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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 1,801 records · Page 100
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

RapidEELS: machine learning for denoising and classification in rapid acquisition electron energy loss spectroscopy

Recent advances in detectors for imaging and spectroscopy have afforded in situ, rapid acquisition of hyperspectral data. While electron energy loss spectroscopy (EELS) data acquisition speeds with electron counting are regularly reaching 400 frames per second with near-zero read noise, signal to noise ratio (SNR) remains a challenge owing to fundamental counting statistics. In order to advance understanding of transient materials phenomena during rapid acquisition EELS, trustworthy analysis of noisy spectra must be demonstrated. In this study, we applied machine learning techniques to denoise high frame rate spectra, benchmarking with slower frame rate “ground truths”. The results provide a foundation for reliable use of low SNR data acquired in rapid, in-situ spectroscopy experiments. Such a tool-set is a first step toward both automation in microscopy as well as use of these methods to interrogate otherwise poorly understood transformations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Transcript and blood-microbiome analysis towards a blood diagnostic tool for goats affected by Haemonchus contortus

The Alpine goat (Capra aegagrus hircus) is parasitized by the barber pole worm (Haemonchus contortus). Hematological parameters from transcript and metagenome analysis in the host are reflective of infestation. We explored comparisons between blood samples of control, infected, infected zoledronic acid-treated, and infected antibody (anti-γδ T cells) treated wethers under controlled conditions. Seven days post-inoculation (dpi), we identified 7,627 transcripts associated with the different treatment types. Microbiome measurements at 7 dpi revealed fewer raw read counts across all treatments and a less diverse microbial flora than at 21 dpi. This study identifies treatment specific transcripts and an increase in microflora abundance and diversity as wethers age. Further, F/B ratio reflect health, based on depression or elevation above thresholds defined by the baseline of non-infected controls. Forty Alpine wethers were studied where blood samples were collected from five goats in four treatment groups on 7 dpi and 21 dpi. Transcript and microbiome profiles were obtained using the Partek Flow (St. Louis, Missouri, USA) software suites pipelines. Inflammation comparisons were based on the Firmicutes/Bacteriodetes ratios that are calculated as well as the reduction of microbial diversity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds

Abstract Battlefield injury management requires specialized care, and wound infection is a frequent complication. Challenges related to characterizing relevant pathogens further complicates treatment. Applying metagenomics to wounds offers a comprehensive path toward assessing microbial genomic fingerprints and could indicate prognostic variables for future decision support tools. Wound specimens from combat-injured U.S. service members, obtained during surgical debridements before delayed wound closure, were subjected to whole metagenome analysis and targeted enrichment of antimicrobial resistance genes. Results did not indicate a singular, common microbial metagenomic profile for wound failure, instead reflecting a complex microenvironment with varying bioburden diversity across outcomes. Genus-level Pseudomonas detection was associated with wound failure at all surgeries. A logistic regression model was fit to the presence and absence of antimicrobial resistance classes to assess associations with nosocomial pathogens. A. baumannii detection was associated with detection of genomic signatures for resistance to trimethoprim, aminoglycosides, bacitracin, and polymyxin. Machine learning classifiers were applied to identify wound and microbial variables associated with outcome. Feature importance rankings averaged across models indicated the variables with the largest effects on predicting wound outcome, including an increase in P. putida sequence reads. These results describe the microbial genomic determinants in combat wound bioburden and demonstrate metagenomic investigation as a comprehensive tool for providing information toward aiding treatment of combat-related injuries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome sequence and characterization of a novel Pseudomonas putida phage, MiCath

Abstract Pseudomonads are ubiquitous bacteria with importance in medicine, soil, agriculture, and biomanufacturing. We report a novel Pseudomonas putida phage, MiCath, which is the first known phage infecting P. putida S12, a strain increasingly used as a synthetic biology chassis. MiCath was isolated from garden soil under a tomato plant using P. putida S12 as a host and was also found to infect four other P. putida strains. MiCath has a ~ 61 kbp double-stranded DNA genome which encodes 97 predicted open reading frames (ORFs); functions could only be predicted for 48 ORFs using comparative genomics. Functions include structural phage proteins, other common phage proteins (e.g., terminase), a queuosine gene cassette, a cas4 exonuclease, and an endosialidase. Restriction digestion analysis suggests the queuosine gene cassette encodes a pathway capable of modification of guanine residues. When compared to other phage genomes, MiCath shares at most 74% nucleotide identity over 2% of the genome with any sequenced phage. Overall, MiCath is a novel phage with no close relatives, encoding many unique gene products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Advances in detection for neutron reflectometry with time-resolved imaging detectors

Thermal neutron detection in neutron scattering science is a challenging endeavour due to a limited number of technologies which are sensitive to these weakly interacting particles. While many improvements to conventional detectors are underway at various facilities, there is a great opportunity to make a leap in performance by combining the spatial resolution benefits of imaging and the temporal resolution and background discrimination of event-driven radiation detectors. This idea has been realized by using a neutron sensitive scintillator read out by a single-photon sensitive camera based on a Timepix3 ASIC. We demonstrate how such data-driven imaging sensors can enable unprecedented performance in neutron reflectometry using the ASTERIX instrument at the Los Alamos Neutron Scattering Center. Several samples were measured with both the new and a conventional 3 He detector systems. The results from this work demonstrate that these imaging based systems can satisfy performance parameters for the future QIKR reflectometer to be built at the Second Target Station at Oak Ridge National Laboratory. Further improvements to the detector are already underway which will allow streamlined and expedited experiments. We demonstrate at least a two order of magnitude increase in detection rate at an acceptable dead time and introduce a new way of tuning the detector efficiency using light collecting optics to accommodate highly intense direct beams which cannot be measured with any current detectors without severe attenuation. This will allow measurements of complete reflectometry profiles and using a single sample measurement combined with fewer direct beam calibration measurements on QIKR and potentially other reflectometers.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Impact of CuInP 2 S 6 –metal interfaces on the stabilization of polar phases and polarization switching

The multifunctionality of two-dimensional ferroelectric CuInP 2 S 6 (CIPS) arises from the existence of multiple polar phases combined with a high ionic conductivity that facilitates polarization switching in unusual ways. The van der Waals (vdW) layered structure provides ultrathin flakes and ideal interfaces to integrate with other materials for microelectronics and neuromorphic elements. However, device integration necessitates metal contacts to read, write, or transmit signals. In this work, we find that different types of metal–CIPS interfaces strongly impact the stabilization of specific polar phases and the field-induced transitions between the polarization states. Cu electrodes initially suppress the piezoresponse, whereas, at CIPS–Ag interfaces, the electromechanical signal is increased. Under electric fields, the Cu electrodes, Ag electrodes and surrounding CIPS surfaces can show distinct switching behavior as different phases and polarization orientations are stabilized. These findings highlight that metal–CIPS interfaces provide the opportunity to optimize functional material properties.

Ferroelectrics and multiferroics↗
DOE OSTI2023

acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens

Abstract High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of engineered and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes via calculation of an optimization metric, thus determining the fitness effect of disrupted genes. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica and acCRISPR was used to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in screens quantifying relative cellular fitness under high salt conditions to identify genes that were related to salt tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

High-throughput feedback-enabled optogenetic stimulation and spectroscopy in microwell plates

Abstract The ability to perform sophisticated, high-throughput optogenetic experiments has been greatly enhanced by recent open-source illumination devices that allow independent programming of light patterns in single wells of microwell plates. However, there is currently a lack of instrumentation to monitor such experiments in real time, necessitating repeated transfers of the samples to stand-alone analytical instruments, thus limiting the types of experiments that could be performed. Here we address this gap with the development of the optoPlateReader (oPR), an open-source, solid-state, compact device that allows automated optogenetic stimulation and spectroscopy in each well of a 96-well plate. The oPR integrates an optoPlate illumination module with a module called the optoReader, an array of 96 photodiodes and LEDs that allows 96 parallel light measurements. The oPR was optimized for stimulation with blue light and for measurements of optical density and fluorescence. After calibration of all device components, we used the oPR to measure growth and to induce and measure fluorescent protein expression in E. coli . We further demonstrated how the optical read/write capabilities of the oPR permit computer-in-the-loop feedback control, where the current state of the sample can be used to adjust the optical stimulation parameters of the sample according to pre-defined feedback algorithms. The oPR will thus help realize an untapped potential for optogenetic experiments by enabling automated reading, writing, and feedback in microwell plates through open-source hardware that is accessible, customizable, and inexpensive.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Next-generation neutron detection using a 6 Li glass scintillator composite

Neutron detectors are crucial in fundamental science, nuclear security, safeguards, and civil applications. 3 He-filled gas proportional counters are the gold standard for thermal neutron detection, prized for their efficiency, neutron/gamma discrimination, and stability; however, the scarcity of 3 He has prompted the search for alternatives. Here, we introduce a neutron detector design based on a scintillating composite consisting of 6 Li glass scintillator particles dispersed in an organic matrix. A detector consisting of this scintillating composite, photomultiplier tubes (PMTs) for optical detection, and electronics for reading out the PMT signal in both pulse and current modes was prototyped and characterized using various neutron and gamma sources. The prototype achieves a measured intrinsic detection efficiency of 6.70 ± 0.01%, a die-away time of 10.3 ± 0.1 μs, a negligible gamma misidentification probability, and response linearity up to at least 3.7 × 10 6 incident neutrons/s established via a cross-calibration technique. This detector holds the potential to outperform traditional 3 He-gas-based neutron detection systems, offering a viable alternative amidst the ongoing 3 He shortage and promising advancements in neutron detection technology.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into ‘iVirus’ on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus’s functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy’s Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as “live” protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

Bolduc, Benjamin (ORCID:0000000324200755)↗
DOE OSTI2018

Auto-generated materials database of Curie and Néel temperatures via semi-supervised relationship extraction

article presents an auto-generated database of 39,822 records containing chemical compounds and their associated Curie and Néel magnetic phase transition temperatures. The database was produced using natural language processing and semi-supervised quaternary relationship extraction, applied to a corpus of 68,078 chemistry and physics articles. Evaluation of the database shows an estimated overall precision of 73%. Therein, records processed with the text-mining toolkit, ChemDataExtractor, were assisted by a modified Snowball algorithm, whose original binary relationship extraction capabilities were extended to quaternary relationship extraction. Consequently, its machine learning component can now train with ≤500 seeds, rather than the 4,000 originally used. Data processed with the modified Snowball algorithm affords 82% precision. Database records are available in MongoDB, CSV and JSON formats which can easily be read using Python, R, Java and MatLab. As a result, this makes the database easy to query for tackling big-data materials science initiatives and provides a basis for magnetic materials discovery.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Barium: An Efficient Cathode Layer for Bulk-heterojunction Solar Cells

We report Barium (Ba) cathode layer for bulk-heterojunction solar cells which enhanced the fill factor (FF) of p-DTS(FBTTh2)2/PC71BM BHJ solar cell up to 75.1%, one of the highest value reported for an organic solar cell. The external quantum efficiency exceeds 80%. Analysis of recombination mechanisms using the current-voltage (J–V) characteristics at various light intensities in the BHJ solar cell layer reveals that Ba prevents trap assisted Shockley-Read-Hall (SRH) recombination at the interface and with different thicknesses of the Ba, the recombination shifts towards bimolecular from monomolecular. Moreover, Ba increases shunt resistance and decreases the series resistance significantly. This results in an increase in the charge collection probability leading to high FF. This work identifies a new cathode interlayer which outclasses the all the reported interlayers in increasing FF leading to high power conversion efficiency and have significant implications in improving the performance of BHJ solar cells.

SOLAR CELLS↗
DOE OSTI2015

Illumina sequencing-based analysis of free-living bacterial community dynamics during an Akashiwo sanguine bloom in Xiamen sea, China

Although phytoplankton are the major source of marine dissolved organic matter (DOM), their blooms are a global problem that can greatly affect marine ecological systems, especially free-living bacteria, which are the primary DOM degraders. In this study, we analyzed free-living bacterial communities from Xiamen sea during an Akashiwo sanguine bloom using Illumina MiSeq sequencing of 16S rRNA gene amplicons. The bloom was probably stimulated by low salinity and ended after abatement of eutrophication pollution. A total of 658,446 sequence reads and 11,807 OTUs were obtained in both bloom and control samples with Alpha-proteobacteria and Gamma-proteobacteria being the predominant classes detected. The bloom decreased bacterial diversity, increased species evenness and significantly changed the bacterial community structure. Bacterial communities within the bloom were more homogeneous than those within the control area. The bacteria stimulated by this bloom included the SAR86 and SAR116 clades and the AEGEAN-169 marine group, but a few were suppressed. In addition, many bacteria known to be associated with phytoplankton were detected only in the bloom samples. This study revealed the great influence of an A. sanguinea bloom on free-living bacterial communities and provided new insights into the relationship between bacteria and A. sanguinea in marine ecosystems.

Science & Technology - Other Topics↗
DOE OSTI2015

Lead-free epitaxial ferroelectric material integration on semiconducting (100) Nb-doped SrTiO3 for low-power non-volatile memory and efficient ultraviolet ray detection

We report lead-free ferroelectric based resistive switching non-volatile memory (NVM) devices with epitaxial (1-x)BaTiO3-xBiFeO3 (x = 0.725) (BT-BFO) film integrated on semiconducting (100) Nb (0.7%) doped SrTiO3 (Nb:STO) substrates. The piezoelectric force microscopy (PFM) measurement at room temperature demonstrated ferroelectricity in the BT-BFO thin film. PFM results also reveal the repeatable polarization inversion by poling, manifesting its potential for read-write operation in NVM devices. The electroforming-free and ferroelectric polarization coupled electrical behaviour demonstrated excellent resistive switching with high retention time, cyclic endurance and low set/reset voltages. X-ray photoelectron spectroscopy was utilized to determine the band alignment at the BT-BFO and Nb:STO heterojunction and it exhibited staggered band alignment. This heterojunction is found to behave as an efficient ultraviolet photo-detector with low rise and fall time. The architecture also demonstrates half-wave rectification under low and high input signal frequencies, where the output distortion is minimal. The results provide avenue for an electrical switch that can regulate the pixels in low or high frequency images. Combined this work paves the pathway towards designing future generation low-power ferroelectric based microelectronic devices by merging both electrical and photovoltaic properties of BT-BFO materials.

Science & Technology - Other Topics↗
DOE OSTI2016

An innovative platform for quick and flexible joining of assorted DNA fragments

Successful synthetic biology efforts rely on conceptual and experimental designs in combination with testing of multi-gene constructs. Despite recent progresses, several limitations still hinder the ability to flexibly assemble and collectively share different types of DNA segments. We describe an advanced system for joining DNA fragments from a universal library that automatically maintains open reading frames (ORFs) and does not require linkers, adaptors, sequence homology, amplification or mutation (domestication) of fragments in order to work properly. Moreover, we find that this system, which is enhanced by a unique buffer formulation, provides unforeseen capabilities for testing, and sharing, complex multi-gene circuitry assembled from different DNA fragments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring

Alkaline sulfide-rich hot springs provide a unique environment for microbial community and arsenic (As) biogeochemistry. In this study, a representative alkaline sulfide-rich hot spring, Zimeiquan in the Tengchong geothermal area, was chosen to study arsenic geochemistry and microbial community using Illumina MiSeq sequencing. Over 0.26 million 16S rRNA sequence reads were obtained from 5-paired parallel water and sediment samples along the hot spring’s outflow channel. High ratios of As(V)/As Sum (total combined arsenate and arsenite concentrations) (0.59–0.78), coupled with high sulfide (up to 5.87 mg/L), were present in the hot spring’s pools, which suggested As(III) oxidation occurred. Along the outflow channel, As Sum increased from 5.45 to 13.86 μmol/L, and the combined sulfide and sulfate concentrations increased from 292.02 to 364.28 μmol/L. These increases were primarily attributed to thioarsenic transformation. Temperature, sulfide, As and dissolved oxygen significantly shaped the microbial communities between not only the pools and downstream samples, but also water and sediment samples. Results implied that the upstream Thermocrinis was responsible for the transformation of thioarsenic to As(III) and the downstream Thermus contributed to derived As(III) oxidation. This study improves our understanding of microbially-mediated As transformation in alkaline sulfide-rich hot springs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome

Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain “universal” 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of “microbial dark matter,” or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Lastly, our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we used an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.

59 BASIC BIOLOGICAL SCIENCES↗

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