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NASA NTRSDate not supplied

Optimizing a Small RNAseq Analysis Pipeline for NASA GeneLab Using Open-Source Tools and Libraries

Small RNA sequencing (small RNAseq) is a powerful tool for studying the regulation of gene expression in various organisms. Small RNAseq has been leveraged in space biology research to study how expression of small RNAs, e.g. micro RNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs), change upon exposure to the space environment. NASA GeneLab currently hosts small RNAseq raw data derived from space-relevant experiments on the Open Science Data Repository (OSDR). To maximize the accessibility of these data to the scientific community, in addition to hosting raw data, which is only interpretable by bioinformaticians, GeneLab plans to process all small RNAseq datasets and make those processed data available to the scientific community via the OSDR. In this study, we present the development of the GeneLab standardized pipeline for processing small RNAseq datasets. Using human, plant, and synthetic small RNAseq datasets, we interrogate various open-source software and publicly available databases to evaluate their accuracy and reproducibility in each step of the pipeline. For quality control and adapter detection and trimming, we evaluated TrimGalore!, FASTX, SeqKit, and DNApi methods to optimize alignment to reference genomes. We compared BWA, Bowtie, and Bowtie2 to determine the optimal alignment tool. For each alignment tool we also assessed various reference databases, including Ensembl reference genomes and different types of small RNA reference databases, including genome, hairpin, and miRNA references from the miRbase and MirGeneDB databases. To quantify the aligned data, we compared SAMtools, HTSeq, and RSEM for counting alignment events from each alignment tool used. Finally, we evaluated various tools, including DESeq2 and EdgeR, for data normalization and subsequent differential expression analysis. We will present the results from our comparative analyses for each pipeline step and propose a consensus pipeline for processing small RNAseq data derived from various organisms exposed to the space environment.

SmallRNAseq, NASA GeneLab, quality control, adapte↗
NASA NTRS2005

Microparticle Flow Sensor

The microparticle flow sensor (MFS) is a system for identifying and counting microscopic particles entrained in a flowing liquid. The MFS includes a transparent, optoelectronically instrumented laminar-flow chamber (see figure) and a computer for processing instrument-readout data. The MFS could be used to count microparticles (including micro-organisms) in diverse applications -- for example, production of microcapsules, treatment of wastewater, pumping of industrial chemicals, and identification of ownership of liquid products.

Morrison, Dennis R.↗
NASA NTRS2012

Restoration and Reexamination of Data from the Apollo 11, 12, 14, and 15 Dust, Thermal and Radiation Engineering Measurements Experiments

As part of an effort by the Lunar Data Node (LDN) we are restoring data returned by the Apollo Dust, Thermal, and Radiation Engineering Measurements (DTREM) packages emplaced on the lunar surface by the crews of Apollo 11, 12, 14, and 15. Also commonly known as the Dust Detector experiments, the DTREM packages measured the outputs of exposed solar cells and thermistors over time. They operated on the surface for up to nearly 8 years, returning data every 54 seconds. The Apollo 11 DTREM was part of the Early Apollo Surface Experiments Package (EASEP), and operated for a few months as planned following emplacement in July 1969. The Apollo 12, 14, and 15 DTREMs were mounted on the central station as part of the Apollo Lunar Surface Experiments Package (ALSEP) and operated from deployment until ALSEP shutdown in September 1977. The objective of the DTREM experiments was to determine the effects of lunar and meteoric dust, thermal stresses, and radiation exposure on solar cells. The LDN, part of the Geosciences Node of the Planetary Data System (PDS), operates out of the National Space Science Data Center (NSSDC) at Goddard Space Flight Center. The goal of the LDN is to extract lunar data stored on older media and/or in obsolete formats, restore the data into a usable digital format, and archive the data with PDS and NSSDC. For the DTREM data we plan to recover the raw telemetry, translate the raw counts into appropriate output units, and then apply calibrations. The final archived data will include the raw, translated, and calibrated data and the associated conversion tables produced from the microfilm, as well as ancillary supporting data (metadata) packaged in PDS format.

McBride, Marie J.↗
NASA NTRS1982

LANDSAT-D flight segment operations manual. Appendix A: Coefficients/calibration data

Telemetry calibration curves for the LANDSAT-4 subsystems are defined by nth order polynomial equations which convert telemetry counts to engineering units. The calibration curve coefficients for each telemetry point are controlled in the data base and are listed along with the unit section number where the sensor is located. Tables showing the coefficients may be obtained from the data base administrator. The tables show telemetry counts versus engineering units.

Gilmore, A.↗
NASA NTRS1991

Determination of confidence limits for experiments with low numbers of counts

Two different methods, classical and Bayesian, for determining confidence intervals involving Poisson-distributed data are compared. Particular consideration is given to cases where the number of counts observed is small and is comparable to the mean number of background counts. Reasons for preferring the Bayesian over the classical method are given. Tables of confidence limits calculated by the Bayesian method are provided for quick reference.

Kraft, Ralph P.↗
NASA NTRS2017

Surface-Height Determination of Crevassed Glaciers-Mathematical Principles of an Autoadaptive Density-Dimension Algorithm and Validation Using ICESat-2 Simulator (SIMPL) Data

Glacial acceleration is a main source of uncertainty in sea-level-change assessment. Measurement of ice-surface heights with a spatial and temporal resolution that not only allows elevation-change calculation, but also captures ice-surface morphology and its changes is required to aid in investigations of the geophysical processes associated with glacial acceleration.The Advanced Topographic Laser Altimeter System aboard NASAs future ICESat-2 Mission (launch 2017) will implement multibeam micropulse photon-counting lidar altimetry aimed at measuring ice-surface heights at 0.7-m along-track spacing. The instrument is designed to resolve spatial and temporal variability of rapidly changing glaciers and ice sheets and the Arctic sea ice. The new technology requires the development of a new mathematical algorithm for the retrieval of height information.We introduce the density-dimension algorithm (DDA) that utilizes the radial basis function to calculate a weighted density as a form of data aggregation in the photon cloud and considers density an additional dimension as an aid in auto-adaptive threshold determination. The auto-adaptive capability of the algorithm is necessary to separate returns from noise and signal photons under changing environmental conditions. The algorithm is evaluated using data collected with an ICESat-2 simulator instrument, the Slope Imaging Multi-polarization Photon-counting Lidar, over the heavily crevassed Giesecke Braer in Northwestern Greenland in summer 2015. Results demonstrate that ICESat-2 may be expected to provide ice-surface height measurements over crevassed glaciers and other complex ice surfaces. The DDA is generally applicable for the analysis of airborne and spaceborne micropulse photon-counting lidar data over complex and simple surfaces.

Herzfeld, Ute C.↗
NASA NTRS1985

A preliminary look at astrometric accuracy as a function of photon counts

The importance of photon counts as a factor in the accuracy of astrometric positions is illustrated by a preliminary look at data collected with the Allegheny Observatory's photon-counting detector, the Multichannel Astrometric Photometer. Twenty estimates are plotted of the standard errors, per hour, of astrometric positions obtained with the photometer and the blue-light lens of the observatory's 30-inch refractor. The agreement between the estimated standard errors in the X and Y coordinates supports the conclusion that, as predicted by Drake, the accuracy is dependent upon the count rate.

Gatewood, G.↗
NASA NTRS1973

RALPH: An online computer program for acquisition and reduction of pulse height data

A background/foreground data acquisition and analysis system incorporating a high level control language was developed for acquiring both singles and dual parameter coincidence data from scintillation detectors at the Radiation Counting Laboratory at the NASA Manned Spacecraft Center in Houston, Texas. The system supports acquisition of gamma ray spectra in a 256 x 256 coincidence matrix (utilizing disk storage) and simultaneous operation of any of several background support and data analysis functions. In addition to special instruments and interfaces, the hardware consists of a PDP-9 with 24K core memory, 256K words of disk storage, and Dectape and Magtape bulk storage.

Davies, R. C.↗
NASA NTRS1999

Parameter Estimation in Astronomy with Poisson-Distributed Data: The (CHI)2(gamma) Statistic - 1

Applying the standard weighted mean formula, [Sigma (sub i)n(sub i)ssigma(sub i, sup -2)], to determine the weighted mean of data, n(sub i), drawn from a Poisson distribution, will, on average, underestimate the true mean by approx. 1 for all true mean values larger than approx.3 when the common assumption is made that the error of the i th observation is sigma(sub i) = max square root of n(sub i), 1).This small, but statistically significant offset, explains the long-known observation that chi-square minimization techniques which use the modified Neyman'chi(sub 2) statistic, chi(sup 2, sub N) equivalent Sigma(sub i)((n(sub i) - y(sub i)(exp 2)) / max(n(sub i), 1), to compare Poisson - distributed data with model values, y(sub i), will typically predict a total number of counts that underestimates the true total by about 1 count per bin. Based on my finding that weighted mean of data drawn from a Poisson distribution can be determined using the formula [Sigma(sub i)[n(sub i) + min(n(sub i), 1)](n(sub i) + 1)(exp -1)] / [Sigma(sub i)(n(sub i) + 1)(exp -1))], I propose that a new chi(sub 2) statistic, chi(sup 2, sub gamma) equivalent, should always be used to analyze Poisson- distributed data in preference to the modified Neyman's chi(exp 2) statistic. I demonstrated the power and usefulness of,chi(sub gamma, sup 2) minimization by using two statistical fitting techniques and five chi(exp 2) statistics to analyze simulated X-ray power - low 15 - channel spectra with large and small counts per bin. I show that chi(sub gamma, sup 2) minimization with the Levenberg - Marquardt or Powell's method can produce excellent results (mean slope errors approx. less than 3%) with spectra having as few as 25 total counts.

Mighell, Kenneth J.↗
NASA NTRS1972

Interplanetary dust and comet orbits

Several years of observational results are available from the Pioneer 8 and 9 interplanetary dust detectors, and these data were used to show dust counts graphically. The characteristics of the five largest dust showers are also summarized.

Roosen, R. G.↗
NASA NTRS1977

Shuttle program: Ground tracking data program document shuttle OFT launch/landing

The equations for processing ground tracking data during a space shuttle ascent or entry, or any nonfree flight phase of a shuttle mission are given. The resulting computer program processes data from up to three stations simultaneously: C-band station number 1; C-band station number 2; and an S-band station. The C-band data consists of range, azimuth, and elevation angle measurements. The S-band data consists of range, two angles, and integrated Doppler data in the form of cycle counts. A nineteen element state vector is used in Kalman filter to process the measurements. The acceleration components of the shuttle are taken to be independent exponentially-correlated random variables. Nine elements of the state vector are the measurement bias errors associated with range and two angles for each tracking station. The biases are all modeled as exponentially-correlated random variables with a typical time constant of 108 seconds. All time constants are taken to be the same for all nine state variables. This simplifies the logic in propagating the state error covariance matrix ahead in time.

Lear, W. M.↗
NASA NTRS1979

The application of laser Rayleigh scattering to gas density measurements in hypersonic helium flows

Measurements of the mean static free-stream gas density have been made in two Langley Research Center helium facilities, the 3-inch leg of the high-Reynolds-number helium complex and the 22-inch hypersonic helium tunnel. Rayleigh scattering of a CW argon ion laser beam at 514.5 nm provided the basic physical mechanism. The behavior of the scattered signal was linear, confirmed by a preliminary laboratory study. That study also revealed the need to introduce baffles to reduce stray light. A relatively simple optical system and associated photon-counting electronics were utilized to obtain data for densities from 10 to the 23rd to 10 to the 25th per cu m. The major purpose, to confirm the applicability of this technique in the hypersonic helium flow, was accomplished.

Hoppe, J. C.↗
NASA NTRS1980

The results from the X ray bremsstrahlung experiment of Project Trigger

Analysis of the bremsstrahlung X-ray data produced the following conclusions. The counting rate observed before the explosion was an expected normal quiet background. An unexpected increase in the counting rate below 20 keV was observed after the explosion, which may have been an effect of the explosion. A significant 0.13-H2 peak in the power spectral density of the X-ray flux was observed, which is interpreted as evidence for a particle-wave-particle interaction involving a bounce resonance stimulated by the explosion. Dispersed continuation of this interaction may have been responsible for delayed long-term precipitation.

Bering, E. A.↗
NASA NTRS1986

Reduction of spermatogonia and testosterone in rat testes flown on Space Lab-3

The effects of space flight on rat testes were investigated. The weight, spermatogonial cell count, and testosterone levels in six rats flown on Space Lab-3 were measured. It is observed that compared to ground control rats the average weight loss was 7.1 percent and the spermatogonial cell count decreased by 7.5 percent. The data reveal that the testosterone level for large control rats was 9.13 ng/ml and 0.31 ng/ml for flight rats; and 2.54 ng/ml and 0.233 ng/ml for smaller control and flight rats, respectively. It is noted that spermatogenesis and testosterone production are reduced during spaceflight.

Philpott, Delbert E.↗
NASA NTRS1998

Atmospheric Depolarization Lidar Experimental Receiver: A Space Shuttle Hitchhiker Payload

Development work is underway at the Goddard Space Flight Center to construct a depolarization measuring atmospheric lidar receiver. The Atmospheric Lidar (AL) is tentatively scheduled to fly on the Space Shuttle in a late-1999 time frame. The AL will fly in conjunction with the Shuttle Laser Altimeter (SLA) and the Infrared Spectral Imaging Radiometer (ISIR) to provide a comprehensive package of atmospheric aerosol and cloud information. The AL operates in conjunction with the SLA laser transmitter and measures profiles of atmospheric backscatter at 532 nm. The receiver system discriminates between the parallel and perpendicular polarizations of the backscattered signal, thus providing depolarization ratios for scattering from clouds. The lidar receiver also provides cloud height and thickness measurements to complement the brightness temperature measurements generated by the ISIR thermal imager. The function of the AL is twofold. The primary function is to provide range-resolved measurements of atmospheric aerosol backscatter and depolarization ratio at 532 nm with 75 m vertical resolution. The scientific purpose of these measurements is to determine composition of clouds based on the depolarization ratio (i.e cloud content is water or ice), to determine cloud height and thickness, and to gain further understanding of the global distribution of aerosols. This information, when coupled with the cloud brightness measured by the ISIR thermal imager will provide a significant amount of information on cloud composition and radiative effects, particularly for cirrus and sub-visual cirrus clouds. A secondary function of the AL is to serve as an in-space test bed for lidar technology advancements, including a fully fiber-coupled receiver and photon counting from space. In addition, the data obtained by the AL will be used to develop software for the Geoscience Laser Altimeter System (GLAS) flight mission.

McGill, Matthew J.↗
NASA NTRS2013

Fiber Treatment Effects on Bioreactor Bulk Fluid Trends

In order to facilitate the exploration of worlds beyond the borders of our planet, it is necessary to maintain sustainable levels of clean water. The remediation of water via Membrane Aerated Bioreactors (MABRs) is one such method, and the focus of this study. MARRs rely on healthy biofilms grown on hollow fiber membranes to clean non-potable water. These biofilms can take weeks to months to establish. Therefore, various fiber treatments and two inoculums were evaluated for their effect on rapid biofilm formation. Fiber treatments are as follows: sanding of the fibers with 1500 and 8000 grit sandpaper, immersion of the fibers in a 1% hydrofluoric acid solution for 12 seconds and 15 minutes, and the immersion of the fibers in a Fluoroetch® solution for 18 seconds and 5 minutes. The two inoculums utilized were sourced from healthy, established MARRs; Texas Tech University (TTU) MABR "TRL5" and Kennedy Space Center (KSC) MABR "R3". Data attained from direct bacterial cell counts of the reactor bulk fluids via fluorescent microscopy, suggests that the fluoroetching treatment combined with the TTU inoculum show the greatest biofilm creation.

Ellis, Ronald II↗
NASA NTRS1998

On the Generation and Use of TCP Acknowledgments

This paper presents a simulation study of various TCP acknowledgment generation and utilization techniques. We investigate the standard version of TCP and the two standard acknowledgment strategies employed by receivers: those that acknowledge each incoming segment and those that implement delayed acknowledgments. We show the delayed acknowledgment mechanism hurts TCP performance, especially during slow start. Next we examine three alternate mechanisms for generating and using acknowledgments designed to mitigate the negative impact of delayed acknowledgments. The first method is to generate delayed ACKs only when the sender is not using the slow start algorithm. The second mechanism, called byte counting, allows TCP senders to increase the amount of data being injected into the network based on the amount of data acknowledged rather than on the number of acknowledgments received. The last mechanism is a limited form of byte counting. Each of these mechanisms is evaluated in a simulated network with no competing traffic, as well as a dynamic environment with a varying amount of competing traffic. We study the costs and benefits of the alternate mechanisms when compared to the standard algorithm with delayed ACKs.

Allman, Mark↗