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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 19 records
All sourcesNASA NTRSDOE OSTI
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 OSTI2019

diBELLA: Distributed Long Read to Long Read Alignment

© 2019 ACM. We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers [29]. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, diBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability. We describe and present analyses for high level design trade-offs and conduct an extensive empirical analysis that compares performance characteristics across state-of-the-art HPC systems as well as a commercial cloud architectures, highlighting the advantages of state-of-the-art network technologies.

Ellis, Marquita↗
DOE OSTI2020

Distributed Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (DiBELLA) v1.0.0

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, DiBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability.

Ellis, Marquita↗
DOE OSTI2026

Data for A Fluorescence-Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants

Scripts for the manuscript "A fluorescence-based transient expression assay for the analysis of upstream open reading frames in plant" by Haas et al. Upstream open reading frames (uORFs) are regulatory elements present in the 5′ leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome- wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild- type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost- efficient alternative to investigate transcript leaders by co- expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO2 assimilation during sun–shade transitions.

Gene Editing↗
DOE OSTI2026

Human RNome Project draft human RNome sequence of GM12878, B-cell line, obtained by mass-spectrometry sequencing, long-read sequencing and short-read sequencing.

Here we report the first draft of the human RNome sequence, a reference map of RNA chemical modifications in a human B-cell line. RNA carries a diverse repertoire of chemical modifications that regulate gene expression, cellular function, and responses to physiological and pathological cues. Yet, unlike the genome, no reference map of RNA modifications is available for any human cell. To generate this resource, the Human RNome Project Consortium analyzed a shared RNA preparation from the well-characterized GM12878 B-cell line using short-read sequencing, long-read direct RNA sequencing, and mass spectrometry, generating more than 7.1 billion sequencing reads spanning approximately 1.2 trillion nucleotides. The resulting maps of the human RNome reveal that RNA modifications are organized according to function, transcript architecture, and cellular identity. Modifications concentrate at functional centers of ribosomal and transfer RNAs, follow the canonical topology of N6-methyladenosine in coding transcripts, and form coordinated hotspots in immune regulatory genes. This first reference human RNome provides a foundation for understanding how RNA chemistry shapes cellular identity, human disease, and the development of RNA-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

ENDFtk: A robust tool for reading and writing ENDF-formatted nuclear data

ENDFtk is a recently developed C++ and Python interface to interact with ENDF-6 formatted nuclear data files. It provides a robust and complete interface, allowing the reading and writing of all formats currently part of the ENDF-6 formats manual, as well as some non-ENDF formats used by the NJOY processing code. It provides an interface that mimics the names in the ENDF-6 formats manual as well as an equivalent interface using human-readable attribute names. It is robust and powerful enogh for nuclear data experts to develop complex applications, while also simple enough to be used non-experts to retrieve and manipulate evaluated nuclear data. ENDFtk offers the ability to easily interrogate and manipulate data either in large-scale code projects or in simple Python scripts. Here, in this paper, a brief overview of the interface is given, as well as more substantial examples demonstrating plotting simple data, interacting with more complex data, and writing new data to files. ENDFtk is open source and available for download via GitHub (https://github.com/njoy/ENDFtk).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

De novo Nanopore read quality improvement using deep learning

BACKGROUND: Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area. RESULTS: Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent "scrubbing" (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments. Applying MiniScrub to real world control datasets under several different parameters, we show that it robustly improves read quality, and improves read error correction in the metagenome setting. Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer mis-assemblies and large indel errors. CONCLUSIONS: MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗
DOE OSTI2024

Enhanced read resolution in reconfigurable memristive synapses for Spiking Neural Networks

Abstract The synapse is a key element circuit in any memristor-based neuromorphic computing system. A memristor is a two-terminal analog memory device. Memristive synapses suffer from various challenges including high voltage, SET or RESET failure, and READ margin issues that can degrade the distinguishability of stored weights. Enhancing READ resolution is very important to improving the reliability of memristive synapses. Usually, the READ resolution is very small for a memristive synapse with a 4-bit data precision. This work considers a step-by-step analysis to enhance the READ current resolution or the read current difference between two resistance levels for a current-controlled memristor-based synapse. An empirical model is used to characterize the $${\hbox {HfO}}_{2}$$ HfO 2 based memristive device. $$1\textrm{st}$$ 1 st and $$2\textrm{nd}$$ 2 nd stage device of our proposed synapse design can be scaled to enhance the READ current margin up to $$\sim$$ ∼ 4.3 $$\times$$ × and $$\sim$$ ∼ 21%, respectively. Moreover, READ current resolution can be enhanced with run-time adaptation techniques such as READ voltage scaling and body biasing. The READ voltage scaling and body biasing can improve the READ current resolution by about 46% and 15%, respectively. TENNLab’s neuromorphic computing framework is leveraged to evaluate the effect of READ current resolution on classification, control, and reservoir computing applications. Higher READ current resolution shows better accuracy than lower resolution even when facing different levels of read noise.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Genomic and phenotypic characterization of multidrug-resistant Salmonella enterica serovar Reading isolates involved in a turkey-associated foodborne outbreak

Salmonella is a global bacterial foodborne pathogen associated with a variety of contaminated food products. Poultry products are a common source of Salmonella -associated foodborne illness, and an estimated 7% of human illnesses in the United States are attributed to turkey products. From November 2017 to March 2019, the Centers for Disease Control and Prevention reported a turkey-associated outbreak of multidrug-resistant (MDR; resistant to ≥3 antimicrobial classes) Salmonella enterica serovar Reading ( S . Reading) linked to 358 human infections in 42 US states and Canada. Since S . Reading was seldom linked to human illness prior to this outbreak, the current study compared genomic sequences of S . Reading isolates prior to the outbreak (pre-outbreak) to isolates identified during the outbreak period, focusing on genes that were different between the two groups but common within a group. Following whole-genome sequence analysis of five pre-outbreak and five outbreak-associated turkey/turkey product isolates of S . Reading, 37 genes located within two distinct chromosomal regions were identified only in the pre-outbreak isolates: (1) an ~5 kb region containing four protein-coding genes including uidA which encodes beta-glucuronidase, pgdA encoding peptidoglycan deacetylase, and two hypothetical proteins and (2) an ~28 kb region comprised of 32 phage-like genes and the xerC gene, which encodes tyrosine recombinase (frequently associated with phage genes). The five outbreak isolates also had a deletional event within the cirA gene, introducing a translational frame shift and premature stop codon. The cirA gene encodes a protein with dual receptor functions: a siderophore receptor for transport of dihydroxybenzoylserine as well as a colicin Ia/b receptor. Significant differences for the identified genetic variations were also detected in 75 S . Reading human isolates. Of the 41 S . Reading isolates collected before or in 2017, 81 and 90% of the isolates contained the uidA and pgdA genes, respectively, but only 24% of the isolates collected after 2017 harbored the uidA and pgdA genes. The truncation event within the cirA gene was also significantly higher in isolates collected after 2017 (74%) compared to before or in 2017 (5%). Phenotypic analysis of the S . Reading isolates for colicin and cefiderocol sensitivities (CirA) and β-methyl-D-glucuronic acid utilization (UidA and accessory proteins) supported the genomic data. Overall, a similar genome reduction pattern was generally observed in both the turkey and human isolates of S . Reading during the outbreak period, and the genetic differences were present in genes that could potentially promote pathogen dissemination due to variation in Salmonella colonization, fitness, and/or virulence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Effects on the Ocular Surface from Reading on Different Smartphone Screens: A Prospective Randomized Controlled Study

The purpose of this study was to investigate the influence of smartphone reading on the ocular surface and to compare the various effects of different screens and light conditions on the ocular surface. One hundred nineteen volunteers were randomly divided into: light + organic light‐emitting diode (OLED), light + electronic ink (eINK), dark + OLED, and dark + eINK. Ocular surface examinations, including noninvasive break‐up time (NIBUT), noninvasive keratograph tear meniscus height (NIKTMH), ocular redness, fluorescein break‐up time (FBUT), corneal fluorescein staining, meibomian gland assessment, Schirmer I Test, and blinking frequency, were performed before and after a reading task. Symptoms were evaluated using the Ocular Surface Disease Index (OSDI) and Computer Vision Syndrome Questionnaire (CVS‐Q). NIBUT and FBUT were decreased statistically significantly after participants read on an OLED screen for 2 hours compared with the baseline in light and dark environments, whereas no statistically significant decrease was observed on an eINK screen. NIKTMH was statistically significantly decreased after reading on an OLED screen in light and dark settings, and the eINK screen had a lesser effect on NIKTMH. An obvious increase in the ocular redness, OSDI and CVS‐Q scores was observed after reading on an OLED screen, whereas the eINK screen had a lesser effect on these indicators. Blink rate increased gradually in OLED subgroups during the reading task, whereas no statistically significant difference was observed in the eINK subgroups. Our research suggested that reading on an OLED screen can cause ocular surface disorder and obvious subjective discomfort, whereas reading on an eINK screen can minimize ocular surface disorder in both dark and light environments.

Yuan, Kelan↗
DOE OSTI2024

Evaluating two live-attenuated vaccines against Salmonella enterica serovar Reading in turkeys: reduced tissue colonization and cecal tonsil transcriptome responses

Vaccines that cross-protect across serovars ofSalmonella enterica(Salmonella) would be a beneficial intervention against emerging and persistentSalmonellaisolates of concern for the turkey industry. The 2017–2019 foodborne outbreak ofSalmonella entericaserovar Reading (S. Reading) revealed the need for effective control of this serovar in turkey production. This study evaluated two live-attenuatedSalmonellavaccines, an internally developed cross-protective vaccine and a commercially available vaccine, against an outbreak-associated strain ofS. Reading in turkeys. At 1 day and 3 weeks of age, male turkey poults were either mock-vaccinated with phosphate buffered saline (PBS) or given one of the vaccines by oral gavage (primary and booster) or aerosol spray (primary) then drinking water (booster). At 7 weeks of age, poults were challenged with 10 9 colony forming units (CFU) ofS. Reading; a mock-vaccinated group was mock-challenged with PBS. Colonization of the cecal contents and cecal tonsil was 1.5–3 log 10 CFU/g lower in vaccinated birds than mock-vaccinated birds at 7 and/or 14 days post-inoculation (DPI).Salmonelladissemination to the spleen was significantly reduced by both vaccines. Gene expression of intestinal transporters (such asSCNN1BandSLC10A2) and tight junction proteins was significantly decreased in the turkey cecal tonsil transcriptome at 2 DPI withS. Reading. Vaccination with either vaccine mitigated most cecal tonsil gene expression responses toS. Reading challenge. Therefore, both the internally developed vaccine and commercial vaccine were cross-protective against colonization and dissemination, and both were able to limit transcriptional changes from challenge in intestinal health-related genes in the cecal tonsil, thereby providing vaccination efficacy and impact data againstS. Reading in turkeys.

Veterinary Sciences↗
NASA NTRS1993

Read buffer optimizations to support compiler-assisted multiple instruction retry

Multiple instruction retry is a recovery mechanism for transient processor faults. We previously developed a compiler-assisted approach to multiple instruction ferry in which a read buffer of size 2N (where N represents the maximum instruction rollback distance) was used to resolve some data hazards while the compiler resolved the remaining hazards. The compiler-assisted scheme was shown to reduce the performance overhead and/or hardware complexity normally associated with hardware-only retry schemes. This paper examines the size and design of the read buffer. We establish a practical lower bound and average size requirement for the read buffer by modifying the scheme to save only the data required for rollback. The study measures the effect on the performance of a DECstation 3100 running ten application programs using six read buffer configurations with varying read buffer sizes. Two alternative configurations are shown to be the most efficient and differed depending on whether split-cycle-saves are assumed. Up to a 55 percent read buffer size reduction is achievable with an average reduction of 39 percent given the most efficient read buffer configuration and a variety of applications.

Alewine, N. J.↗
NASA NTRS1995

The Empirical Investigation of Perspective-Based Reading

We consider reading techniques a fundamental means of achieving high quality software. Due to 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 requirement documents. The goal of PBR is to provide operation scenarios where members of a review team read a document from a particular perspective (eg., tester, developer, user). Our assumption is that the combination of different perspective provides better coverage of the document than the same number of readers using their usual technique. To test the efficacy of PBR, we conducted two runs of a controlled experiment in the environment of NASA GSFC Software Engineering Laboratory (SEL), using developers from the environment. The subjects read two types of documents, one generic in nature and the other from the NASA Domain, using two reading techniques, PBR and their usual technique. The results from these experiment as well as the experimental design, are presented and analyzed. When there is a statistically significant distinction, PBR performs better than the subjects' usual technique. However, PBR appears to be more effective on the generic documents than on the NASA documents.

Basili, Victor R.↗
NASA NTRS1992

Improved accuracy in ground-based facilities - 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 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↗