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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.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections

Co-infections or secondary infections with SARS-CoV-2 have the potential to affect disease severity and morbidity. Additionally, the potential influence of the nasal microbiome on COVID-19 illness is not well understood. In this study, we analyzed 203 residual samples, originally submitted for SARS-CoV-2 testing, for the presence of viral, bacterial, and fungal pathogens and non-pathogens using a comprehensive microarray technology, the Lawrence Livermore Microbial Detection Array (LLMDA). Eighty-seven percent of the samples were nasopharyngeal samples, and 23% of the samples were oral, nasal and oral pharyngeal swabs. We conducted bioinformatics analyses to examine differences in microbial populations of these samples, as a proxy for the nasal and oral microbiome, from SARS-CoV-2 positive and negative specimens. We found 91% concordance with the LLMDA relative to a diagnostic RT-qPCR assay for detection of SARS-CoV-2. Sixteen percent of all the samples (32/203) revealed the presence of an opportunistic bacterial or frank viral pathogen with the potential to cause co-infections. The two most detected bacteria, Streptococcus pyogenes and Streptococcus pneumoniae , were present in both SARS-CoV-2 positive and negative samples. Human metapneumovirus was the most prevalent viral pathogen in the SARS-CoV-2 negative samples. Sequence analysis of 16S rRNA was also conducted to evaluate bacterial diversity and confirm LLMDA results.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A Comprehensive Study of the Impact of Inverter-Based Resource (IBR) Modeling and Control on Protection Relay Elements

Inverter-based resources (IBRs) exhibit fault responses that differ significantly from those of synchronous generators, which can challenge the reliable operation of many commonly used power system protection elements. The fault response of IBRs is primarily influenced by their control algorithms and configurations, but the impact of these controls on protection relays is not yet fully understood. This presentation provides a comprehensive study of how IBR modeling and controls affect transmission line protection. Key modeling and control aspects include the DC source, inverter model, power level control, current control, and current limiting. The study reveals that certain aspects - such as the type of DC source (battery, PV, or hybrid), inverter model (average vs. switching), and power level control methods (PQ dispatch vs. Vdc-Vac control for grid-following IBRs, and droop vs. VSM for grid-forming IBRs) - do not significantly affect relay response. However, faster control loops, such as current control and current limiting, do influence the relay behavior. Additionally, the study explores the effects of other factors, including momentary cessation, operating points, fast/slow current responses, and grid strength on relay performance. Finally, the study offers recommendations for both IBR and protection engineers to improve IBR fault response and enhance the reliability of protection systems.

14 SOLAR ENERGY↗
DOE OSTI2026

Evaluation of a Reduced-Order Model for IBR Fault Response Representation via OEM Blackbox Models: Preprint

Driven by the need to capture the electromagnetic transients of transmission lines, inverter switching behavior, and detailed control systems, electromagnetic transient (EMT) studies have become increasingly important in industry, such as IBR interconnection study and fault study. However, original equipment manufacturer (OEM) inverter models typically include extensive parameters and proprietary settings that are unavailable to protection engineers. This paper introduces a data-driven, reduced-order model (ROM) developed as a PSCAD library component for use in EMT-based fault studies. The ROM replicates key OEM model behaviors without requiring detailed knowledge of control design or parameterization. The accompanying Python automation scripts streamline data generation, parameter fitting, and validation. The ROM's performance is demonstrated through comparison with both IEEE 2800-compliant and non-compliant OEM models in a real-world power system. Relay responses show nearly identical results, while simulation runtime is reduced by an average of 32.8\%, highlighting the ROM's practicality for protection engineers.

14 SOLAR ENERGY↗
DOE OSTI2022

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Impact of K-factor on Short Circuit Program Convergence for Inverter-Based Resources during Faults

Classical short-circuit programs that linearize the power network are no longer applicable for inverter based resources (IBRs), necessitating an iterative approach. Phasor domain programs can model the IBRs using an iterative approach considering nonlinear fault responses. In phasor domain models, the IBR can be modeled as a voltage controlled current source (VCCS) in tabular form with positive, negative, and zero sequence information for balanced and unbalance short-circuit faults. In the VCCS modeling of the IBR, positive and negative incremental reactive current, also known as the k-factor, plays an important role in short circuit program convergence. In this work, a few approaches: conventional VCCS modeling with a k-factor of 2, conventional VCCS modeling with a k-factor of 2 with modified pre-fault voltages, VCCS characteristics based on the power flow solution with a k-factor of 2, and VCCS characteristics based on the power flow solution with a k-factor of 1 are investigated for short circuit program convergence under higher IBR penetration. The IEEE 39 bus New England Test System is taken as the test system, and simulations are carried out in PSS®CAPE 15.0.26 simulation software. Simulation results demonstrate that IBR penetration is higher for the VCCS model, which corresponds to the power flow solution with k-factor 1, compared to other approaches.

42 ENGINEERING↗
DOE OSTI2020

Identifying sequence perturbations to an intrinsically disordered protein that determine its phase-separation behavior

Phase separation of intrinsically disordered proteins (IDPs) commonly underlies the formation of membraneless organelles, which compartmentalize molecules intracellularly in the absence of a lipid membrane. Identifying the protein sequence features responsible for IDP phase separation is critical for understanding physiological roles and pathological consequences of biomolecular condensation, as well as for harnessing phase separation for applications in bioinspired materials design. To expand our knowledge of sequence determinants of IDP phase separation, we characterized variants of the intrinsically disordered RGG domain from LAF-1, a model protein involved in phase separation and a key component of P granules. Based on a predictive coarse-grained IDP model, we identified a region of the RGG domain that has high contact probability and is highly conserved between species; deletion of this region significantly disrupts phase separation in vitro and in vivo. We determined the effects of charge patterning on phase behavior through sequence shuffling. We designed sequences with significantly increased phase separation propensity by shuffling the wild-type sequence, which contains well-mixed charged residues, to increase charge segregation. This result indicates the natural sequence is under negative selection to moderate this mode of interaction. We measured the contributions of tyrosine and arginine residues to phase separation experimentally through mutagenesis studies and computationally through direct interrogation of different modes of interaction using all-atom simulations. Finally, we show that despite these sequence perturbations, the RGG-derived condensates remain liquid-like. Together, these studies advance our fundamental understanding of key biophysical principles and sequence features important to phase separation.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Development and validation of a next-generation sequencing-based multigene assay to predict the prognosis of estrogen receptor-positive, HER2-negative breast cancer

Purpose: Multigene assays provide useful prognostic information regarding hormone receptor (HR)-positive breast cancer. Next-generation sequencing (NGS)-based platforms have numerous advantages including reproducibility and adaptability in local laboratories. Here we aimed to develop and validate an NGS-based multigene assay to predict the distant recurrence risk. Experimental Design: In total, 179 genes including 30 reference genes highly correlated with the 21-gene recurrence score (RS) algorithm were selected from public databases. Targeted RNA-sequencing was performed using 250 and 93 archived breast cancer samples with a known RS in the training and verification sets, respectively, to develop the algorithm and NGS–Prognostic Score (NGS-PS). The assay was validated in 413 independent samples with long-term follow-up data on distant metastasis. Results: In the verification set, the NGS-PS and 21-gene RS displayed 91.4% concurrence (85/93 samples). In the validation cohort of 413 samples, area under the receiver operating characteristic curve plotted using NGS-PS values classified for distant recurrence was 0.76. The best NGS-PS cut-off value predicting distant metastasis was 20. Furthermore, 269 and 144 patients were classified as low- and high-risk patients in accordance with the cut-off. Five- and 10-year estimates of distant metastasis–free survival (DMFS) for low- versus high-risk groups were 97.0% versus 77.8% and 93.2% versus 64.4%, respectively. The age-related HR for distant recurrence without chemotherapy was 9.73 (95% CI, 3.59–26.40) and 3.19 (95% CI, 1.40–7.29) for patients aged ≤50 and >50 years, respectively. Conclusions: The newly developed and validated NGS-based multigene assay can predict the distant recurrence risk in ER-positive, HER2-negative breast cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Hidden Markov Model: a shortest unique representative approach to detect the protein toxins, virulence factors and antibiotic resistance genes

Objective: Currently, next generation sequencing (NGS) is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. However, the efficient identification of novel or diverged pathogenomic compositions remains a big challenge. It is especially true for short DNA sequence fragments from NGS, since sequence similarity searching is vulnerable to false negatives or false positives, as is mismatching or matching with unrelated proteins. Therefore, this study aimed to establish a bioinformatics approach that can generate unique motif sequences for profiling searching, resulting in high specificity and sensitivity. Results: In this study, we introduced a Shortest Unique Representative Hidden Markov Model (HMM) approach to identify bacterial toxin, virulence factor (VF), and antimicrobial resistance (AR) in short sequence reads. We first construct unique representative domain sequences of toxin genes, VFs, and ARs to avoid potential false positives, and then to use HMM models to accurately identify potential toxin, VF, and AR fragments. The benchmark shows this approach can achieve relatively high specificity and sensitivity if the appropriate cutoff value is applied. Our approach can be used to recognize the protein sequences of known toxins and pathogens, identifies their common characteristics and then searches for similar sequences in other organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Suppression of Richtmyer-Meshkov Instability via Special Pairs of Shocks and Phase Transitions

The classical Richtmyer-Meshkov instability (RMI) is a hydrodynamic instability characterizing the evolution of an interface following shock loading. In contrast to other hydrodynamic instabilities such as Rayleigh-Taylor, it is known for being unconditionally unstable: regardless of the direction of shock passage, any deviations from a flat interface will be amplified. In this article, we show that for negative Atwood numbers, there exist special sequences of shocks which result in a nearly perfectly suppressed instability growth. Here, we demonstrate this principle computationally and experimentally with stepped fliers and phase transition materials. A fascinating immediate corollary is that in specific instances, a phase-transitioning material may self-suppress RMI.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Post-compression of long-wave infrared 2 picosecond sub-terawatt pulses in bulk materials

We have experimentally demonstrated the post-compression of a long-wave infrared (9.2 μm) 150 GW peak power pulse from 2 ps to less than 500 fs using a sequence of two bulk materials with negative group velocity dispersion (GVD). The compression resulted in up to 1.6-fold increase of the peak power and up to 2.8-fold increase of the intensity in the center of a quasi-Gaussian beam. The partial decoupling of the self-phase modulation and chirp compensation stages by using two materials with significantly different ratios of nonlinear refractive index to GVD provides accurate optimization of the compression mechanism and promises a viable path to scaling peak powers to supra-terawatt levels. During the preparatory study, we measured, for the first time to our knowledge, the nonlinear refractive indices of NaCl, KCl, and BaF 2 for picosecond pulses in the long-wave infrared region.

43 PARTICLE ACCELERATORS↗
DOE OSTI2026

Origin of replication discovery for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products

Leveraging predicted origin sequences from a previously characterized groundwater plasmidome, we constructed a barcoded plasmid library to screen for previously unknown origins. Testing this library against a panel of representative bacterial strains led to the identification of 3 previously unknown origins that replicate in gram-negative bacteria not previously associated with these origin sequences. Experimental validation confirmed that a plasmid bearing origin 6911 as the sole origin could replicate with a copy number of 9 (±2) in Pantoea sp. MT58, a fast growing and metal tolerant, environmentally important bacterium. Plasmids based on this new origin were used to express the reporter protein GFP, and non-native metabolite pathways for the natural product indigoidine and the terpenoid compound isoprenol. Functional previously unknown origins of replication in such non-model organisms can expand the toolkit for genetic manipulations of both model and less-studied bacteria.

molecular biology↗
DOE OSTI2020

A robust benchmark for detection of germline large deletions and insertions

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Stacked filters: learning to filter by structure

We present Stacked Filters, a new probabilistic filter which is fast and robust similar to query-agnostic filters (such as Bloom and Cuckoo filters), and at the same time brings low false positive rates and sizes similar to classifier-based filters (such as Learned Filters). The core idea is that Stacked Filters incorporate workload knowledge about frequently queried non-existing values. Instead of learning, they structurally incorporate that knowledge using hashing and several sequenced filter layers, indexing both data and frequent negatives. Stacked Filters can also gather workload knowledge on-the-fly and adaptively build the filter. We show experimentally that for a given memory budget, Stacked Filters achieve end-to-end query throughput up to 130x better than the best alternative for a workload, either query-agnostic or classifier-based filters, and depending on where data is (SSD or HDD).

Computer Science↗
DOE OSTI2021

Nanosecond isomers and the evolution of collectivity in stable, even- A Hg isotopes

Isomeric states and associated collective structures have been studied up to high spin in 198,200,202 Hg using multinucleon transfer reactions and the Gammasphere array. A coupled rotational band, with possible four-quasiparticle character, is established in 198 Hg. Sequences built on two-quasiparticle, positive- and negative-parity levels are assigned to 202 Hg. New isomers in 202 Hg with I π = (7 – ) and (9 – ), and T 1/2 = 10.4(4) ns and 1.4(3) ns, respectively, have been identified. A half-life of 1.0(3) ns is established for the I π = 12 + state in 200 Hg. B(E2) values deduced from isomeric transitions in Hg isotopes indicate that, while collectivity near the ground state gradually diminishes from N = 112 to N = 124, it is found to increase for the 12 + and 9 – states up to N = 118, followed by a reduction for higher neutron numbers. Calculations using the ultimate cranker code provide insight into the variation of deformation with spin and allow for an understanding of observed band crossings. As a result, the evolution of collectivity with spin, and along the isotopic chain, is described.

190 ≤ A ≤ 219↗
DOE OSTI2025

On resistive interchange, double tearing, and resonant and non-resonant infernal modes in spherical tokamak negative central shear discharges

We examine the linear and nonlinear stability of a sequence of reversed shear NSTX equilibria with the same toroidal current density and pressure profile but with different toroidal field strengths. All equilibria have two q = 2 surfaces and have q > 1 everywhere. For this sequence, which all have β P ∼ 0.5, as the minimum value of q decreases below about 1.4, the localized resistive interchange criterion is strongly violated, and the unstable mode with toroidal mode number n=1 changes its dominant poloidal mode number m from a (m,n)=(2,1) double tearing mode to a non-resonant (1,1) infernal mode. This (1,1) mode nonlinearly flattens both the current density and the pressure near the magnetic axis. The higher-n unstable modes are all resistive infernal modes localized around the surface where q has a minimum and the magnetic shear vanishes. They generally saturate nonlinearly at low amplitude but can cause magnetic surface breakup near the axis.

Spitzer resistivity↗
DOE OSTI2023

Case report: Fatal Legionella infection diagnosed via by metagenomic next-generation sequencing in a patient with chronic myeloid leukemia

Legionella is an aerobic, gram-negative, intracellular pathogen and is an important cause of community-acquired pneumonia. Legionella pneumophila is the most common causative agent of Legionella pneumonia. Clinical diagnosis of Legionella pneumonia is challenging due to the lack of specific clinical manifestations and the low positive rates of conventional pathogen detection methods. In this study, we report a case of a patient with chronic myeloid leukemia who developed rigors and high fever after chemotherapy and immunotherapy. Chest computed tomography revealed consolidation in the left lower lobe of the lung and ground-glass opacities in both lower lobes. Multiple blood cultures showed Escherichia coli , Staphylococcus aureus , Bacillus licheniformis , and positive results in the β-D-glucan test (G test). The patient was treated with various sensitive antimicrobial agents, including meropenem plus fluconazole, meropenem plus carpofungin, and vancomycin. Unfortunately, the patient’s condition gradually worsened and eventually resulted in death. On the following day of death, metagenomic next-generation sequencing (mNGS) of 1whole blood revealed L. pneumophila pneumonia with concurrent bloodstream infection (blood mNGS reads 114,302). These findings suggest that when conventional empirical antimicrobial therapy proves ineffective for critically ill patients with pneumonia, the possibility of combined Legionella infection must be considered, and mNGS can provide a diagnostic tool in such cases.

Bu, Chunhong↗
DOE OSTI2024

Stress Testing California's Hydroclimatic Whiplash: Potential Challenges, Trade‐Offs and Adaptations in Water Management and Hydropower Generation

Abstract Inter‐annual precipitation in California is highly variable, and future projections indicate an increase in the intensity and frequency of hydroclimatic “whiplash.” Understanding the implications of these shocks on California's water system and its degree of resiliency is critical from a planning perspective. Therefore, we quantify the resilience of reservoir services provided by water and hydropower systems in four basins in the western Sierra Nevada. Using downscaled runoff from 10 climate model outputs, we generated 200 synthetic hydrologic whiplash sequences of alternating dry and wet years to represent a wide range of extremes and transitional conditions used as inputs to a water system simulation model. Sequences were derived from upper (wet) and lower (dry) quintiles of future streamflow projections (2030–2060). Results show that carryover storage was negatively affected in all basins, particularly in those with lower storage capacity. All basins experienced negative impacts on hydropower generation, with losses ranging from 5% to nearly 90%. Reservoir sizes and inflexible operating rules are a particular challenge for flood control, as in extremely wet years spillage averaged nearly the annual basins' total discharge. The reliability of environmental flows and agricultural deliveries varied depending on the basin, intensity, and duration of whiplash sequences. Overall, wet years temporarily rebound negative drought effects, and greater storage capacity results in higher reliability and resiliency, and lesser volatility in services. We highlight potential policy changes to improve flexibility, increase resilience, and better equip managers to face challenges posed by whiplash while meeting human and environmental needs.

Environmental Sciences & Ecology↗
DOE OSTI2020

Boron and Lithium in Calcium Sulfate Veins: Tracking Precipitation of Diagenetic Materials in Vera Rubin Ridge, Gale Crater

The NASA Curiosity rover's ChemCam instrument suite has detected boron in calcium-sulfate-filled fractures throughout the sedimentary strata of Gale crater including Vera Rubin ridge. The presence of elevated B concentration provides insights into Martian subsurface aqueous processes. Here, we extend the data set of B in Ca-sulfate veins across Gale crater, comparing the detection frequency and relative abundances with Li. We report 33 new detections of B within veins analyzed between Sols 1548 and 2311 where detections increase in Pettegrove Point and Jura members, which form Vera Rubin ridge. The presence of B and Li in the Ca-sulfate veins is possibly due to dissolution of preexisting B in clays of the bedrock by acids or neutral water and redistribution of the elements into the veins. Elevated frequency of B detection in veins of Gale crater correlates with presence of dehydration features such as desiccation cracks, altered clay minerals and detections of evaporites such as Mg-sulfates and chloride salts in the host rocks. The increased observations of B also coincide with decreased Li concentration in the veins (average Li concentration of veins drops by ~15 ppm). Boron and Li have varying solubilities, and Li does not form salts as readily upon dehydration as B, causing it to remain in the solution. So the weak negative correlation between B and Li may reflect the crystallization sequence during dehydration on Vera Rubin ridge.

58 GEOSCIENCES↗