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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS1992

Development of an automated film-reading system for ballistic ranges

Software for an automated film-reading system that uses personal computers and digitized shadowgraphs is described. The software identifies pixels associated with fiducial-line and model images, and least-squares procedures are used to calculate the positions and orientations of the images. Automated position and orientation readings for sphere and cone models are compared to those obtained using a manual film reader. When facility calibration errors are removed from these readings, the accuracy of the automated readings is better than the pixel resolution, and it is equal to, or better than, the manual readings. The effects of film-reading and facility-calibration errors on calculated aerodynamic coefficients is discussed.

Yates, Leslie A.↗
NASA NTRS2015

Results from On-Board CSA-CP and CDM Sensor Readings During the Burning and Suppression of Solids II (BASS-II) Experiment in the Microgravity Science Glovebox (MSG)

For the first time on ISS, BASS-II utilized MSG working volume dilution with gaseous nitrogen (N2). We developed a perfectly stirred reactor model to determine the N2 flow time and flow rate to obtain the desired reduced oxygen concentration in the working volume for each test. We calibrated the model with CSA-CP oxygen readings offset using the Mass Constituents Analyzer reading of the ISS ambient atmosphere data for that day. This worked out extremely well for operations, and added a new vital variable, ambient oxygen level, to our test matrices. The main variables tested in BASS-II were ambient oxygen concentration, ventilation flow velocity, and fuel type, thickness, and geometry. BASS-II also utilized the on-board CSA-CP for oxygen and carbon monoxide readings, and the CDM for carbon dioxide readings before and after each test. Readings from these sensors allow us to evaluate the completeness of the combustion. The oxygen and carbon dioxide readings before and after each test were analyzed and compared very well to stoichiometric ratios for a one step gas-phase reaction. The CO versus CO2 followed a linear trend for some datasets, but not for all the different geometries of fuel and flow tested. Lastly, we calculated the heat release rates during each test from the oxygen consumption and burn times, using the constant 13.1 kJ of heat released per gram of oxygen consumed. The results showed that the majority of the tests had heat release rates well below 100 Watts.

combustion products↗
DOE OSTI2021

Impact of short-read sequencing on the misassembly of a plant genome

Abstract Background Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with highly uneven read coverages indicative of sequencing and assembly issues that could significantly impact any downstream analysis of plant genomes. In tomato for example, 0.6% (5.1 Mb) and 9.7% (79.6 Mb) of short-read based assembly had significantly higher and lower coverage compared to background, respectively. Results To understand what the causes may be for such uneven coverage, we first established machine learning models capable of predicting genomic regions with variable coverages and found that high coverage regions tend to have higher simple sequence repeat and tandem gene densities compared to background regions. To determine if the high coverage regions were misassembled, we examined a recently available tomato long-read based assembly and found that 27.8% (1.41 Mb) of high coverage regions were potentially misassembled of duplicate sequences, compared to 1.4% in background regions. In addition, using a predictive model that can distinguish correctly and incorrectly assembled high coverage regions, we found that misassembled, high coverage regions tend to be flanked by simple sequence repeats, pseudogenes, and transposon elements. Conclusions Our study provides insights on the causes of variable coverage regions and a quantitative assessment of factors contributing to plant genome misassembly when using short reads and the generality of these causes and factors should be tested further in other species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Deconvolute individual genomes from metagenome sequences through short read clustering

Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads by species before assembly offers a unique opportunity for parallel downstream assembly of genomes with individualized optimization. However, current read clustering methods suffer either false negative (under-clustering) or false positive (over-clustering) problems. Here we extended our previous read clustering software, SpaRC, by exploiting statistics derived from multiple samples in a dataset to reduce the under-clustering problem. Using synthetic and real-world datasets we demonstrated that this method has the potential to cluster almost all of the short reads from genomes with sufficient sequencing coverage. The improved read clustering in turn leads to improved downstream genome assembly quality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Calibration of multisite raters for prospective visual reads of amyloid PET scans

Abstract INTRODUCTION In multicenter Alzheimer's disease studies, amyloid positron emission tomography (PET) visual reads are typically performed centrally by a few experts. Incorporating a broader reader network enhances scalability and generalizability. METHODS Ten neuroimaging experts from eight Alzheimer's Disease Research Centers (ADRCs) visually read 180 amyloid PET scans (30 scans and 15 duplicate scans for each of four tracers, imaged across a wide variety of scanners), using preferred reading software without anatomical imaging or quantitation. Scans were classified as elevated or non‐elevated per tracer‐specific criteria. Inter‐ and intra‐rater agreement was assessed. RESULTS Inter‐rater agreement was substantial (Fleiss’κ = 0.78), with full consensus on 69% of scans. Inter‐rater reliability was substantial to perfect across tracers (Fleiss’κ = 0.70–0.87). Intra‐rater agreement was substantial to perfect (Cohen'sκ = 0.79‐1). Scans with intermediate (10–40 Centiloid) quantitation had lower reader agreement. DISCUSSION A multicenter expert network achieved substantial agreement classifying amyloid PET scans. These scans provide a standard for reader training and reliability assurance in future studies. Highlights Calibration methods ensure reliable amyloid positron emission tomography (PET) visual reads across multiple raters. Substantial agreement is possible across readers using their preferred tools. Agreement is also substantial regardless of the amyloid PET tracer used. Scans with intermediate (10–40 Centiloid) quantitation have lower reader agreement. The calibration set will become a training tool for amyloid PET visual read studies.

Neurosciences & Neurology↗
DOE OSTI2023

Utility of Shockley–Read–Hall analysis to extract defect properties from semiconductor minority carrier lifetime data

The semiconductor minority carrier lifetime contains information about several important material properties, including Shockley–Read–Hall defect levels/concentrations and radiative/Auger recombination rates, and the complex relationships between these parameters produce a non-trivial temperature-dependence of the measured lifetime. It is tempting to fit temperature-dependent lifetime data to extract the properties of the Shockley–Read–Hall recombination centers; however, without a priori knowledge of the distribution of the Shockley–Read–Hall states across the bandgap, this fit problem is under-constrained in most circumstances. Shockley–Read–Hall lifetime data are not well-suited for the extraction of Shockley–Read–Hall defect levels but can be used effectively to extract minority carrier recombination lifetimes. The minority carrier recombination lifetime is observed at temperatures below 100 K in a Si-doped n-type InGaAs/InAsSb superlattice, and deviation from its expected temperature-dependence indicates that the capture cross section of the defect associated with Si-doping has an activation energy of 1.5 meV or a characteristic temperature of 17 K. This lower temperature regime is also preferrable for the analysis of the physics of defect introduction with displacement-damage-generating particle irradiation.

Physics↗
DOE OSTI2024

Deformed Fredkin model for the ν = 5 / 2 Moore-Read state on thin cylinders

We propose a frustration-free model for the Moore-Read quantum Hall state on sufficiently thin cylinders with circumferences ≲ 7 magnetic lengths. While the Moore-Read Hamiltonian involves complicated long-range interactions between triplets of electrons in a Landau level, our effective model is a simpler one-dimensional chain of qubits with deformed Fredkin gates. We show that the ground state of the Fredkin model has high overlap with the Moore-Read wave function and accurately reproduces the latter's entanglement properties. Moreover, we demonstrate that the model captures the dynamical response of the Moore-Read state to a geometric quench, induced by suddenly changing the anisotropy of the system. We elucidate the underlying mechanism of the quench dynamics and show that it coincides with the linearized bimetric field theory. The minimal model introduced here can be directly implemented as a first step towards quantum simulation of the Moore-Read state, as we demonstrate by deriving an efficient circuit approximation to the ground state and implementing it on an IBM quantum processor. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

ABSTRACT Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances. IMPORTANCE Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.

Lui, Lauren M.↗
DOE OSTI2018

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies

Genome graphs are emerging as an important novel approach to the analysis of high-throughput human sequencing data. By explicitly representing genetic variants and alternative haplotypes in a mappable data structure, they can enable the improved analysis of structurally variable and hyperpolymorphic regions of the genome. In most existing approaches, graphs are constructed from variant call sets derived from short-read sequencing. As long-read sequencing becomes more cost-effective and enables de novo assembly for increasing numbers of whole genomes, a method for the direct construction of a genome graph from sets of assembled human genomes would be desirable. Such assembly-based genome graphs would encompass the wide spectrum of genetic variation accessible to long-read-based de novo assembly, including large structural variants and divergent haplotypes. We present NovoGraph, a method for the construction of a human genome graph directly from a set of de novo assemblies. NovoGraph constructs a genome-wide multiple sequence alignment of all input contigs and creates a graph by merging the input sequences at positions that are both homologous and sequence-identical. NovoGraph outputs resulting graphs in VCF format that can be loaded into third-party genome graph toolkits. To demonstrate NovoGraph, we construct a genome graph with 23,478,835 variant sites and 30,582,795 variant alleles from de novo assemblies of seven ethnically diverse human genomes (AK1, CHM1, CHM13, HG003, HG004, HX1, NA19240). Initial evaluations show that mapping against the constructed graph reduces the average mismatch rate of reads from sample NA12878 by approximately 0.2%, albeit at a slightly increased rate of reads that remain unmapped.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Long-read sequencing transcriptome quantification with lr-kallisto

RNA abundance quantification has become routine and affordable thanks to high-throughput “short-read” technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full-length, transcript isoforms has remained a stubborn challenge, despite its obvious biological significance across a wide range of problems. “Long-read” sequencing platforms now produce data-types that can, in principle, drive routine definitive isoform quantification. However some particulars of contemporary long-read datatypes, together with isoform complexity and genetic variation, present bioinformatic challenges. We show here, using ONT data, that fast and accurate quantification of long-read data is possible and that it is improved by exome capture. To perform quantifications we developed lr-kallisto, which adapts the kallisto bulk and single-cell RNA-seq quantification methods for long-read technologies.

Loving, Rebekah K. (ORCID:0000000187250376)↗
NASA NTRS1996

The Empirical Investigation of Perspective-Based Reading

We consider reading techniques a fundamental means of achieving high quality software. Due to the lack of research in this area, we are experimenting with the application and comparison of various reading techniques. This paper deals with our experiences with Perspective-Based Reading (PBR), a particular reading technique for requirements documents. The goal of PBR is to provide operational scenarios where members of a review team read a document from a particular perspective (e.g., tester, developer, user). Our assumption is that the combination of different perspectives provides better coverage of the document than the same number of readers using their usual technique.

Basili, Victor R.↗
NASA NTRS2003

Software for Automated Reading of STEP Files by I-DEAS(trademark)

A program called "readstep" enables the I-DEAS(tm) computer-aided-design (CAD) software to automatically read Standard for the Exchange of Product Model Data (STEP) files. (The STEP format is one of several used to transfer data between dissimilar CAD programs.) Prior to the development of "readstep," it was necessary to read STEP files into I-DEAS(tm) one at a time in a slow process that required repeated intervention by the user. In operation, "readstep" prompts the user for the location of the desired STEP files and the names of the I-DEAS(tm) project and model file, then generates an I-DEAS(tm) program file called "readstep.prg" and two Unix shell programs called "runner" and "controller." The program "runner" runs I-DEAS(tm) sessions that execute readstep.prg, while "controller" controls the execution of "runner" and edits readstep.prg if necessary. The user sets "runner" and "controller" into execution simultaneously, and then no further intervention by the user is required. When "runner" has finished, the user should see only parts from successfully read STEP files present in the model file. STEP files that could not be read successfully (e.g., because of format errors) should be regenerated before attempting to read them again.

Pinedo, John↗
DOE OSTI2023

Automated gauge reading and related systems, methods, and devices

Computing devices and methods for reading gauges are disclosed. A gauge reading method includes capturing image data corresponding to a captured image of one or more gauges, detecting one or more gauges in the captured image, cropping a detected gauge in the captured image to provide a use image including the detected gauge, and classifying the detected gauge to correlate the detected gauge with a template image. The gauge reading method also includes attempting to perform feature detection rectification on the use image to produce a rectified image of the detected gauge, performing template matching rectification on the use image to produce the rectified image responsive to a failure to perform the feature detection rectification, and estimating a gauge reading responsive to the rectified image. A computing device may implement at least a portion of a gauge reading method.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

A Novel Scalable Array Design for III-V Compound Semiconductor-based Nonvolatile Memory (UltraRAM) with Separate Read-Write Paths

The dream of achieving a universal memory that can provide robust non-volatile memory states along with low-energy operation has been the key driving force of memory research. Despite dominating the memory market, conventional charge-based memories cannot satisfy these requirements. However, UltraRAM, an oxide-free charge-based memory cell, aims to achieve both of these requirements. This device achieves non-volatility (with an endurance of over 10 7 cycles and a retention of over 1000 years) along with switching at low-voltage (±2.3 V) utilizing a triple-barrier resonant tunneling (TBRT) structure made of InAs/AlSb. In this work, we propose an array design for UltraRAM-based memory devices. Our proposed memory array features separate read-write path and eliminates the possibility of accidentally switching the memory states stored in the array. Moreover, our design allows us to read all the cells in a column in one cycle without imposing any limit on the scalability. Besides, since the read operation in our proposed design is independent of the write mechanism, there is flexibility to optimize the read operation for memory and in-memory computing applications.

Alam, Shamiul↗
DOE OSTI2020

Python Library For Reading Endf Files

Evaluated Nuclear Data Files (ENDFs) are the most common way to store nuclear data. However, they are a hard-to-read format that few people or programs can read. OpenMC, an open source project, developed a way to read Evaluated Nuclear Data Files (ENDF) into a useful form for python. This library will remove all unnecessary code from OpenMC to focus solely on reading nuclear data. In addition, it will handle parsing Grouped cross-section data from an ENDF file, which OpenMC does not currently handle.

Gale, MicahD.↗
DOE OSTI2018

Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

Switchgrass ( Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. Here, we present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.

09 BIOMASS FUELS↗
DOE OSTI2024

C2C Expert Match Technical Assistance: City of Reading, Pennsylvania [Slides]

The City of Reading, located in southeastern Pennsylvania, is the main city in the Greater Reading Area and the county seat of Berks County, with a population of approximately 95,112 as of 2020. Historically a disinvested manufacturing community, it has a poverty rate of around 40%, a housing stock averaging 90 years old, and an owner-occupied housing rate below 40%. In 2019, Reading adopted a resolution to achieve 100% renewable energy by 2050. The city aims to transition residential, small commercial, and small manufacturing sectors to renewable energy for electricity and heating, bypassing natural gas. This C2C Expert Match aimed to improve the energy efficiency and comfort of older rowhomes in Reading, which often rely on home heating oil and lack cooling systems. A representative energy model of a typical rowhome was developed to evaluate retrofit strategies focused on reducing overheating risk, as well as the potential impacts of heat pump installation. Additionally, resources such as case studies and best practices on energy efficiency, thermal resilience, and electrification retrofits were gathered to support the implementation of effective measures in the community.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2021

Impact of BBDuk metagenomic read trimming and decontamination

Background Investigators using metagenomic sequencing to study their microbiomes are often provided data that has been trimmed and decontaminated or do it themselves without knowing the effect these procedures can have on their downstream analyses. Here we evaluated the impact that JGI trimming and decontamination procedures had on assembly and binning metrics, placement of metagenome assembled genomes into species trees, and functional profiles of metagenome-assembled genomes (MAGs) extracted from twenty three complex rhizosphere metagenomes. We also investigated how more aggressive trimming impacts these binning metrics. Results We found that JGI trimmed and decontamination of input reads had some significant impacts in assembly and binning metrics compared to raw reads, and that differences in placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. More aggressive trimming beyond those used by JGI were found to reduce MAG counts. Conclusions Mild trimming and decontamination of metagenomics reads prior to assembly can change an investigator’s answer to the questions, “Who is there and what are they doing? However, mild trimming and decontamination of metagenomic reads with high quality scores is recommended for those who elect to do so.

59 BASIC BIOLOGICAL SCIENCES↗