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All sourcesNASA NTRSDOE OSTI
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 OSTI2016

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data

In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine. Pipelines that do not use a reference genome assign arbitrary names to SNPs, making meta-analysis across projects difficult. We created the software TagDigger, which includes three programs for analyzing GBS and RAD-seq data. The first script, tagdigger_interactive.py, rapidly extracts read counts and genotypes from FASTQ files using user supplied sets of barcodes and tags. Input and output is in CSV format so that it can be opened by spreadsheet software. Tag sequences can also be imported from the Stacks, TASSEL-GBSv2, TASSEL-UNEAK, or pyRAD pipelines, and a separate file can be imported listing the names of markers to retain. A second script, tag_manager.py, consolidates marker names and sequences across multiple projects. A third script, barcode_splitter.py, assists with preparing FASTQ data for deposit in a public archive by splitting FASTQ files by barcode and generating MD5 checksums for the resulting files. TagDigger is open-source and freely available software written in Python 3. It uses a scalable, rapid search algorithm that can process over 100 million FASTQ reads per hour. TagDigger will run on a laptop with any operating system, does not consume hard drive space with intermediate files, and does not require programming skill to use.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Analysis of read-out heating rate effects on the glow peaks of TLD-100 using WinGCF software

This study was done to analyze the effects of the read-out heating rate on the LiF:Mg,Ti (TLD-100) thermoluminescent dosimeters (TLD) glow peaks using WinGCF computer software. The TLDs were exposed to X-ray photons with a potential difference of 72 kVp and 200 mAs in air and were read-out using a Harshaw 3500 TLD reader. The TLDs were read-out using four read-out heating rates at 10, 7, 4 and 1 °C s{sup −1}. It was observed that lowering the heating rate could separate more glow peaks. The activation energy for peak 5 was found to be lower than that for peak 4. The peak maximum temperature and the integral value of the main peak decreased as the heating rate decreases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Do morphemes matter when reading compound words with transposed letters? Evidence from eye-tracking and event-related potentials

We investigate the online processing consequences of encountering compound words with transposed letters (TLs), in order to determine if cross-morpheme TLs are more disruptive to reading than those within a single morpheme, as would be predicted by accounts of obligatory morpho-orthopgrahic decomposition. Two measures of online processing, eye movements and event-related potentials (ERPs), were collected in separate experiments. Participants read sentences containing correctly spelled compound words (cupcake), or compounds with TLs occurring either across morphemes (cucpake) or within one morpheme (cupacke). Results showed that between- and within-morpheme transpositions produced equal processing costs in both measures, in the form of longer reading times (Experiment 1) and a late posterior positivity (Experiment 2) that did not differ between conditions. Our findings converge to suggest that within- and between-morpheme TLs are equally disruptive to recognition, providing evidence against obligatory morpho-orthographic processing and in favour of whole-word access of English compound words during sentence reading.

97 MATHEMATICS AND COMPUTING↗
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 OSTI2016

Technical Note: Statistical dependences between channels in radiochromic film readings. Implications in multichannel dosimetry

Purpose: This note studies the statistical relationships between color channels in radiochromic film readings with flatbed scanners. The same relationships are studied for noise. Finally, their implications for multichannel film dosimetry are discussed. Methods: Radiochromic films exposed to wedged fields of 6 MV energy were read in a flatbed scanner. The joint histograms of pairs of color channels were used to obtain the joint and conditional probability density functions between channels. Then, the conditional expectations and variances of one channel given another channel were obtained. Noise was extracted from film readings by means of a multiresolution analysis. Two different dose ranges were analyzed, the first one ranging from 112 to 473 cGy and the second one from 52 to 1290 cGy. Results: For the smallest dose range, the conditional expectations of one channel given another channel can be approximated by linear functions, while the conditional variances are fairly constant. The slopes of the linear relationships between channels can be used to simplify the expression that estimates the dose by means of the multichannel method. The slopes of the linear relationships between each channel and the red one can also be interpreted as weights in the final contribution to dose estimation. However, for the largest dose range, the conditional expectations of one channel given another channel are no longer linear functions. Finally, noises in different channels were found to correlate weakly. Conclusions: Signals present in different channels of radiochromic film readings show a strong statistical dependence. By contrast, noise correlates weakly between channels. For the smallest dose range analyzed, the linear behavior between the conditional expectation of one channel given another channel can be used to simplify calculations in multichannel film dosimetry.

60 APPLIED LIFE SCIENCES↗
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↗
NASA NTRS1984

Report-reading patterns of technical managers and nonmanagers

A survey to determine the review and reading processes used by technical managers and nonmanagers indicates that the summary, abstract, conclusion, title page, and introduction are the components used most frequently by both groups to decide whether to read a NASA technical report. In the review process, significantly more managers than nonmanagers use the summary and conclusion, whereas significantly more nonmanagers use the abstract and title page. The most common sequence of review consists of the title page, abstract, and summary, in that order, for both groups. In the reading process, the conclusion, results and discussion, and summary are the components read by the highest percentage of both groups.

Pinelli, T. E.↗
NASA NTRS1984

The Explorer's Guide to the Universe: A Reading List for Planetary and Space Science

During the last decade, both scientists and the public have been engulfed by a flood of discoveries and information from outer space. Distant worlds have become familiar landscapes. Instruments in space have shown us a different Sun by the "light" of ultraviolet radiation and X-rays. Beyond the solar system, we have detected a strange universe of unsuspected violence, unexplained objects, and unimaginable energies. We are completely remarking our picture of the universe around us, and scientists and the general public alike are curious and excited about what we see. The public has participated in this period of exploration and discovery to an extent never possible before. In real time, TV screens show moonwalks, the sands of Mars, the volcanoes of Io, and the rings of Saturn. But after the initial excitement, it is hard for the curious non-scientist to learn more details or even to stay in touch with what is going on. Each space mission or new discovery is quickly skimmed over by newspapers and TV and then preserved in technical journals that are neither accessible nor easily read by the average reader. This reading list is an attempt to bridge the gap between the people who make discoveries in space and the people who would like to read about them. The aim has been to provide to many different people--teachers, students, scientists, other professionals, and curious citizens of all kinds--a list of readings where they can find out what the universe is like and what we have learned about it. We have included sections on the objects that seem to be of general interest--the Moon, the planets, the Sun, comets, and the universe beyond. We have also included material on related subjects that people are interested in--the history of space exploration, space habitats, extraterrestrial life, and U F O ' s . The list is intended to be self-contained; it includes both general references to supply background and more specific sources for new discoveries. Although the list can be used by a wide range of people, it has been compiled with the non-scientist specifically in mind. A s a general rule, we have not included technical symposia or the special issues of

French, Bevan M.↗
NASA NTRS2004

Clarissa Spoken Dialogue System for Procedure Reading and Navigation

Speech is the most natural modality for humans use to communicate with other people, agents and complex systems. A spoken dialogue system must be robust to noise and able to mimic human conversational behavior, like correcting misunderstandings, answering simple questions about the task and understanding most well formed inquiries or commands. The system aims to understand the meaning of the human utterance, and if it does not, then it discards the utterance as being meant for someone else. The first operational system is Clarissa, a conversational procedure reader and navigator, which will be used in a System Development Test Objective (SDTO) on the International Space Station (ISS) during Expedition 10. In the present environment one astronaut reads the procedure on a Manual Procedure Viewer (MPV) or paper, and has to stop to read or turn pages, shifting focus from the task. Clarissa is designed to read and navigate ISS procedures entirely with speech, while the astronaut has his eyes and hands engaged in performing the task. The system also provides an MPV like graphical interface so the procedure can be read visually. A demo of the system will be given.

Hieronymus, James↗
NASA NTRS2009

Real-Time Detection of Dust Devils from Pressure Readings

A method for real-time detection of dust devils at a given location is based on identifying the abrupt, temporary decreases in atmospheric pressure that are characteristic of dust devils as they travel through that location. The method was conceived for use in a study of dust devils on the Martian surface, where bandwidth limitations encourage the transmission of only those blocks of data that are most likely to contain information about features of interest, such as dust devils. The method, which is a form of intelligent data compression, could readily be adapted to use for the same purpose in scientific investigation of dust devils on Earth. In this method, the readings of an atmospheric- pressure sensor are repeatedly digitized, recorded, and processed by an algorithm that looks for extreme deviations from a continually updated model of the current pressure environment. The question in formulating the algorithm is how to model current normal observations and what minimum magnitude deviation can be considered sufficiently anomalous as to indicate the presence of a dust devil. There is no single, simple answer to this question: any answer necessarily entails a compromise between false detections and misses. For the original Mars application, the answer was sought through analysis of sliding time windows of digitized pressure readings. Windows of 5-, 10-, and 15-minute durations were considered. The windows were advanced in increments of 30 seconds. Increments of other sizes can also be used, but computational cost increases as the increment decreases and analysis is performed more frequently. Pressure models were defined using a polynomial fit to the data within the windows. For example, the figure depicts pressure readings from a 10-minute window wherein the model was defined by a third-degree polynomial fit to the readings and dust devils were identified as negative deviations larger than both 3 standard deviations (from the mean) and 0.05 mbar in magnitude. An algorithm embodying the detection scheme of this example was found to yield a miss rate of just 8 percent and a false-detection rate of 57 percent when evaluated on historical pressure-sensor data collected by the Mars Pathfinder lander. Since dust devils occur infrequently over the course of a mission, prioritizing observations that contain successful detections could greatly conserve bandwidth allocated to a given mission. This technique can be used on future Mars landers and rovers, such as Mars Phoenix and the Mars Science Laboratory.

Wagstaff, Kiri↗
DOE OSTI2015

Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

Precision medicine or personalized medicine has been proposed as a modernized and promising medical strategy. Genetic variants of patients are the key information for implementation of precision medicine. Next-generation sequencing (NGS) is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make a decision on which alignment algorithm to use in their studies. Selection of the right alignment algorithm determines not only the alignment algorithm but also the set of suitable parameters to be used by the algorithm. Understanding these algorithms helps in selecting the appropriate alignment algorithm for different applications in precision medicine. Here, we review current available algorithms and their major strategies such as seed-and-extend and q-gram filter. We also discuss the challenges in current alignment algorithms, including alignment in multiple repeated regions, long reads alignment and alignment facilitated with known genetic variants.

59 BASIC BIOLOGICAL SCIENCES↗