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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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

SU-E-T-98: Dependence of Radiotherapy Couch Transmission Factors On Field Size and Couch-Isocenter Distance

Purpose: The dosimetric effect of the treatment couch is non-negligible in today's radiotherapy treatment. To accurately include couch in dose calculation, we investigated the dependence of couch transmission factors on field size and couch-isocenter distance. Methods: Couch transmission factors for Varian Exact Couch were determined by taking the ratios of ionization of a posterior-anterior beam with and without the couch in the beam path. Measurements were performed at the isocenter using a PTW cylindrical ionization chamber (Model 31030) with an Aluminum buildup cap of 1.1 cm thick for the 6 MV photon beam. Ionization readings for beam sizes ranging from 2 × 2 cm2 to 40 × 40 cm2 were taken. Transmission factors for couch-isocenter distances ranging from 3 cm to 20 cm were also investigated. Results: The couch transmission factors increased with the field size approximately in an exponential manner. For the field sizes that we tested, the transmission factor ranged from 0.976 to 0.992 for couch-isocenter distance of 3 cm. The transmission factor was also monotonically dependent on couch-isocenter separation distance, but in a lighter magnitude. For the tested couch heights, the transmission factor ranged from 0.974 – 0.972 for 2 × 2 cm2 field size and 0.992 – 0.986 for 40 × 40 cm2 field size. The dependence on couch-isocenter distance is stronger for larger field size. Conclusions: The transmission factor of a radiotherapy treatment couch increases with field size of the radiation beam and its distance from the isocenter. Such characterization of the couch transmission factor helps improve the accuracy of couch modeling for radiotherapy treatment planning.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information

Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility. Using these simulations, we monitored the behavior of several correlation statistics, including the Pearson’s R and Spearman’s ρ coefficients as well as Kendall’s τ and Top–Down correlation. We also test the behavior of association measures, including the coefficient of determination R 2 , Kendall’s W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spear man’s ρ, Kendall’s τ, and Kendall’s W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, the R 2 coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships. Collectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Experimental Physical Sciences Vistas Performance through Science Winter 2017

This issue of Experimental Physical Sciences Vistas focuses on the integrated science that plays a critical role in Los Alamos National Laboratory’s support of the nation’s nuclear deterrent. I hope you will enjoy reading about these accomplishments, opportunities, and challenges.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Accelerated Data Analytics for Power-System Time-Series (ADAPT) [Final Project Report]

Over the past decade, electric utilities have made significant progress in deploying networks of phasor measurement units (PMUs). The high-speed measurements provided by PMUs are valuable for offline analysis, but the sheer volume of data presents a challenge for utilities. The Accelerated Data Analytics for Power-System Time-Series (ADAPT) project was created to address this challenge by developing SciSync, an open-source software tool that enables utilities to rapidly read, process, analyze, and review grid measurements. SciSync was designed to provide the capabilities of Archive Walker, a research tool developed by PNNL, along with the reliability and performance of commercial-grade software.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Benchmarking DAOS Filesystem on Aurora

We benchmark the DAOS filesystem on Argonne's Aurora supercomputer (127 nodes, 4,064 targets) using fio, IOR, mdtest, and IO500 to characterize I/O and metadata performance across the DFS API and DFuse+POSIX. Single-client fio shows POSIX bandwidth saturating at 1–2 MiB I/O sizes, with write-heavy workloads outperforming reads. Multi-node IOR shows DFS bandwidth scaling well up to ~32 tasks/node, with write latency growing faster than read latency. An 8-node IO500 evaluation shows DFS achieving ~5x higher bandwidth and ~190x higher IOPS than POSIX. Results indicate DAOS is well-suited to read-heavy workloads like AI training data loading, given appropriately sized transfers and concurrency.

George, Rebecca [College of William and Mary, Will↗
NASA NTRS1983

Blue compact dwarf galaxies. II - Near-infrared studies and stellar populations

An IR photometric survey was performed of 36 blue compact dwarf galaxies (BCDG) where intense bursts of star formation have been observed. The survey covered the J, H, and K lines, with all readings taken at the level of a few mJy. Although the near-IR fluxes observed in the galaxies are due to K and M giants, the bursts have calculated ages of less than 50 million yr. However, the BCDG galaxies surveyed are not young, with the least chemically evolved galaxy observed, I Zw 18, featuring 50 pct of its stars formed prior to its last burst, but with a missing mass that is not accounted for by H I interferometric observations. It is concluded that the old stars must be more spatially extended than the young stars, and a mixture of OB stars with the K and M giants is projected as capable of displaying the colors observed. The star formation processes in the BCDG galaxies is defined as dependent on the total mass of the galaxies, with low mass galaxies having a high ratio of star formation, compared to their previous rates.

Thuan, T. X.↗
NASA NTRS1983

A 20-GHz IMPATT transmitter, summary

A three stage IMPATT diode amplifier capable of a 16 W CW output and a 2 dB bandwidth of 117 MHz was developed. On the component side, high performance circulators with a 0.2 dB insertion loss and bandwidth of 5 GHz were fabricated. State of the art GaAs IMPATT diodes incorporating diamond heat sink and double Read doping profile were also developed. The diodes are capable of a 2.5 W CW output. A few diodes achieved power outputs as high as 3 W. On the circuit side, high gain (up to 12 dB per stage) single diode, multituned circuits capable of 2 GHz and 930 MHx bandwidth were developed as the first and second stages, respectively, of the amplifier. A 12 diode waveguide cavity combiner was developed as the output stage. The output stage utilized commercially available single drift GaAs IMPATT diodes.

Source record↗
NASA NTRS2017

MS Non-Pharmacological Countermeasure to Decrease Landing Sickness and Improve Functional Performance While Disorientad

Upon return from spaceflight, a majority of crewmembers experience motion sickness (MS) symptoms. The interactions between crewmembers' adaptation to a gravitational transition, the performance decrements resulting from MS and/or use of promethazine (PMZ), and the constraints imposed by mission task demands could significantly challenge and limit an astronaut's ability to perform functional tasks during gravitational transitions. No operational countermeasure currently exists to mitigate the risks associated with these sensorimotor disturbances. Stochastic resonance (SR) can be thought of simply as "noise benefit" or an increase in information transfer by a system when in the presence of a non-zero level of noise. We have shown that low levels of stochastic vestibular stimulation (SVS) improve balance and locomotor performance due to SR (Goel et al. 2015, Mulavara et al. 2011, 2015). Additionally, a study in a 6-hydroxydopamine (6-OHDA) hemi-lesioned rat model of Parkinson's disease demonstrated improvements in locomotor activity after low-level SVS delivery possibly due to an increase in nigral gamma-aminobutyric acid (GABA) release in a dopamine independent way (Samoudi et al. 2012). SVS specifically increased GABA release on the lesioned, but not the intact side. These results suggest that SVS can cause targeted alterations of GABA release to affect performance of functional tasks. Activation of the GABA pathway is important in modulating MS and promoting adaptability (Cohen 2008). Magnusson et al. (2000) supported this finding by showing that the administration of a GABAB agonist caused a reversal of the symptoms that is normally seen after unilateral labyrinthectomy. Thus, GABA could play a significant role in reducing MS and promoting adaptability. We have taken advantage of the SR mechanism as a modulator of neurotransmitters to develop a unique SVS countermeasure system to mitigate MS symptoms and improve functional performance after landing. Healthy subjects (n=20) participated in two test sessions, one in which they received +/-400 microA of SVS and one where they received no stimulation (0 microA); the study design was counterbalanced. Subjects began by performing a series of four functional tasks 3-5 times as baseline measurements of task performance. Then, to induce MS, subjects walked an obstacle course with up-down reversing prisms. If they completed the course before achieving our pre-determined level of MS, they were asked to read a poster while making large up-down head movements to a metronome while still wearing the reversing prism goggles. Subjects were stopped every two minutes and asked to report their MS symptoms. Using the Pensacola Scale for motion sickness, test operators evaluated the level of MS of each subject. Once a subject reached an 8 on this scale, which is equivalent to mild malaise, or 30 minutes had passed since the start of the MS induction, this protocol was stopped. Finally, immediately after MS induction, subjects were asked to complete the four functional tasks again. Although, 100% of our subjects experienced at least one MS symptom, only 55% of our subjects experienced stomach awareness to any degree. Without SVS, only 40% of subjects lasted the full 30-minute MS induction protocol, while 65% of subjects lasted the full 30 minutes with SVS, which is nearly a significant increase (p=0.056). In addition, subjects showed significant improvement from baseline when performing a tandem walk and a prone-to-stand test immediately after the MS induction protocol was stopped but the stimulation level was continued. The results are promising and future work includes comparing MS progression between PMZ and SVS directly in subjects that are provoked to a minimum of nausea. Low levels of SVS stimulation may serve as a non-pharmacological countermeasure to replace or reduce the PMZ dosage requirements and concurrently improve functional performance during transitions to new gravitational environments after spaceflight.

Rosenberg, M. J. F.↗
DOE OSTI2012

Analysis of the Salt Feed Tank Core Sample

The Saltstone Production Facility (SPF) immobilizes and disposes of low-level radioactive and hazardous liquid waste (salt solution) remaining from the processing of radioactive material at the Savannah River Site (SRS). Low-level waste (LLW) streams from processes at SRS are stored in Tank 50 until the LLW can be transferred to the SPF for treatment and disposal. The Salt Feed Tank (SFT) at the Saltstone Production Facility (SPF) holds approximately 6500 gallons of low level waste from Tank 50 as well as drain water returned from the Saltstone Disposal Facility (SDF) vaults. Over the past several years, Saltstone Engineering has noted the accumulation of solids in the SFT. The solids are causing issues with pump performance, agitator performance, density/level monitoring, as well as taking up volume in the tank. The tank has been sounded at the same location multiple times to determine the level of the solids. The readings have been 12, 25 and 15 inches. The SFT is 8.5 feet high and 12 feet in diameter, therefore the solids account for approximately 10 % of the tank volume. Saltstone Engineering has unsuccessfully attempted to obtain scrape samples of the solids for analysis. As a result, Savannah River National Laboratory (SRNL) was tasked with developing a soft core sampler to obtain a sample of the solids and to analyze the core sample to aid in determining a path forward for removing the solids from the SFT. The source of the material in the SFT is the drain water return system where excess liquid from the Saltstone disposal vaults is pumped back to the SFT for reprocessing. It has been shown that fresh grout from the vault enter the drain water system piping. Once these grout solids return to the SFT, they settle in the tank, set up, and can't be reprocessed, causing buildup in the tank over time. The composition of the material indicates that it is potentially toxic for chromium and mercury and the primary radionuclide is cesium-137. Qualitative measurements show that the material is not cohesive and will break apart with some force.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

ALICE-USA Barrel Tracking Upgrade (Project Final Report)

The ALICE-USA Barrel Tracking Upgrade (BTU) project began in 2015 to participate in a major upgrade of the Time Projection Chamber (TPC) and the Inner Tracking System (ITS) of the ALICE Experiment at CERN in Geneva, Switzerland. This upgrade increased the maximum readout rate of the ALICE detector to accommodate the increased heavy ion interaction rates following Long Shutdown 2 of the Large Hadron Collider, and greatly improved the vertexing performance of the detector. The original scope was completed and reviewed in November 2019. The BTU project document BTU.19.v1 "ALICE Barrel Tracking Upgrade Project Closeout / Transition to Operations (2019)" from November 2019 describes the status in detail and is attached as Appendix 1 below. At that point, all delivery milestones had been met on time, all Key Performance Parameters (KPPs) of the project had been satisfied, and the project was under budget. Several subsequent No Cost Extensions (NCEs) supported integration and pre-commissioning of the BTU project deliverables at CERN, as well as study and assessment of performance with Pb-Pb collisions at 50 kHz. The BTU project was successfully completed on 30 September 2024.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

A Conceptual Design for a Mobile Application to Support Infield Inventory Activities

This paper introduces an inventory assistant being developed at Oak Ridge National Laboratory (ORNL) that we believe will empower users to perform inventory activities at nuclear facilities more accurately, reliably, and quickly. Inventory activities at nuclear facilities are often conducted using pen and paper, which can be time-consuming, tedious, and susceptible to reading or transcription errors. The proposed inventory assistant would replace the paper-based process used by International Atomic Energy Agency (IAEA) inspectors, nuclear facility operators, or verification monitors to complete an inventory of nuclear and non-nuclear items. In general, the inventory assistant would ingest an inventory list, distribute assigned items from the inventory list to one or more mobile devices, enable inventory teams to record their observations in the field, and then enable an inventory lead to integrate and reconcile the observations to produce a final report. The assistant consists of two software components—one for the inventory teams to record observations in the field (In-Field Observations App [IFOA]) and one for the inventory lead to reconcile the inventory list with observations (Distribution, Integration, and Reconciliation Application [DIRA]). This paper introduces the overall workflow of the inventory assistant and describes the IFOA user experience in more detail. To demonstrate the concept, the authors present a use case of IAEA inspectors conducting item counting and tag checking activities of UF6 cylinders at a gas centrifuge enrichment plant with a large number of UF6 cylinders (e.g., thousands). These activities can currently require 30–40 person-days of inspection to complete. Based on experiences during an exercised performed at the IAEA by the ORNL team in 2016, we believe an inventory assistant could allow the IAEA to complete item counting and tag checking using the global identifier or the operator’s barcode in 8–10 person-days of inspection. We would expect other users (e.g., facility operators or verification monitors) to also benefit from significant time savings.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

AGR 5/6/7 Data Qualification Report for ATR Cycles 162B through 168A

This report provides the qualification status of experimental data for the Advanced Gas Reactor (AGR) 5/6/7 fuel irradiation. AGR-5/6/7 was conducted in the Advanced Test Reactor (ATR) at Idaho National Laboratory (INL) in support of development and qualification of tri-structural isotropic (TRISO) low-enriched fuel for use in high temperature gas-cooled reactors. The objectives of the AGR-5/6/7 experiments are to: (i) irradiate reference-design fuel particles to support fuel qualification, (ii) establish operating margins for the fuel beyond normal operating conditions, and (iii) provide irradiated-fuel performance data and irradiated-fuel samples for post-irradiation examination (PIE) and safety testing. The test train contains five separate capsules that were independently controlled and monitored. Each capsule contains multiple 12.51-mm-long compacts filled with low enriched uranium carbide/oxide (UCO) TRISO fuel particles. The primary objective of the AGR-5/6 test (Capsules 1, 2, 4, and 5) is to verify successful performance of the reference-design fuel under normal operating conditions. The AGR-7 test (Capsule 3) was designed to explore fuel performance at higher temperatures to demonstrate the capability of the fuel to withstand conditions beyond normal operating conditions in support of plant design and licensing. AGR 5/6/7 will also provide irradiated-fuel performance data on fission-gas release from failed particles during irradiation. The AGR-5/6/7 capsules were irradiated in the ATR northeast flux trap location. The experiment began on February 16, 2018 and ended on July 22, 2020, spanning nine ATR cycles over two and a half years. Thus, the AGR-5/6/7 fuel compacts were irradiated for a total of 360.9 effective full power days. The AGR 5/6/7 experiment was able to remain in the reactor core during all three Powered Axial Locator Mechanism (PALM) cycles (163A, 165A, and 167A) without overheating its fuel compacts. This report includes irradiation monitoring data from nine ATR Cycles: 162B, 163A, 164A, 164B, 165A, 166A, 166B, 167A, and 168A, as stored in the Nuclear Data Management and Analysis System (NDMAS). During irradiation, data records consisted of instantaneous measurements recorded every minute and provided by text files automatically every 2 hours. The AGR 5/6/7 data streams addressed in this report include thermocouple (TC) temperatures, sweep gas data (flow rates [capsule inlet, outlet, and downstream at detector], pressure, and moisture content), and Fission Product Monitoring System (FPMS) data (release rates and release to birth rate ratios [R/Bs]) for each of the five capsules. A total of 94,989,908 TC temperature and sweep gas data records were received and processed by NDMAS for AGR 5/6/7 irradiation. Of these records, 41,593,387 (or 43.7% of the total) met data collection and accuracy requirements and are labeled as Qualified. A total of 57,746,693 TC temperature readings were captured from 54 installed TCs. Among them, 10,034,676 TC temperature records (only 17.4%) were Qualified and 47,701,371 TC temperatures (or 82.6%) are Failed due to 48 TC failures (63.5%) and due to missing values (19.1%). To assess performance of the operational TCs, analysis of daily correlations between TCs found no evidence of virtual junction failure for any TCs. Analyses on control charts of TC temperature differences revealed trending in TC readings for TC2, 4, 5, and 13 in Capsule 3, but there is no conclusive indication of TC drift failure that caused those trends. Therefore, TC control charts are not used to disqualify TC data, but only for users’ consideration. For sweep gas flow rates, a total of 31,519,747 gas flow records (84.4%) are Qualified for use for AGR-5/6/7 experiment; 5,723,468 gas flow records (15.4%) are Failed due mostly to missing values; and 74,641 high sweep gas flow rates (0.2 %) are Trend. A large number of Failed missing TC temperature and gas flow values were caused by an error in the data output script that outputted a ‘NULL’ value when values were unchanged. This problem was fixed during the outage of Cycle 166B, which led to a substantially decreased number of missing values during the last three cycles. Nonetheless, a large amount of non-missing data remained because of the high data acquisition frequency (1-minute) and still provided sufficient data to effectively monitor the experiment as designed. For FPMS data, NDMAS received and processed fission product release and R/B data for nine ATR cycles, when ATR core reached full power during AGR 5/6/7 irradiation. These data consist of 110,388 release rate records and 110,388 R/B records for the twelve radionuclides (Kr 85m, Kr 87, Kr 88, Kr 89, Kr 90, Xe 131m, Xe 133, Xe 135, Xe 135m, Xe 137, Xe 138, and Xe 139) for each of the five capsules. Equivalent numbers of uncertainty records associated the release rates and R/B values were provided. To date, qualification status of the FPMS data stored in the NDMAS dat

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
NASA NTRS2010

Tool for Forecasting Cool-Season Peak Winds Across Kennedy Space Center and Cape Canaveral Air Force Station

The expected peak wind speed for the day is an important element in the daily morning forecast for ground and space launch operations at Kennedy Space Center (KSC) and Cape Canaveral Air Force Station (CCAFS). The 45th Weather Squadron (45 WS) must issue forecast advisories for KSC/CCAFS when they expect peak gusts for >= 25, >= 35, and >= 50 kt thresholds at any level from the surface to 300 ft. In Phase I of this task, the 45 WS tasked the Applied Meteorology Unit (AMU) to develop a cool-season (October - April) tool to help forecast the non-convective peak wind from the surface to 300 ft at KSC/CCAFS. During the warm season, these wind speeds are rarely exceeded except during convective winds or under the influence of tropical cyclones, for which other techniques are already in use. The tool used single and multiple linear regression equations to predict the peak wind from the morning sounding. The forecaster manually entered several observed sounding parameters into a Microsoft Excel graphical user interface (GUI), and then the tool displayed the forecast peak wind speed, average wind speed at the time of the peak wind, the timing of the peak wind and the probability the peak wind will meet or exceed 35, 50 and 60 kt. The 45 WS customers later dropped the requirement for >= 60 kt wind warnings. During Phase II of this task, the AMU expanded the period of record (POR) by six years to increase the number of observations used to create the forecast equations. A large number of possible predictors were evaluated from archived soundings, including inversion depth and strength, low-level wind shear, mixing height, temperature lapse rate and winds from the surface to 3000 ft. Each day in the POR was stratified in a number of ways, such as by low-level wind direction, synoptic weather pattern, precipitation and Bulk Richardson number. The most accurate Phase II equations were then selected for an independent verification. The Phase I and II forecast methods were compared using an independent verification data set. The two methods were compared to climatology, wind warnings and advisories issued by the 45 WS, and North American Mesoscale (NAM) model (MesoNAM) forecast winds. The performance of the Phase I and II methods were similar with respect to mean absolute error. Since the Phase I data were not stratified by precipitation, this method's peak wind forecasts had a large negative bias on days with precipitation and a small positive bias on days with no precipitation. Overall, the climatology methods performed the worst while the MesoNAM performed the best. Since the MesoNAM winds were the most accurate in the comparison, the final version of the tool was based on the MesoNAM winds. The probability the peak wind will meet or exceed the warning thresholds were based on the one standard deviation error bars from the linear regression. For example, the linear regression might forecast the most likely peak speed to be 35 kt and the error bars used to calculate that the probability of >= 25 kt = 76%, the probability of >= 35 kt = 50%, and the probability of >= 50 kt = 19%. The authors have not seen this application of linear regression error bars in any other meteorological applications. Although probability forecast tools should usually be developed with logistic regression, this technique could be easily generalized to any linear regression forecast tool to estimate the probability of exceeding any desired threshold . This could be useful for previously developed linear regression forecast tools or new forecast applications where statistical analysis software to perform logistic regression is not available. The tool was delivered in two formats - a Microsoft Excel GUI and a Tool Command Language/Tool Kit (Tcl/Tk) GUI in the Meteorological Interactive Data Display System (MIDDS). The Microsoft Excel GUI reads a MesoNAM text file containing hourly forecasts from 0 to 84 hours, from one model run (00 or 12 UTC). The GUI then displays e peak wind speed, average wind speed, and the probability the peak wind will meet or exceed the 25-, 35- and 50-kt thresholds. The user can display the Day-1 through Day-3 peak wind forecasts, and separate forecasts are made for precipitation and non-precipitation days. The MIDDS GUI uses data from the NAM and Global Forecast System (GFS), instead of the MesoNAM. It can display Day-1 and Day-2 forecasts using NAM data, and Day-1 through Day-5 forecasts using GFS data. The timing of the peak wind is not displayed, since the independent verification showed that none of the forecast methods performed significantly better than climatology. The forecaster should use the climatological timing of the peak wind (2248 UTC) as a first guess and then adjust it based on the movement of weather features.

Barrett, Joe H., III↗
DOE OSTI2016

Stride Search v. 1.0

Stride Search provides a flexible tool for detecting storms or other extreme climate events in high-resolution climate data sets saved on uniform latitude-longitude grids in standard NetCDF format. Users provide the software a quantitative description of a meteorological event they are interested in; the software searches a data set for locations in space and time that meet the user’s description. In its first stage, Stride Search performs a spatial search of the data set at each timestep by dividing a search domain into circular sectors of constant geodesic radius. Data from a netCDF file is read into memory for each circular search sector. If the data meet or exceed a set of storm identification criteria (defined by the user), a storm is recorded to a linked list. Finally, the linked list is examined and duplicate detections of the same storm are removed and the results are written to an output file. The first stage’s output file is read by a second program that builds storm. Additional identification criteria may be applied at this stage to further classify storms. Storm tracks are the software’s ultimate output and routines are provided for formatting that output for various external software libraries for plotting and tabulating data.

Bosler, Peter↗
DOE OSTI2013

PCR-Induced Transitions Are the Major Source of Error in Cleaned Ultra-Deep Pyrosequencing Data

Ultra-deep pyrosequencing (UDPS) is used to identify rare sequence variants. The sequence depth is influenced by several factors including the error frequency of PCR and UDPS. This study investigated the characteristics and source of errors in raw and cleaned UDPS data. UDPS of a 167-nucleotide fragment of the HIV-1 SG3Δenv plasmid was performed on the Roche/454 platform. The plasmid was diluted to one copy, PCR amplified and subjected to bidirectional UDPS on three occasions. The dataset consisted of 47,693 UDPS reads. Raw UDPS data had an average error frequency of 0.30% per nucleotide site. Most errors were insertions and deletions in homopolymeric regions. We used a cleaning strategy that removed almost all indel errors, but had little effect on substitution errors, which reduced the error frequency to 0.056% per nucleotide. In cleaned data the error frequency was similar in homopolymeric and non-homopolymeric regions, but varied considerably across sites. These site-specific error frequencies were moderately, but still significantly, correlated between runs (r = 0.15–0.65) and between forward and reverse sequencing directions within runs (r = 0.33–0.65). Furthermore, transition errors were 48-times more common than transversion errors (0.052% vs. 0.001%; p<0.0001). Collectively the results indicate that a considerable proportion of the sequencing errors that remained after data cleaning were generated during the PCR that preceded UDPS. A majority of the sequencing errors that remained after data cleaning were introduced by PCR prior to sequencing, which means that they will be independent of platform used for next-generation sequencing. The transition vs. transversion error bias in cleaned UDPS data will influence the detection limits of rare mutations and sequence variants.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

A high speed CMOS correlator

A full custom, 25 MHz, 1.6 microns CMOS Correlator chip is presented. The 5.15mm by 4.23mm chip performs either autocorrelation or crosscorrelation, consuming less than 10mW per channel. The correlator, designed for a space borne spectrometer, contains 32 channels. The 24 bit accumulator registers can be read independent of the input data path, in either 8 bit bytes, or 16 bit words. The device is cascadable and allows integration periods of up to 1.78 seconds, at 25 Megasamples/second. The controllers, for the input data path and the data output section, are implemented with Sequence Invariant State Machines.

Canaris, J.↗
NASA NTRS2005

The Different Wavelengths of Radio Science

Radio Science covers many different avenues. This summer I attempted to work in each of the different avenues to learn the full range of subjects covered by Radio Science. I began my summer by traveling to Greece for the 3rd International Planetary Probe Workshop (IPPW-3). I went as a co-author of the Doppler Wind Experiment (DWE) team paper. My first job when I returned from Greece was to update the Radio Science activities webpage. I then used Fast Fourier Transforms (FFT) to find radio signals in recorded Radio Science experimental data and determine frequencies and powers. I read about and ran Fortran code being used to determine wind measurements on Huygens. I formatted and revised the abstracts and data lengths for the DVD data sets. By performing these tasks, I also learned the Unix operating system as well as a small amount of shell programming.

Malecha, Jessica L.↗