SIC BASED PHOTON COUNTING DETECTOR FOR SCINTILLATOR READ-OUT IN HARSH ENVIRONMENT APPLICATIONS
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Neher, Steven↗
SEARCH · Engineering Papers
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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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Quantitative Literature Review (QLR): Did the Agent Read the Paper or Memorize It?
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97 MATHEMATICS AND COMPUTING↗
Erratum to: “The Fluorescence and Electronic Structure of Phenyl-Substituted Tetraazachlorin Molecules” [Optics and Spectroscopy 117, 722 (2014)]
should read “porphyrazine” instead of “porphyrazin”;should read “intersystem crossing” instead of “intercombinational conversion”;should read “mirror-symmetrical” instead of “reflection-symmetric”;should read “fluorescence enhancement” instead of “fluorescence buildup.”Page 722, Abstract, lines 9–10 from the top, the sentence should read:This characteristic increases upon tetrapyrrole phenylation.Page 727, left column, lines 17–18 from the top, the sentence should read:The vibronic transition parts of the emission spectrum are diffuse, (…)Page 727, left column, lines 29–30 from the top, the sentence should read:Note that the Stokes shift in these cases is relatively large.Page 729, left column, lines 8–10 from the bottom, the sentence should read:For H{sub 2}Ph{sub 8}TAC{sup mp} and H{sub 2}Ph{sub 6}TAC{sup tm}, the enhancement of fluorescence is weaker than in the former case: on cooling, τ{sub F} is increased by a factor of 4–5 in MTHF and by a factor of only 2.6–3 in toluene.Page 729, right column, lines 9–10 from the footnote, the sentence should read:It is seen from Table 1 that our results agree reasonably well with previously reported data.Page 730, left column, lines 16–19 from the top, the sentence should read:The lifetime for the outgassed H{sub 2}TAP solution intoluene (τ{sub T}{sup 0}) was measured by A.S. Stasheuski as phosphorescence decay at λ{sub reg} = 1070 nm using the setup described in [29].Page 730, left column, lines 20–23 from the top, the sentence should read:The τ{sub T} value derived from the kinetics of the rise of singlet oxygen luminescence [26] for the nonoutgassed solution at λ{sub reg} = 1272 nm is 162 ns;Page 730, right column, lines 25–27 from the top, the sentence should read:Therefore, for H{sub 2}TAP (λ{sub F}{sup 00}≈ 620 nm), the internal conversion probability should not be high.Page 731, left column, the heading of Table 2 should read:Bond lengths in the porphine macrocycle (Å).Page 731, left column, lines 3–6 from the top, the sentence should read:For elucidating the mechanism of the deactivation of the S{sub 1} state, it was of essential interest to see whether the enhancement of H{sub 2}TAP fluorescence would be observed at 77 K.Page 733, left column, lines 2–3 from the top, the sentence should read:The corresponding difference for the H{sub 2}P–H{sub 2}C pair is 0.013 Å.Page 733, left column, lines 14–16 from the top, the sentence should read:The macrocycle undergoes additional contraction, and the symmetry of its conjugated system is very close to D{sub 2h}.Page 733, right column, line 21 from the top should read:Replacement of the methine bridges (…)Page 734, left column, lines 8–11 from the figure caption, the sentence should read:This is the main reason of the large bathochromic shift of the Soret band of H{sub 2}Ph{sub 8}TAP and MgPh{sub 8}TAP [16] relative to H{sub 2}TAP and MgTAP, respectively.Page 734, left column, lines 1–4 from the bottom, the sentence should read:The complete INDO/Sm calculation yields the corresponding quantitative characteristics, which are in good agreement with experimental data (see below).Page 740, left column, reference no. 25 should read:25. V. A. Galievsky, A. S. Stasheuski, V. V. Kiselyov, A. I. Shabusov, M. V. Belkov, and B. M. Dzhagarov, Instrum. Exp. Tech. 53, 568 (2010).25. V. A. Galievsky, A. S. Stasheuski, V. V. Kiselyov, A. I. Shabusov, M. V. Belkov, and B. M. Dzhagarov, Instrum. Exp. Tech. 53, 568 (2010).30. V. L. Ermolaev and E. B. Sveshnikova, Acta Phys. Pol. 34, 771 (1968).
74 ATOMIC AND MOLECULAR PHYSICS↗
Preliminary Analysis of Photoreading
The purpose of this project was to provide a preliminary analysis of a reading strategy called PhotoReading. PhotoReading is a technique developed by Paul Scheele that claims to increase reading rate to 25,000 words per minute (Scheele, 1993). PhotoReading itself involves entering a "relaxed state" and looking at, but not reading, each page of a text for a brief moment (about I to 2 seconds). While this technique has received attention in the popular press, there had been no objective examinations of the technique's validity. To examine the effectiveness of PhotoReading, the principal investigator (i.e., trainee) participated in a PhotoReading workshop to learn the technique. Parallel versions of two standardized and three experimenter-created reading comprehension tests were administered to the trainee and an expert user of the PhotoReading technique to compare the use of normal reading strategies and the PhotoReading technique by both readers. The results for all measures yielded no benefits of using the PhotoReading technique. The extremely rapid reading rates claimed by PhotoReaders were not observed; indeed, the reading rates were generally comparable to those for normal reading. Moreover, the PhotoReading expert generally showed an increase in reading time when using the PhotoReading technique in comparison to when using normal reading strategies to process text. This increase in reading time when PhotoReading was accompanied by a decrease in text comprehension.
McNamara, Danielle S.↗
Page turning system
A device for holding reading materials for use by readers without arm mobility is presented. The device is adapted to hold the reading materials in position for reading with the pages displayed to enable turning by use of a rubber tipped stick that is held in the mouth and has a pair of rectangular frames. The frames are for holding and positioning the reading materials opened in reading posture with the pages displayed at a substantially unobstructed sighting position for reading. The pair of rectangular frames are connected to one another by a hinge so the angle between the frames may be varied thereby varying the inclination of the reading material. A pair of bent spring mounted wires for holding opposing pages of the reading material open for reading without substantial visual interference of the pages is mounted to the base. The wires are also adjustable to the thickness of the reading material and have a variable friction adjustment. This enables the force of the wires against the pages to be varied and permits the reader to manipulate the pages with the stick.
Kerley, James J.↗
How Much is Remembered as a Function of Presentation Modality?
According to a widespread claim often used for teaching recommendations, students remember 10 percent of what they read, 20 percent of what they hear, 30 percent of what they see, and 50 percent of what they see and hear. Clearly, the percentages cannot be correct, and there is no empirical evidence even for the ordering. To investigate the ordering, we used a laboratory paradigm that has already revealed some findings regarding the ordering of modalities for remembering information. In this paradigm, subjects are given messages instructing them to move in a grid of four stacked matrices by clicking a computer mouse. The current experiment compared 3 modalities presented either once, see (visual arrows), hear (auditory words), read (visual words); twice in succession, see see, hear hear, read read; or in two different successive modalities, see hear, hear see, see read, read see, hear read, read hear. We found better performance for messages presented twice than for those presented once, regardless of modality. For the twice-presented messages performance varied as a function of the second modality, with best performance for see and worst for read.
information↗
Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry
PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7–12 per sample) compared to commercial kits (US$30–50 per sample).
Parris, D. Joshua↗
Extracting the Data From the LCM vk4 Formatted Output File
These are slides about extracting the data from the LCM vk4 formatted output file. The following is covered: vk4 file produced by Keyence VK Software, custom analysis, no off the shelf way to read the file, reading the binary data in a vk4 file, various offsets in decimal lines, finding the height image data, directly in MATLAB, binary output beginning of height image data, color image information, color image binary data, color image decimal and binary data, MATLAB code to read vk4 file (choose a file, read the file, compute offsets, read optical image, laser optical image, read and compute laser intensity image, read height image, timing, display height image, display laser intensity image, display RGB laser optical images, display RGB optical images, display beginning data and save images to workspace, gamma correction subroutine), reading intensity form the vk4 file, linear in the low range, linear in the high range, gamma correction for vk4 files, computing the gamma intensity correction, observations.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
CMS Storage Performance with RNTuple
CMS is transitioning to use ROOT’s new RNTuple data storage format for the files CMS will write in the HL-LHC era. Based on initial tests, CMS expects faster I/O and smaller files compared to the present TTree storage format. This contribution will show a comprehensive performance comparison between RNTuple and TTree I/O using CMS AOD and MiniAOD data formats as test cases for both simulation and collision data corresponding to similar data taking conditions of LHC Run 3. Quantities such as the resulting file size, the memory usage of the I/O components, and the rate of events being read from a file or written to a file will be measured. CMS’ data processing relies heavily on reading files over the local or wide area networks. The file read patterns are important because the latencies have been seen to influence the total production job times. Therefore a study on the file read patterns will be conducted by recording traces of the offset, size, and timestamp of each read request for both RNTuple and TTree. The behavior of network reads will be mimicked by reading local files where artificial latency will be added to the read requests. The effect of different latency values on the job times will be studied.
Jones, Christopher D. [Fermilab]↗
Multisensor Arrays for Greater Reliability and Accuracy
Arrays of multiple, nominally identical sensors with sensor-output-processing electronic hardware and software are being developed in order to obtain accuracy, reliability, and lifetime greater than those of single sensors. The conceptual basis of this development lies in the statistical behavior of multiple sensors and a multisensor-array (MSA) algorithm that exploits that behavior. In addition, advances in microelectromechanical systems (MEMS) and integrated circuits are exploited. A typical sensor unit according to this concept includes multiple MEMS sensors and sensor-readout circuitry fabricated together on a single chip and packaged compactly with a microprocessor that performs several functions, including execution of the MSA algorithm. In the MSA algorithm, the readings from all the sensors in an array at a given instant of time are compared and the reliability of each sensor is quantified. This comparison of readings and quantification of reliabilities involves the calculation of the ratio between every sensor reading and every other sensor reading, plus calculation of the sum of all such ratios. Then one output reading for the given instant of time is computed as a weighted average of the readings of all the sensors. In this computation, the weight for each sensor is the aforementioned value used to quantify its reliability. In an optional variant of the MSA algorithm that can be implemented easily, a running sum of the reliability value for each sensor at previous time steps as well as at the present time step is used as the weight of the sensor in calculating the weighted average at the present time step. In this variant, the weight of a sensor that continually fails gradually decreases, so that eventually, its influence over the output reading becomes minimal: In effect, the sensor system "learns" which sensors to trust and which not to trust. The MSA algorithm incorporates a criterion for deciding whether there remain enough sensor readings that approximate each other sufficiently closely to constitute a majority for the purpose of quantifying reliability. This criterion is, simply, that if there do not exist at least three sensors having weights greater than a prescribed minimum acceptable value, then the array as a whole is deemed to have failed.
Immer, Christopher↗
Telomere-to-telomere assemblies of chromosome 10 reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by Helitrons
The model woody plant Populus trichocarpa displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of 3-ketoacyl-CoA synthases ( KCS ), which has been difficult to confirm with short-read assemblies. Long-read sequencing enables the development of telomere-to-telomere resources to detect cryptic variation, including CNVs, which are currently missed. Integrating this information can improve genomic prediction for breeding and provide insights into the evolutionary basis of important traits. Our analysis of 78 long-read haplotypes from chromosome 10 identified more than twice as many KCS genes as previously reported, and numerous intragenic non-synonymous substitutions. Random Forest predictive models highlighted the importance of Potri.010G079500 in producing very long chain alkenes; however, its absence did not predict previously reported alkene-deficient phenotypes. Instead, alkene levels are best predicted by the combinations of KCS copies. Additionally, amino acid substitutions clustered around ligand and donor binding pockets, suggesting they contribute to differing wax cuticle composition. Finally, each KCS gene and copy was linked to a Helitron transposon. A phylogenetic analysis suggests Helitrons are the evolutionary mechanism for generating KCS tandem arrays. Long-read generated telomere-to-telomere assemblies of P. trichocarpa chromosome 10 revealed large-effect loci critical to genetic studies that are unattainable from short-reads. This new resource produced novel insights into genome structure and function, and a novel mechanism for generating tandem gene duplication. Our results highlight that, given current challenges in annotation and assembly, detailed and focused long-read sequences are key to interpreting complex genomic regions that contain tandem copy number variants.
09 BIOMASS FUELS↗
Fault detection and analysis in nuclear research facility using artificial intelligence methods
In this article, an online detection of transducer and actuator condition is discussed. A case study is on the reading of area radiation monitor (ARM) installed at the chimney of PUSPATI TRIGA nuclear reactor building, located at Bangi, Malaysia. There are at least five categories of abnormal ARM reading that could happen during the transducer failure, namely either the reading becomes very high, or very low/ zero, or with high fluctuation and noise. Moreover, the reading may be significantly higher or significantly lower as compared to the normal reading. An artificial neural network (ANN) and adaptive neuro-fuzzy inference system (ANFIS) are good methods for modeling this plant dynamics. The failure of equipment is based on ARM reading so it is then to compare with the estimated ARM data from ANN/ ANFIS function. The failure categories in either ‘yes’ or ‘no’ state are obtained from a comparison between the actual online data and the estimated output from ANN/ ANFIS function. It is found that this system design can correctly report the condition of ARM equipment in a simulated environment and later be implemented for online monitoring. This approach can also be extended to other transducers, such as the temperature profile of reactor core and also to include other critical actuator conditions such as the valves and pumps in the reactor facility provided that the failure symptoms are clearly defined.
42 ENGINEERING↗
CAPG: comprehensive allopolyploid genotyper
Genotyping by sequencing is a powerful tool for investigating genetic variation in plants, but many economically important plants are allopolyploids, where homoeologous similarity obscures the subgenomic origin of reads and confounds allelic and homoeologous SNPs. Recent polyploid genotyping methods use allelic frequencies, rate of heterozygosity, parental cross or other information to resolve read assignment, but good subgenomic references offer the most direct information. The typical strategy aligns reads to the joint reference, performs diploid genotyping within each subgenome, and filters the results, but persistent read misassignment results in an excess of false heterozygous calls. We introduce the Comprehensive Allopolyploid Genotyper (CAPG), which formulates an explicit likelihood to weight read alignments against both subgenomic references and genotype individual allopolyploids from whole-genome resequencing data. We demonstrate CAPG in allotetraploids, where it performs better than Genome Analysis Toolkit’s HaplotypeCaller applied to reads aligned to the combined subgenomic references.
59 BASIC BIOLOGICAL SCIENCES↗
Usage Pattern-Driven Dynamic Data Layout Reorganization
As scientific simulations and experiments move toward extremely large scales and generate massive amounts of data, the data access performance of analytic applications becomes crucial. A mismatch often happens between write and read patterns of data accesses, typically resulting in poor read performance. Data layout reorganization has been used to improve the locality of data accesses. However, current data reorganizations are static and focus on generating a single (or set of) optimized layouts that rely on prior knowledge of exact future access patterns. We propose a framework that dynamically recognizes the data usage patterns, replicates the data of interest in multiple reorganized layouts that would benefit common read patterns, and makes runtime decisions on selecting a favorable layout for a given read pattern. This framework supports reading individual elements and chunks of a multi-dimensional array of variables. Our pattern-driven layout selection strategy achieves multi-fold speedups compared to reading from the original dataset.
97 MATHEMATICS AND COMPUTING↗
Parallel programming of an ionic floating-gate memory array for scalable neuromorphic computing
Neuromorphic computers could overcome efficiency bottlenecks inherent to conventional computing through parallel programming and readout of artificial neural network weights in a crossbar memory array. However, selective and linear weight updates and <10-nanoampere read currents are required for learning that surpasses conventional computing efficiency. We introduce an ionic floating-gate memory array based on a polymer redox transistor connected to a conductive-bridge memory (CBM). Selective and linear programming of a redox transistor array is executed in parallel by overcoming the bridging threshold voltage of the CBMs. Synaptic weight readout with currents <10 nanoamperes is achieved by diluting the conductive polymer with an insulator to decrease the conductance. The redox transistors endure >1 billion write-read operations and support >1-megahertz write-read frequencies.
bio-inspired, energy storage (including batteries ↗
Validation Testing for Automated Solubility Measurement Equipment Final Report
Laboratory tests have been completed to test the validity of automated solubility measurement equipment using sodium nitrate and sodium chloride solutions (see test plan WRPS-1404441, “Validation Testing for Automated Solubility Measurement Equipment”). The sodium nitrate solution results were within 2-3% of the reference values, so the experiment is considered successful using the turbidity meter. The sodium chloride test was done by sight, as the turbidity meter did not work well using sodium chloride. For example, the “clear” turbidity reading was 53 FNU at 80 °C, 107 FNU at 55 °C, and 151 FNU at 20 °C. The sodium chloride did not work because it is granular and large; as the solution was stirred, the granules stayed to the outside of the reactor and just above the stir bar level, having little impact on the turbidity meter readings as the meter was aimed at the center of the solution. Also, the turbidity meter depth has an impact. The salt tends to remain near the stir bar level. If the meter is deeper in the slurry, it will read higher turbidity, and if the meter is raised higher in the slurry, it will read lower turbidity (possibly near zero) because it reads the “clear” part of the slurry. The sodium chloride solution results, as measured by sight rather than by turbidity instrument readings, were within 5-6% of the reference values.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis
Background: Investigators using metagenomic sequencing to study microbiomes often trim and decontaminate reads without knowing their effect on downstream analyses. Objective: This study was designed to evaluate the impacts JGI trimming and decontamination procedures have on assembly and binning metrics, placement of MAGs into species trees, and functional profiles of MAGs extracted from complex rhizosphere metagenomes, as well as how more aggressive trimming impacts these binning metrics. Methods: Twenty-three Miscanthus x giganteus rhizosphere metagenomes were subjected to different combinations and thresholds of force, kmer, and quality trimming and decontamination using BBDuk. Reads were assembled and binned in KBase. Phylogenomic and statistical analyses were applied to evaluate the effects of trimming and decontamination on downstream analyses. Results: We found that JGI trimmed and decontaminated reads had significant impacts on assembly and binning metrics compared to raw reads, including significantly higher total contig counts, more contigs greater than 10k bp in length, and larger total lengths of raw assemblies compared to QC assemblies, and 2.0% lower average contamination of QC MAGs compared to raw MAGs. We also found that differences in the placement of MAGs in species trees increased with decreasing completeness and contamination thresholds. Furthermore, aggressive trimming (Q20) was found to significantly reduce MAG counts. Conclusion: 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 are recommended for removing sample processing and sequencing artifacts.
Whitham, Jason M.↗
JAN transistor and diode characterization test program, JANTX diode 1N5623
A statistical summary of the electrical characterization of diodes and transistors is presented. Each parameter is presented with test conditions, mean, standard deviation, lowest reading, 10% point (where 10% of all readings are equal to or less than the indicated reading), 90% point (where 90% of all readings are equal to or less than indicated reading) and the highest reading.
Takeda, H.↗