtual Biotechnology Laboratory (NVBL) to address key challenges associated with COVID-19. As part of that effort, Pacific Northwest National Laboratory (PNNL) established a capability to collect and analyze specimens from employees who self-reported symptoms consistent with the disease. During the spring and fall of 2021, 688 specimens were screened for SARS-CoV-2, with 64 (9.3%) testing positive using reverse-transcriptase quantitative PCR (RT-qPCR). Of these, 36 samples were released for research. All 36 positive samples released for research were sequenced and genotyped. Here, the relationship between patient age and viral load as measured by Ct values was measured and determined to be only weakly significant. Consensus sequences for each sample were placed into a global phylogeny and transmission dynamics were investigated, revealing that the closest relative for many samples was from outside of Washington state, indicating mixing of viral pools within geographic regions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

CovS inactivation reduces CovR promoter binding at diverse virulence factor encoding genes in group A Streptococcus

The control of virulence gene regulator (CovR), also called caspsule synthesis regulator (CsrR), is critical to how the major human pathogen group A Streptococcus fine-tunes virulence factor production. CovR phosphorylation (CovR~P) levels are determined by its cognate sensor kinase CovS, and functional abrogating mutations in CovS can occur in invasive GAS isolates leading to hypervirulence. Presently, the mechanism of CovR-DNA binding specificity is unclear, and the impact of CovS inactivation on global CovR binding has not been assessed. Thus, we performed CovR chromatin immunoprecipitation sequencing (ChIP-seq) analysis in the emm1 strain MGAS2221 and its CovS kinase deficient derivative strain 2221-CovS-E281A. We identified that CovR bound in the promoter regions of nearly all virulence factor encoding genes in the CovR regulon. Additionally, direct CovR binding was observed for numerous genes encoding proteins involved in amino acid metabolism, but we found limited direct CovR binding to genes encoding other transcriptional regulators. The consensus sequence AATRANAAAARVABTAAA was present in the promoters of genes directly regulated by CovR, and mutations of highly conserved positions within this motif relieved CovR repression of the hasA and MGAS2221_0187 promoters. Analysis of strain 2221-CovS-E281A revealed that binding of CovR at repressed, but not activated, promoters is highly dependent on CovR~P state. CovR repressed virulence factor encoding genes could be grouped dependent on how CovR~P dependent variation in DNA binding correlated with gene transcript levels. Taken together, the data show that CovR repression of virulence factor encoding genes is primarily direct in nature, involves binding to a newly-identified DNA binding motif, and is relieved by CovS inactivation. These data provide new mechanistic insights into one of the most important bacterial virulence regulators and allow for subsequent focused investigations into how CovR-DNA interaction at directly controlled promoters impacts GAS pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The measurement of muon $g-2$ at Fermilab

The Muon g - 2 Experiment at Fermilab (E989) was built to repeat and improve the previous E821 Experiment at Brookhaven National Laboratory (BNL), aiming to reduce the experimental error by a factor of 4 to the final accuracy of 140 parts per billion (ppb). On April 7th, 2021, the E989 collaboration published the first result based on the first year of data taking (Run-1), measuring a μ = 0.001 165 920 40(54) with a precision of 460 ppb. The measured value is consistent with the BNL measurement and strengthens the long-standing tension with the data-driven SM prediction to a combined discrepancy of 4.2σ. On the theory side, however, new efforts involving lattice-QCD techniques are starting to question the current consensus on the theoretical prediction, demanding new improvements on both the experimental and theoretical sides. The Muon g - 2 Experiment at Fermilab has now concluded its sixth and final year of data taking, and a new result based on the Run-2 and Run-3 data was published in August 2023. This paper briefly describes the Muon g - 2 Experiment at Fermilab and its current status.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

REopt Lite Geothermal Heat Pump Design Requirements

This document describes the design requirements for the geothermal heat pump (GHP) module being added to the existing REopt Lite web tool. This document describes the purpose, users, and functional requirements to which the modified web tool shall conform. This document will be revised, as required, throughout the development phase with consensus between the Department of Energy (DOE) Geothermal Technologies Office (GTO) and NREL. The GHP module will expand existing REopt Lite capabilities to include techno-economic optimization of GHP systems, either stand alone, or integrated with the other existing technology types, namely solar photovoltaics (PV), wind power, battery energy storage, thermal energy storage, combined hear and power (CHP), and absorption chiller. Included in this submission are links to the REopt Lite web tool and open-source Git-Hub page. The REopt Lite tool can also be accessed directly via the NREL Developer Network. A link is also provided for the REopt report that overviews the module's capabilities.

15 GEOTHERMAL ENERGY↗
DOE OSTI2025

Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces

These data are from Bandopadhyay et al., "Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces". This study aims to understand the soil microbial ecology along terrestrial-aquatic interfaces of a freshwater and estuarine region and how it relates to organic matter. We analyzed soil microbial (16S rRNA gene) and organic matter (Fourier-transform ion cyclotron resonance mass spectrometry, FTICR-MS) composition from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. This dataset includes 16S rRNA gene amplicon data (only processed file types included here) and organic matter composition from FTICR-MS data (raw and processed files included here) from upland (forested), transition (stressed forest), and wetland positions at three sites in each of the Lake Erie and Chesapeake Bay regions. These sites are part of the COMPASS-FME project (https://compass.pnnl.gov/FME/COMPASSFME). File formats and software needed to access files: 16S rRNA gene amplicon data: These files follow the format reported here https://ess-dive.gitbook.io/amplicon-sequencing-reporting-format#updates-in-v1.0.1. As per this format, there are four file types reported: 1. Taxon tables (also called sequence-by-sample or OTU (operational taxonomic unit)/ESV (exact sequence variant) tables) : available in a .txt file format and accessible using TextEdit or MS Excel. 2. Representative sequences (also called consensus sequences) : available in a .fasta format and accessible using TextEdit. 3. Sequencing metadata : available in a MS Excel workbook file format and CSV file format 4. Bioinformatic metadata : available in a MS Excel workbook file format and CSV file format FTICR-MS data: 1. Raw data converted to a processed file with intensities of the peaks in the given samples : available in a MS Excel CSV file format 2. Processed file used in analyses and visualizations (appended as icr_long_) : available in a MS Excel CSV file format 3. Metadata file for ICR features (appended as icr_meta) : available in a MS Excel CSV file format

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Changes in short- and medium-range order in metallic liquids during undercooling

It has been widely speculated that dominant motifs, such as short-range icosahedral order, can influence glass formation and the properties of glasses. Experimental data on both fragile and strong undercooled liquids demonstrate corresponding changes in their thermophysical properties consistent with increasing development of a network of interconnect motifs based on molecular dynamics. Describing these regions of local order, how they connect, and how they are related to property changes have been challenging issues, both computationally and experimentally. Yet the consensus is that metallic liquids develop interconnected medium-range order consisting of some regions with lower mobility with deeper undercooling. Less well understood is how these motifs (or “crystal genes”) in the liquid can inhibit nucleation in the deeply undercooled liquid or influence phase selection upon devitrification. These motifs tend to have local packing unlike stable compounds with icosahedral order tending to dominate the best glass formers. The underlying kinetic and thermodynamic forces that guide the formation of these motifs and how they interconnect during undercooling remain open questions.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Do solar panels contain PFAS?

The presence and potential leaching of PFAS (Per- and Polyfluoroalkyl Substances) from solar panels are increasingly mentioned in news articles, raising public concerns. Such concerns may slow the adoption of photovoltaic (PV) technology, despite its central role in the renewable energy sector. The limited transparency from manufacturers about fluorinated materials used in PV modules, along with the scarcity of publicly available testing data, contributes to uncertainty and speculation. This perspective aims to clarify the current state of PFAS presence in solar PV. Although certain fluoropolymers are used in PV manufacturing, the scientific consensus on their toxicity indicates they should not be classified as PFAS. Portraying fluoropolymers as toxic PFAS unnecessarily amplifies concerns and unfairly undermines the perceived environmental sustainability of PV technology.

environmental impact↗
DOE OSTI2020

Challenges and Opportunities in Turning Large U.S. Archives of Analog Seismograms into a Modern Usable Resource

Abstract Quantitative seismology is based firmly on the analysis of actual ground motions, and the transition to digital recording in the 1980s enabled sophisticated new capabilities to extract useful results from waveforms. With some effort, these tools can also be applied to analog records. Focusing on assets available within U.S. institutions, we review the necessary steps and the challenges in enabling “data rescue”—that is, preserving the scientific information latent in large analog seismogram archives and making it usable. They include: determining what assets are available (the analog seismogram archives held by various institutions, with associated metadata on instrument responses, station locations, and timing information); developing a consensus on the top level of a triage process (which analog records most definitely should be rescued?); deciding the level of quality needed in copying original seismograms to media suitable for digitizing; assessing the relative merits of scanning and digitizing; and, the need for a community service in distributing scans and digital records, as they accumulate. The necessary level of effort can benefit from practical experience. For example, specific studies have used digitized versions of analog recordings to model earthquake sources and assess seismic hazard. Other studies have used them to gain experience with nuclear explosion signals recorded at regional distances, noting that regional signals enable explosions to be monitored down to levels much lower than those attainable teleseismically. The opportunities presented by large archives of analog seismograms include the insights they present to current and future seismologists studying earthquakes and explosions, into the practical areas of assessing seismic hazard, monitoring for test ban compliance down to low explosion yields—and prompt characterization of actual explosions should they occur, as well the traditional academic pursuit of a better understanding of earthquake physics.

Geochemistry & Geophysics↗
DOE OSTI2023

Origins of quench in buffered chemical polished and low temperature baked SRF cavities

Electropolishing (EP) and buffered chemical polishing (BCP) are conventional surface preparation techniques for superconducting radiofrequency (SRF) cavities that remove damaged material from the cavity surface. One main issue with EP and BCP treated SRF cavities is high field Q-slope (HFQS), a drop in quality factor at high gradients that limits quench field. High gradient performance in EP cavities can be improved by applying a low temperature bake (LTB), but LTB does not consistently remove HFQS in BCP cavities. There is no consensus as to the why LTB is not effective on BCP prepared cavities, and the cause of HFQS in BCP cavities is not well understood. We examine the origins of quench in EP, BCP, EP+LTB, and BCP+LTB treated SRF cavities. We also show the effect of these treatments on the onset of HFQS, heating within the cavity up to quench, concentration of free hydrogen, and surface roughness.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Design of a PIP-II Era Mu2e Experiment

We propose a design of an upgraded Mu2e experiment for the future Fermilab PIP-II era based on the muon collider front end. The consensus is that such an upgrade should provide a factor of 10 increase in the rate of stopping muons in the experimental target. The current Mu2e design is optimized for 8 kW of protons at 8 GeV. The PIP-II upgrade project is a 250-meter-long CW linac capable of accelerating a 2-mA proton beam to a kinetic energy of 800 MeV (total power 1.6 MW). This would significantly improve the Fermilab proton source to enable next-generation intensity frontier experiments. But using this 800 MeV beam poses challenges to the Mu2E experiment. Bright muon beams generated from sources designed for muon collider and neutrino factory facilities have been shown to generate two orders of magnitude more muons per proton than the current Mu2e production target and solenoid. In contrast to the current Mu2e, the muon collider design has forward-production of muons from the target.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Comparing the Effectiveness of Low Temperature Bake in EP and BCP Cavities

Electropolishing (EP) and buffered chemical polishing (BCP) are conventional surface preparation techniques for superconducting radiofrequency (SRF) cavities. Both EP and BCP treated SRF cavities display high field Q-slope (HFQS) which degrades performance at high gradients. While high gradient performance in EP cavities can be improved by introducing oxygen via a low temperature bake (LTB) of 120^{°}C by 48 hours, LTB does not consistently remove HFQS in BCP cavities. There is no consensus as to why LTB is not effective on BCP prepared cavities. We examine quench in EP, BCP, EP+LTB, and BCP+LTB treated 1.3 GHz single-cell Nb cavities by studying the heating behavior with field using a temperature mapping system. Cavity performance is correlated to characterizations of surface impurity profile obtained via time of flight secondary ion mass spectrometry studies. We observe a difference in near surface hydrogen concentration following BCP compared to EP that may suggest that the causes of quench in EP and BCP cavities are different.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Four no-go theorems on the existence of spin and orbital angular momentum of massless bosons

The past decades have seen substantial interest in the so-called orbital angular momentum (OAM) of light, driven largely by its diverse range of applications. However, there are fundamental theoretical issues with decomposing the angular momentum of massless particles, such as photons, into spin (SAM) and orbital angular momentum parts. While the angular momentum of massive particles has a natural splitting into the Wigner SAM and OAM, there are numerous proposed splittings for photons and no consensus about which is correct. Moreover, it has been shown that most of the proposed SAM and OAM operators do not satisfy the defining commutation relations of angular momentum operators and are thus not legitimate splittings. Here, we prove that it is generally impossible to split the total angular momentum operator of massless bosons, such as photons and gravitons, into spin and orbital parts. We prove two further generalizations of this result, showing that there are no SAM-OAM splittings even if (1) the SAM operator generates non-internal symmetries or (2) if one allows the SAM and OAM operators to generate non-SO(3) symmetries.

Chern numbers↗
DOE OSTI2021

Evaluation of the Large-Scale and Regional Climatic Response Across North Africa to Natural Variability in Oceanic Modes and Terrestrial Vegetation Among the CMIP5 Models

Hydrologic variability is a serious threat to the poverty-stricken regions of North Africa. Meanwhile, the scientific community struggles to attribute these extreme climatic episodes to specific oceanic and land drivers. Prior modeling studies have not assessed simulated feedbacks over North Africa against an established observational benchmark, so their results are considered as untested, model-specific findings. The Coupled Model Intercomparison Project Phase Five (CMIP5) archive represents the state-of-the-art in climate projections, with most CMIP5 models now containing interactive vegetation phenology; however, there have been no studies to date of their simulated vegetation feedbacks. The capability of CMIP5 models at accurately simulating the forcing of both sea-surface temperature (SST) and regional leaf area index (LAI) anomalies on North African climate needs to be a key consideration in assessing the models’ overall credibility and determining appropriate model weighting for developing climate projections. The Generalized Equilibrium Feedback Assessment (GEFA) is a promising statistical method, which can be applied to either model output or observations, for isolating the local and remote impacts of individual oceanic or terrestrial forcings on regional climate. We performed a combined observational and modeling assessment of land-ocean-atmosphere interactions across the distinct ecological and moisture gradients of North Africa. We evaluated and demonstrated the reliability of the GEFA statistical method over North Africa using the Community Earth System Model (CESM), applied GEFA to observational data to quantify the observed forcing of ocean basin SST anomalies and regional LAI anomalies on North African climate, evaluated the CMIP5 models’ performance in terms of representing these key observed feedbacks, and formulated CMIP5 feedback performance metrics for weighting North African climate projections. Our study represented the first attempt to separate the observed roles of oceanic and vegetation feedbacks across North Africa, the first systematic assessment and intercomparison of land-ocean-atmosphere feedbacks in CMIP5, and the first exploration of vegetation feedbacks among CMIP5 models. The following work was accomplished. (1) The team generated 14 scientific publications and 30 presentations based on the DOE-funded research. (2) A stepwise version of the GEFA statistical method was developed in which unimportant forcings were dropped to increase the reliability of the results. (3) SGEFA was successfully validated through experiments with CESM in terms of its ability to isolate the atmospheric responses to individual oceanic or land forcings. (4) Observational evidence was revealed for the Sahel’s positive vegetation-rainfall feedback on the seasonal to interannual time scale, and it was attributed to a moisture recycling mechanism rather than an albedo mechanism. (5) An approach with SGEFA was developed in which the individual contributions of soil moisture versus vegetation forcings could be separated, revealing that the former forcing outweighed the latter for sub-Saharan Africa. (6) Tropical ocean temperatures were found to be key regulators of pan-tropical vegetation variability, especially for arid and semi-arid regions, including sub-Saharan Africa. (7) The CMIP5 models largely underestimated the importance of land feedbacks across the Sahel. (8) The general consensus among CMIP5 models indicates, for the late 21st century, a diminished seasonal predictability of sub-Saharan African regional climate and an elevated role of the land surface compared to oceanic drivers in regulating regional climate variability. (9) Land-ocean-atmosphere interactions were demonstrated to be key contributors to the seasonal predictability of African wildfire activity. (10) The El Djouf was determined to be of greater importance than the Bodélé depression in terms of providing trans-Atlantic dust transport to the Americas.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Clustering Analysis of Commercial Vehicles Using Automatically Extracted Features from Time Series Data

Standard of practice approaches to time series cluster analysis involve careful feature engineering, often utilizing expert input to tune and select features by hand. In many cases, expert input may not be readily available, or there may not yet exist a community consensus on the ideal features for a given application. This paper compares the results of several cluster analysis methods, using both hand selected features and those extracted automatically, when applied to large geospatial time series telematics data from commercial trucking fleets. The impacts of feature selection, dimensionality reduction, and choice of clustering algorithm on the quality of clustering results are explored. Results from this analysis confirm prior results that domain agnostic features are competitive with the hand engineered features with respect to clustering quality metrics. These results also provide new insight into the most successful strategies for identifying structure in large unstructured vehicle telematics data, and suggest that time series clustering using automatic feature extraction can be an effective approach to extract structure from large scale geospatial time series data in cases when hand selected features are not available.

33 ADVANCED PROPULSION SYSTEMS↗