Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “information quality”

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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Improving White Dwarfs as Chronometers with Gaia Parallaxes and Spectroscopic Metallicities

White dwarfs (WDs) offer unrealized potential in solving two problems in astrophysics: stellar age accuracy and precision. WD cooling ages can be inferred from surface temperatures and radii, which can be constrained with precision by high-quality photometry and parallaxes. Accurate and precise Gaia parallaxes along with photometric surveys provide information to derive cooling and total ages for vast numbers of WDs. Here we analyze 1372 WDs found in wide binaries with main-sequence (MS) companions and report on the cooling and total age precision attainable in these WD+MS systems. The total age of a WD can be further constrained if its original metallicity is known because the MS lifetime depends on metallicity at fixed mass, yet metallicity is unavailable via spectroscopy of the WD. We show that incorporating spectroscopic metallicity constraints from 38 wide binary MS companions substantially decreases internal uncertainties in WD total ages compared to a uniform constraint. Averaged over the 38 stars in our sample, the total (internal) age uncertainty improves from 21.04% to 16.77% when incorporating the spectroscopic constraint. Higher mass WDs yield better total age precision; for eight WDs with zero-age MS masses ≥2.0 M ⊙ , the mean uncertainty in total ages improves from 8.61% to 4.54% when incorporating spectroscopic metallicities. We find that it is often possible to achieve 5% total age precision for WDs with progenitor masses above 2.0 M ⊙ if parallaxes with ≤1% precision and Pan-STARRS g, r, and i photometry with ≤0.01 mag precision are available.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

A Bayesian approach to evaluation of soil biogeochemical models

Abstract. To make predictions about the carbon cycling consequences of rising global surface temperatures, Earth system scientists rely on mathematical soil biogeochemical models (SBMs). However, it is not clear which models have better predictive accuracy, and a rigorous quantitative approach for comparing and validating the predictions has yet to be established. In this study, we present a Bayesian approach to SBM comparison that can be incorporated into a statistical model selection framework. We compared the fits of linear and nonlinear SBMs to soil respiration data compiled in a recent meta-analysis of soil warming field experiments. Fit quality was quantified using Bayesian goodness-of-fit metrics, including the widely applicable information criterion (WAIC) and leave-one-out cross validation (LOO). We found that the linear model generally outperformed the nonlinear model at fitting the meta-analysis data set. Both WAIC and LOO computed higher overfitting risk and effective numbers of parameters for the nonlinear model compared to the linear model, conditional on the data set. Goodness of fit for both models generally improved when they were initialized with lower and more realistic steady-state soil organic carbon densities. Still, testing whether linear models offer definitively superior predictive performance over nonlinear models on a global scale will require comparisons with additional site-specific data sets of suitable size and dimensionality. Such comparisons can build upon the approach defined in this study to make more rigorous statistical determinations about model accuracy while leveraging emerging data sets, such as those from long-term ecological research experiments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

AGC-4 Experiment Irradiation Monitoring Data Qualification Final Report

The Graphite Technology Development Program ran a series of six experiments to quantify the effects of irradiation on nuclear grade graphite. This report focuses on the fourth experiment, Advanced Graphite Creep 4 (AGC 4). The Advanced Reactor Development (ARD) Technology Development Office (TDO) Program for research and development activities require documentation of qualified monitoring data to design and license the first high-temperature reactor nuclear plant. Qualified data meets the requirements for use as described in the experiment planning and quality assurance documents. Failed data do not meet the requirements and provide no useable information. Trend data may not meet all requirements but still provide some useable information. Use of Trend data requires assessment of how any deficiencies affect a particular use of the data. AGC-4 began with Advanced Test Reactor (ATR) Cycle 157D on May 30, 2015. After irradiating the graphite for two cycles, the capsule was removed from the reactor after ATR Cycle 158A, which ended on January 2, 2016, due to interference with another experiment. Irradiation was resumed with Cycle 162A on October 7, 2017 after the interfering experiment was removed from the reactor. AGC-4 irradiation completed by the end of Cycle 166B on January 10, 2020. Between Cycles 162A and 166B, AGC-4 capsule was removed from the reactor core during two Powered Axial Locator Mechanism (PALM) Cycles 163A and 165A to avoid overheating. All thermocouples (TCs) have functioned throughout the AGC-4 experiment. A total of 9,256,184 out of all 11,167,213 temperature records (or 82.9%) are Qualified for use by the ARD Program and 1,911,029 missing values are Failed. Argon, helium, and total gas flow data were within expected ranges, except only eight out-of-range values occurred during outages. A total of 21,240,627 out of all 22,288,5103 gas flow rates (or 92.8%) are Qualified for use by the ARD Program and 1,644,476 are Failed records mostly due to missing values. Discharge gas line moisture values were consistently low during full ATR power, except for 162B, when moisture content was increasing to more than 200 ppmv by the end of this cycle. During outages, moisture content reached as high as 700 ppmv. 1,089,941 out of a total of 1,107,331 moisture values (or 98.4%) are within the measurement range of the instrument and are Qualified for use by the ARD Program and 17,390 missing moisture values are Failed. Graphite creep specimens were subjected to one of three loads: 393, 491, or 589 lbf. For a brief period during Cycle 157D between 12:19 on June 2, 2015, and 08:23 on June 11, 2015, the load cells were wired incorrectly, resulting in missing stack load data. Missing stack loads were estimated from measured ram pressures using regression equations developed from the existing data from Cycle 157D. Estimated stack loads during this period are considered to be an accurate representation of actual load applied to the stacks. These loads deviate slightly from the planned loads. This deviation does not prevent the data from being Qualified for use but must be taken into account when analyzing the effect of load on creep. 6,095,728 out of a total of 6,403,985 moisture values (or 95.2%) are within the measurement range of the instrument and are Qualified for use by the ARD Program and 308,257 missing load values are Failed. Stack displacement increased consistently throughout the eight cycles, with total displacement reached highest value of 2.4 in by the end of irradiation. During ATR outages, a set of pneumatic rams raised the stacks of graphite creep specimens to ensure the specimens were not stuck within the test train. This stack raising was performed seven times throughout irradiation. All stacks were raised successfully each time. 4,744,974 out of a total of 6,094,513 displacement values (or 77.9%) are within the measurement range of the instrument and are Qualified for use by the ARD Program and 1,349,539 displacement values are Failed mostly due to missing values. Analyses were conducted on correlations between TCs to look for trends and step changes that might indicate instrument degradation or failure. Correlation analysis was used to identify instances when TCs form short circuits, referred to as virtual junctions, which result in TCs reporting temperatures from some location in the capsule other than the location where they were intended to read. No evidence of virtual junctions was found. Analyses were also conducted on control charts of temperature differences of between two TCs, which are expected to behave consistently throughout the entire irradiation period. Upward or downward trend over time indicates at least one TC in the pair was drifted. Examining control charts for all 66 possible pairs out of twelve TCs installed in the AGC-4 capsules reveal no clear drift failures occurred, except unstable behavior of two TCs in Zone 3, TC-7 and TC-8, over irradiation time. In conclus

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Healthy Indoor Air Quality: A Guide to Understanding Pollutants in Extreme Cold Climates

Internal air quality management through commonly supported recommendations in extreme cold weather climates is complicated by cold air infiltration. Air filtration and IAQ monitoring, through central and stand-alone systems can improve internal air quality to the benefit of occupant health and safety. This fact sheet includes reference information for pollutants, sources, health effects, and mitigation strategies.

cold climate↗
DOE OSTI2023

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Abstract Motivation Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery. Results In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures. Availability and implementation The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A Risk-Informed Approach to Trustworthiness Assessment in Digital Twins-Based Autonomous Control

In autonomous control systems, digital twins (DTs) are used to perform diagnostic and prognostic functions. The trustworthiness of these DTs is dependent on quality and coverage of the training data, model accuracy and integrity of sensor data. This work introduces a methodology to determine the trustworthiness of a DT system given faulty sensor data using a risk informed approach. Bayesian Belief Networks (BBNs) are used to propagate uncertainties and determine the probability of trustable recommendations. The decision to trust the control action provided by the DT is based on the DT output, expert opinion, and severity of problems. The performance of DTs is reliant on the data they are trained on. When they encounter out of distribution data, the trustworthiness of the recommendations decreases. To address this issue, we include an expert component that provides input on sensor degradation. For this, we utilize a generative artificial intelligence (AI) model, such as Generative Pretrained Transformer (GPT). The GPT functions as an expert with broad knowledge. The GPT is fine-tuned to understand and discriminate sensor degradation scenarios using manufactured data. This methodology is demonstrated through a case study on a Nearly Autonomous Management and Control System (NAMAC) during a steady state scenario. Various sensor degradation types with different severity levels are considered. Degraded sensor data is processed by the DT system and the fine-tuned GPT. Finally, using the BBN, we combine the GPT information and the DT output with its sources of uncertainty. This provides an output regarding the trustworthiness of the DT recommendation.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2025

Lithography-Defined Semiconductor Moirés with Anomalous In-Gap Quantum Hall States

Quantum materials and phenomena have attracted great interest for their potential applications in next-generation microelectronics and quantum-information technologies. In one especially interesting class of quantum materials, moiré superlattices (MSLs) formed by twisted bilayers of 2D materials, a wide range of novel phenomena are observed. However, there exist daunting challenges such as reproducibility and scalability of utilizing 2D MSLs for microelectronics and quantum technologies due to their exfoliate-tear-stack method. Here, we propose lithography-defined semiconductor MSLs, in which three fundamental parameters electron−electron interaction, spin−orbit coupling, and band topology are designable. We experimentally investigate quantum-transport properties in a moiré specimen made in an InAs quantum well. Strong anomalous in-gap states are observed within the same integer quantum Hall state. Our work opens up new horizons for studying 2D quantum-materials phenomena in semiconductors featuring superior industry-level quality and state-of-the-art technologies, and they may potentially enable new quantum-information and microelectronics technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Nonlinear Multiobjective MPC-Based Optimal Operation of a High Consistency Refining System in Papermaking

As one of the most important unit in the papermaking industry, the high consistency (HC) refining system is confronted with challenges such as improving pulp quality, energy saving, and emissions reduction in its operation processes. Here in this correspondence, an optimal operation of HC refining system is presented using nonlinear multiobjective model predictive control strategies that aim at set-point tracking objective of pulp quality, economic objective, and specific energy (SE) consumption objective, respectively. First, a set of input and output data at different times are employed to construct the subprocess model of the state process model for the HC refining system, and then the Wiener-type model can be obtained through combining the mechanism model of Canadian Standard Freeness and the state process model that determines their structures based on Akaike information criterion. Second, the multiobjective optimization strategy that optimizes both the set-point tracking objective of pulp quality and SE consumption is proposed simultaneously, which uses NSGA-II approach to obtain the Pareto optimal set. Furthermore, targeting at the set-point tracking objective of pulp quality, economic objective, and SE consumption objective, the sequential quadratic programming method is utilized to produce the optimal predictive controllers. In conclusion, the simulation results demonstrate that the proposed methods can make the HC refining system provide a better performance of set-point tracking of pulp quality when these predictive controllers are employed. In addition, while the optimal predictive controllers orienting with comprehensive economic objective and SE consumption objective, it has been shown that they have significantly reduced the energy consumption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2021

Publication and Impact of Preprints Included in the First 100 Editions of the CDC COVID-19 Science Update: Content Analysis

Preprints are publicly available manuscripts posted to various servers that have not been peer reviewed. Although preprints have existed since 1961, they have gained increased popularity during the COVID-19 pandemic due to the need for immediate, relevant information. The aim of this study is to evaluate the publication rate and impact of preprints included in the Centers for Disease Control and Prevention (CDC) COVID-19 Science Update and assess the performance of the COVID-19 Science Update team in selecting impactful preprints. All preprints in the first 100 editions (April 1, 2020, to July 30, 2021) of the Science Update were included in the study. Preprints that were not published were categorized as “unpublished preprints.” Preprints that were subsequently published exist in 2 versions (in a peer-reviewed journal and on the original preprint server), which were analyzed separately and referred to as “peer-reviewed preprint” and “original preprint,” respectively. Time to publish was the time interval between the date on which a preprint was first posted and the date on which it was first available as a peer-reviewed article. Impact was quantified by Altmetric Attention Score and citation count for all available manuscripts on August 6, 2021. Preprints were analyzed by publication status, publication rate, preprint server, and time to publication. Of the 275 preprints included in the CDC COVID-19 Science Update during the study period, most came from three servers: medRxiv (n=201, 73.1%), bioRxiv (n=41, 14.9%), and SSRN (n=25, 9.1%), with 8 (2.9%) coming from other sources. Additionally, 152 (55.3%) were eventually published. The median time to publish was 2.3 (IQR 1.4-3.7). When preprints posted in the last 2.3 months were excluded (to account for the time to publish), the publication rate was 67.8%. Moreover, 76 journals published at least one preprint from the CDC COVID-19 Science Update, and 18 journals published at least three. The median Altmetric Attention Score for unpublished preprints (n=123, 44.7%) was 146 (IQR 22-552) with a median citation count of 2 (IQR 0-8); for original preprints (n=152, 55.2%), these values were 212 (IQR 22-1164) and 14 (IQR 2-40), respectively; for peer-review preprints, these values were 265 (IQR 29-1896) and 19 (IQR 3-101), respectively. Prior studies of COVID-19 preprints found publication rates between 5.4% and 21.1%. Preprints included in the CDC COVID-19 Science Update were published at a higher rate than overall COVID-19 preprints, and those that were ultimately published were published within months and received higher attention scores than unpublished preprints. These findings indicate that the Science Update process for selecting preprints had a high fidelity in terms of their likelihood to be published and their impact. The incorporation of high-quality preprints into the CDC COVID-19 Science Update improves this activity’s capacity to inform meaningful public health decision-making.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Electrical control of magnetism by electric field and current-induced torques

The remanent magnetization of ferromagnets has long been studied and used to store binary information. While early magnetic memory designs relied on magnetization switching by locally generated magnetic fields, key insights in condensed matter physics later suggested the possibility of doing it by electrical means instead. In the 1990s, Slonczewski and Berger formulated the concept of current-induced spin torques in magnetic multilayers through which a spin-polarized current generated by a first ferromagnet may be used to switch the magnetization of a second one. This discovery drove the development of spin-transfer-torque magnetic random-access memories (MRAMs). More recent fundamental research revealed other types of current-induced torques named spin-orbit torques (SOTs) and will lead to a new generation of devices including SOT MRAMs and skyrmion-based devices. Parallel to these advances, multiferroics and their magnetoelectric coupling, first investigated experimentally in the 1960s, experienced a renaissance. Dozens of multiferroic compounds with new magnetoelectric coupling mechanisms were discovered and high-quality multiferroic films were synthesized (notably of BiFeO 3 ), also leading to novel device concepts for information and communication technology such as the magnetoelectric spin-orbit (MESO) transistor. The story of the electrical switching of magnetization, which is discussed in this review, is that of a dance between fundamental research (in spintronics, condensed matter physics, and materials science) and technology (MRAMs, MESO transistors, microwave emitters, spin diodes, skyrmion-based devices, components for neuromorphics, etc.). This pas de deux has led to major scientific and technological breakthroughs in recent decades (such as the conceptualization of pure spin currents, the observation of magnetic skyrmions, and the discovery of spin-charge interconversion effects). As a result, this field has not only propelled MRAMs into consumer electronics products but also fueled discoveries in adjacent research areas such as ferroelectrics or magnonics. Here, in this review, recent advances in the control of magnetism by electric fields and by current-induced torques are covered. Fundamental concepts in these two directions are reviewed first, their combination is then discussed, and finally current various families of devices harnessing the electrical control of magnetic properties for various application fields are addressed. The review concludes by giving perspectives in terms of both emerging fundamental physics concepts and new directions in materials science.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A Robust Event Diagnostics Platform: Integrating Tensor Analytics and Machine Learning into Real-time Grid Monitoring

The objective of this project is to develop a robust event diagnostics (RED) platform by integrating state-of-the-art tensor analytics and machine learning into real-time grid monitoring. The proposed platform can effectively analyze and discover the information hiding within the provided PMU data for effective real-time grid monitoring. The proposed RED platform provides a set of robust diagnostics tools for grid operation and management, including 1) data quality assessment, 2) data completion, 3) event detection, and 4) robust event classification. All the functionalities of the RED platform can help the operator to make informed decisions and respond in a timely manner. The developed RED platform will serve as an innovative advisory tool to reliably identify key events and discover new insights about the events and grid characteristics in the PMU data, and contribute to the efficient, safe, reliable operation and design of the nation’s electric system.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Tantalum alloy–based resonators for quantum information systems

Utilizing tantalum (Ta) in superconducting circuits has led to significant improvements, such as high qubit lifetime (T 1 ) and quality factors in both qubits and resonators, suggesting that material optimization plays an important role in the development of superconducting circuits. Thus we here explore superconducting gap engineering in Ta-based devices as a powerful strategy for expanding the range of suitable host materials. By alloying 20 atomic percent (at.%) hafnium into Ta thin films, we achieve a superconducting transition temperature (T c ) of 6.09 K as observed in direct current (DC) transport measurements, reflecting an increase in the superconducting gap. We systematically vary deposition conditions to control film orientation and transport properties of Ta-Hf alloy thin films. We then confirm the enhancement in T c via microwave measurements at millikelvin temperatures. We verify the ~40 increase in T c relative to bare Ta devices, while the loss contributions from two-level systems and quasi-particles remain unchanged in the low temperature regime. These findings emphasize the promise of material engineering in superconducting circuits and point to many potential material candidates for further exploration.

Ta-Hf alloy thin films↗
DOE OSTI2020

Panel Session 68: Key EFCOG Actions: Risk Communication, Supply Chain Management, Human Capital and More

Overview on the Energy Facility Contractor Group's (EFCOG) most recent work in partnership with DOE to improve performance and EFCOG's mission is to ensure safety, security, and quality across the US DOE complex. Best practices were highlighted in discussions with US DOE/ NNSA leaders and key project executives. EFCOG's key priorities for 2020 were featured in the panel discussions to include: addressing human capital issues to ensure future mission needs can be met; addressing supply chain issues for nuclear projects; improving the data quality and performance assurance; and improving risk communication and stakeholder relations. EFCOG accomplishes its mission through working groups that provide forums to address common challenges and exchange proven techniques and other management and technical information among member contractors. Panelists with presentations: WM EFCOG Panel Slides (Morgan Smith); EFCOG DOE Supply Chain Initiative (SCI) - Enabling The DOE Mission - (Darrell Graddy); Data Quality and Performance Assurance (JD Dowell); Risk Communication - Different Events - Very Different Responses from the Community (Rick McLeod); Current State of Cybersecurity (Liz Porter)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

The Mira–Titan Universe – IV. High-precision power spectrum emulation

Modern cosmological surveys are delivering data sets characterized by unprecedented quality and statistical completeness; this trend is expected to continue in the future as new ground- and space-based surveys come online. In order to maximally extract cosmological information from these observations, matching theoretical predictions are needed. At low redshifts, the surveys probe the non-linear regime of structure formation where cosmological simulations are the primary means of obtaining the required information. The computational cost of sufficiently resolved large-volume simulations makes it prohibitive to run very large ensembles. Nevertheless, precision emulators built on a tractable number of high-quality simulations can be used to build very fast prediction schemes to enable a variety of cosmological inference studies. We have recently introduced the Mira–Titan Universe simulation suite designed to construct emulators for a range of cosmological probes. This gravity-only set of simulations covers the standard six cosmological parameters {ω m , ω b , σ 8 , $h, n_s, w_0$} and, in addition, includes massive neutrinos and a dynamical dark energy equation of state {ω ν , $w_a$}. In this paper, we present the final emulator for the matter power spectrum based on 111 cosmological simulations, each covering a (2.1 Gpc) 3 volume and evolving 3200 3 particles. In this work, an additional set of 1776 lower resolution simulations and TimeRG perturbation theory results for the power spectrum are used to cover scales straddling the linear to mildly non-linear regimes (maximum wavenumber $\textit{k}$ = 5 Mpc –1 ). The emulator provides predictions at the 2–3 percent level of accuracy over a wide range of cosmological parameters and is publicly released as part of this paper.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Improving Building Footprint Extraction Using NAIP and 3DEP Lidar Derived Features with Deep Learning

Accurate building footprint extraction is critical for applications ranging from population estimation to disaster management. Although optical imagery provides detailed spectral information, it often struggles with shadows, occlusions, and background clutter in dense urban environments. Lidar data, by contrast, offer precise elevation and structural attributes but face challenges such as variable point density and noise. This study integrates multispectral imagery from the U.S. Department of Agriculture (USDA) National Agriculture Imagery Program (NAIP) with lidar-derived feature height and intensity from the U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) to improve footprint extraction using a U-Net–based deep learning model. A six-band input stack (RGB, near-infrared, height, intensity) was developed, normalized, and tiled for training and evaluation against Microsoft Global Building Footprints (GBF). Results from the Houston, TX test site show that the six-band model achieved a precision of 0.86, recall of 0.88, F1 score of 0.87, and Intersection-over-Union (IoU) of 0.76, consistently outperforming four-band baselines by reducing false positives while maintaining sensitivity. Predictions on withheld Houston tiles confirmed strong within-region generalization, yielded a precision of 0.78, recall of 0.81, F1 score of 0.79, and IoU of 0.66. Qualitative analysis further revealed limitations stemming from both training label quality and vegetation–building confusion. These findings demonstrate the complementary value of integrating spectral and structural information for robust building footprint extraction and how domain adaptation strategies can be used to enhance cross-regional transferability.

Liu, Jung Kuan [United States Geological Survey (U↗
DOE OSTI2026

High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes

The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated “high” quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.

Acinetobacter baumannii↗
DOE OSTI2020

Data-guided Multi-Map variables for ensemble refinement of molecular movies

Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. In this study, the three-dimensional electron density of a protein, as it would be determined by cryo-EM or x-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work employs the recently developed Multi-Map methodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along the chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along the reaction coordinates derived from electron densities can capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein Data Bank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution density information coupled to comparatively large structural transitions. Practical considerations for probing the transitions between multiple intermediate density states are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

How deep to dig: effects of web-scraping search depth on hyperlink network analysis of environmental stewardship organizations

Abstract Social network analysis (SNA) tools and concepts are essential for addressing many environmental management and sustainability issues. One method to gather SNA data is to scrape them from environmental organizations’ websites. Web-based research can provide important opportunities to understand environmental governance and policy networks while potentially reducing costs and time when compared to traditional survey and interview methods. A key parameter is ‘search depth,’ i.e., how many connected pages within a website to search for information. Existing research uses a variety of depths and no best practices exist, undermining research quality and case study comparability. We therefore analyze how search depth affects SNA data collection among environmental organizations, if results vary when organizations have different objectives, and how search depth affects social network structure. We find that scraping to a depth of three captures the majority of relevant network data regardless of an organization’s focus. Stakeholder identification (i.e., who is in the network) may require less scraping, but this might under-represent network structure (i.e., who is connected). We also discuss how scraping web-pages of local programs of larger organizations may lead to uncertain results and how our work can combine with mixed methods approaches.

Sayles, Jesse S. (ORCID:0000000218378920)↗