Results for “Functional data analysis” — Page 59

DOE OSTI2021

TListSpectrum

TListSpectrum is a C++ class developed inside the CERN high-energy physics analysis C++ framework ROOT. This class structure was developed to assist in the processing, visualization, and analysis of list-mode or time-stamped radiation spectroscopy data. The class structure currently contains parsing and functionality to synthesize list-mode data from CAEN and Mirion Lynx radiation spectroscopy digital acquisition systems along with feature functionality to post-process data sets and build coincident data sets from the instrument.

Pierson, Bruce↗

DOE OSTI2020

Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor–acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. In this work, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Submersible Multistage Centrifugal Pump for Versatile Test Reactor Cartridge Test Loop

Submersible multistage centrifugal pumps are ideal for pumping in narrow confined spaces and achieving necessary head pressures and flow rates. Once a diameter is determined then manipulation of the number of stages and motor speed are all that are required to meet desired flow conditions. The Versatile Test Reactor (VTR) closed loop cartridge systems will need forced convection cooling independent of the main reactor. A multistage centrifugal pump can meet the necessary flow rates and pumping pressures while minimizing space taken. The pump considered for this work was based off a deep well submersible pump, a variation of a multistage centrifugal pump. We experimented with two pump sizes, 5 cm (2 inch) and 7.5 cm (3 inch) diameters. These diameters were chosen to fit into the inner diameter of standard 5 and 7.5 (2 and 3 inch) Schedule 40 pipe, respectively. This made the design for the test loop both simpler and less expensive as the need for an engineered pump housing was eliminated. Initial test cartridge planning indicated space for only a 5 cm (2 inch) diameter pump, though early testing of this size showed the need for an abnormally high-speed and high-power motor. Fine tuning of the cartridge design allowed a pump size increase to 7.5 cm (3 inches), which was the pump size most extensively tested in this work. The test loop is composed of various sizes of PVC and aluminum piping components in a loop configuration. The pump is driven by a Pittman 250 W (1/3 horsepower) electric motor with maximum speed of 3,450 RPM. Testing consisted of running the pump at a constant motor speed while varying a control valve to restrict flow through the loop, with differential pressure and flow rate recorded. This was done for one and two stage configurations for the 5 cm (2 inch) diameter impeller design and one, two, and three stage configurations for the 7.5 cm (3 inch diameter) impeller design, respectively. Due to pumping power requirements, two and three stage 7.5 cm (3 inch) diameter impeller testing at higher flowrates lowered the motor speed substantially. In regions where motor speed could not be maintained constant, the data were discarded. The test loop was also reconfigured to allow for the pump to be tested for pressure drop in a stalled or inoperable (0 RPM) flow condition. Demonstration of adequate natural convection cooling of the test cartridge fuel type is necessary under accident conditions, and this will depend upon the flow resistance through the impeller assembly when the pump is not operating. Thus, accurate knowledge of the effective impeller assembly loss coefficient is important for safety evaluations. The test loop was modified to provide water inlet and outlets on either side of the pump impeller stack, and a metered flow of lab water was provided in order to measure the pressure drop across the cartridges as a function of flowrate. Data from the pump head curve testing developed as part of this work and supported by analysis using pump head affinity laws indicates that a three stage 7.5 cm (3 inch) pump impeller design will meet target requirements for coolant flow within the VTR cartridge sodium cartridge at full power conditions [1] with margin; this corresponds to a flowrate of 45 l/min (12 gpm) at a pressure drop of 6.1 m (20 feet) of water head. The results of the pressure loss measurements across the impeller assembly when the pump is stationary (i.e., at 0 RPM) indicate that the pressure loss coefficient is 0.921 for a two impeller stack configuration; this value is calculated based on the flow velocity through the minimum available flow area within a single stage of the impeller which corresponds to 1.4 cm2.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Process–Property–Performance Mapping of Additively Manufactured 316H Stainless Steel Components

The Advanced Materials and Manufacturing Technologies Program is focused on accelerating the development of advanced materials and components fabricated via additive manufacturing, and is using laser powder bed fusion (LPBF) of 316H stainless steel as an initial case study. In the previous fiscal year, miniature high-throughput specimens were printed on multiple LPBF systems to provide initial processing windows to minimize porosity and limit epitaxial grain growth during prints. This fiscal year, scaled builds were completed on three different LPBF systems at ORNL: a GE Concept Laser M2, a Renishaw AM400, and an EOS M290. Builds on the Concept Laser were conducted on multiple powder lots and processing parameter ranges to provide microstructure effects on time-independent and time-dependent mechanical properties. Builds on the Renishaw were produced using Oak Ridge National Laboratory (ORNL)-optimized printing parameters and Argonne National Laboratory (ANL)-optimized printing parameters to compare outcomes of parallel process optimization efforts at different national laboratories on the same LPBF system. Similarly, the build completed on the EOS M290 replicated the processing parameters of builds completed at Los Alamos National Laboratory (LANL). Optical microscopy and electron backscatter diffraction characterization was completed on all builds. In addition to the general round robin characterization, this work-package generated time-independent data, including tensile and fracture toughness test data on scaled Concept Laser builds as a function of processing parameters and post-build heat treatment. This analysis is complimentary to work in parallel work packages aiming to establish heat treatment and processing effects on time-dependent properties. It was found that although the stress-relief heat treatment provides the highest strength at lower-temperatures, tensile strength begins to converge at higher temperatures regardless of heat treatment condition. In addition, the more rigorous solution annealing and hot-isostatic pressing post-build heat treatments result in higher fracture toughness than the stress-relieved condition. The root-causes of the lower fracture toughness of the stress-relieved LPBF 316H material was informed via a stress-relief optimization study on a scaled concept laser print, where it was found that although dislocation recovery was largely complete after only a couple hours at 650°C, the extended hold of the current 24h heat treatment employed on scaled builds likely caused increased carbide volume fractions along the LPBF 316H grain boundaries, thereby deteriorating crack propagation resistance. This trend was seen to become more deleterious with additional increases of stress-relief temperature to 750°C or 850°C. These results have helped inform a new optimal stress-relief annealing condition for LPBF 316H for future campaign testing (650°C for 2h).

36 MATERIALS SCIENCE↗

DOE OSTI2024

Process–Property–Performance Mapping of Additively Manufactured 316H Stainless Steel Components

The Advanced Materials and Manufacturing Technologies Program is focused on accelerating the development of advanced materials and components fabricated via additive manufacturing, and is using laser powder bed fusion (LPBF) of 316H stainless steel as an initial case study. In the previous fiscal year, miniature high-throughput specimens were printed on multiple LPBF systems to provide initial processing windows to minimize porosity and limit epitaxial grain growth during prints. This fiscal year, scaled builds were completed on three different LPBF systems at ORNL: a GE Concept Laser M2, a Renishaw AM400, and an EOS M290. Builds on the Concept Laser were conducted on multiple powder lots and processing parameter ranges to provide microstructure effects on time-independent and time-dependent mechanical properties. Builds on the Renishaw were produced using Oak Ridge National Laboratory (ORNL)-optimized printing parameters and Argonne National Laboratory (ANL)-optimized printing parameters to compare outcomes of parallel process optimization efforts at different national laboratories on the same LPBF system. Similarly, the build completed on the EOS M290 replicated the processing parameters of builds completed at Los Alamos National Laboratory (LANL). Optical microscopy and electron backscatter diffraction characterization was completed on all builds. In addition to the general round robin characterization, this work-package generated time-independent data, including tensile and fracture toughness test data on scaled Concept Laser builds as a function of processing parameters and post-build heat treatment. This analysis is complimentary to work in parallel work packages aiming to establish heat treatment and processing effects on time-dependent properties. It was found that although the stress-relief heat treatment provides the highest strength at lower-temperatures, tensile strength begins to converge at higher temperatures regardless of heat treatment condition. In addition, the more rigorous solution annealing and hot-isostatic pressing post-build heat treatments result in higher fracture toughness than the stress-relieved condition. The root-causes of the lower fracture toughness of the stress-relieved LPBF 316H material was informed via a stress-relief optimization study on a scaled concept laser print, where it was found that although dislocation recovery was largely complete after only a couple hours at 650°C, the extended hold of the current 24h heat treatment employed on scaled builds likely caused increased carbide volume fractions along the LPBF 316H grain boundaries, thereby deteriorating crack propagation resistance. This trend was seen to become more deleterious with additional increases of stress-relief temperature to 750°C or 850°C. These results have helped inform a new optimal stress-relief annealing condition for LPBF 316H for future campaign testing (650°C for 2h).

36 MATERIALS SCIENCE↗

DOE OSTI2023

3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism

The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.

3’ RNA-seq↗

DOE OSTI2024

Incidence and predictors of loss to follow-up among adult patients receiving antiretroviral therapy in Central Ethiopia: a multi-center retrospective cohort study

Background: Globally, loss to follow-up (LTFU) remains a significant public health concern despite the rapid expansion of antiretroviral medication programs. It is a significant cause of treatment failure and threatens the enhancement of HIV treatment outcomes among patients on antiretroviral therapy (ART). However, there is a paucity of evidence on its incidence and predictors in Ethiopia. Thus, this study aimed to examine the incidence and predictors of LTFU among adult HIV patients receiving ART at hospitals in Central Ethiopia. Methods: A multi-centered facility-based retrospective cohort study was conducted among 432 randomly selected adult patients who received antiretroviral therapy. Data were entered into EpiData version 3.1 and exported to Stata version 14 for analysis. The Kaplan–Meier failure function was employed to determine the overall failure estimates, and the log-rank test was used to compare the probability of failure among the different categories of variables. The Cox proportional hazard model was used to identify independent predictors of LTFU. Results: Overall, 172 (39.8%) study participants were lost to follow-up over the 10-year follow-up period with an incidence rate of 8.12 (95% CI: 7.11, 9.09) per 1,000 person-months. Undisclosed HIV status (AHR: 1.96, 95% CI: 1.14, 3.36), not able to work (AHR: 1.84, 95% CI: 1.13, 2.22), opportunistic infections (AHR: 3.13, 95% CI: 2.17, 4.52), CD4 < 200 cell/mL (AHR: 1.95, 95% CI: 1.18, 3.21), not receiving isoniazid preventive therapy (IPT) (AHR: 2.57, 95% CI: 1.62, 4.06), not participating in clubs (AHR: 1.68, 95% CI: 1.10, 2.22), side effects of drugs (AHR: 1.44, 95% CI: 1.02, 2.04), and high viral load (AHR: 3.15, 95% CI: 1.81, 5.47) were identified as significant predictors of loss to follow-up. Conclusion: In this study, the incidence of LTFU was high. The focus should be on creating awareness and prevention programs that aim to reduce loss to follow-up by continuing counseling, especially on the negative effects of loss to follow-up and the benefits of ART care.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Automating Analysis of Neutron Scattering Time-of-Flight Single Crystal Phonon Data

This article introduces software called Phonon Explorer that implements a data mining workflow for large datasets of the neutron scattering function, S(Q, ω), measured on time-of-flight neutron spectrometers. This systematic approach takes advantage of all useful data contained in the dataset. It includes finding Brillouin zones where specific phonons have the highest scattering intensity, background subtraction, combining statistics in multiple Brillouin zones, and separating closely spaced phonon peaks. Using the software reduces the time needed to determine phonon dispersions, linewidths, and eigenvectors by more than an order of magnitude.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS1973

Meteorological utility of high resolution multispectral data

There are no author-identified significant results in this report. This investigation is directed towards determining the meteorological information content of ERTS-1 MSS bulk data at 0.6 - 0.7 microns as a function of resolution. To accomplish this, the resolution of the MSS data is degraded incrementally to 0.5 min. Subsequent analysis of the processed photographs in conjunction with surface and upper air observations will then determine to what extent significant meteorological information has been lost in the degradation process.

Danko, J. M.↗

NASA NTRS1974

Tracking system analytic calibration activities for the Mariner Mars 1971 mission

This report describes the functions of the Tracking System Analytic Calibration activity for Mariner Mars 1971 (MM'71), its objectives for this and future missions, and the support provided to the MM'71 Navigation Team during operations. The support functions encompass calibration of tracking data by estimating physical parameters whose uncertainties represent limitations to navigational accuracy, and detailed analysis of the tracking data to uncover and resolve any anomalies. Separate articles treat the activities and results of producing calibrations for the various error sources: Deep Space Station Locations, timing and polar motion, charged particles, and the troposphere. Two other articles are also included dis- - cussing the effects of the media error sources on orbit determination and the merits of the smoothing technique used for DRIVID.

Facilities↗

NASA NTRS1974

The tracking system analytic calibration activity for Mariner Mars 1971: Its function and scope

The functions of the Tracking System Analytic Calibration activity for Mariner Mars 1971 (MM'71), its objectives for this and future missions, and the support provided to the MM'71 Navigation Team during operations are described. Support functions encompass calibration of tracking data by estimating physical parameters whose uncertainties represent limitations to navigational accuracy, and detailed analysis of the tracking data to uncover and resolve any anomalies. Separate articles treat the activities and results of producing calibrations for the various error sources: Deep Space Station Locations, timing and polar motion, charged particles, and the troposphere. Two other articles are also included discussing the effects of the media error sources on orbit determination and the merits of the smoothing technique used for DRIVID.

Madrid, G. A.↗

NASA NTRS1975

Ride quality of terminal-area flight maneuvers

Complex terminal-area flight maneuvers being considered for airline operations may not be acceptable to passengers. To provide technology in this area, a series of flight experiments was conducted by NASA using the U. S. Air Force Total In-Flight Simulator (TIFS) aircraft to obtain subjective responses of a significant number of passenger test subjects to closely controlled and repeatable flight maneuvers. Regression analysis of the data produced a mathematical model which closely predicts mean passenger ride-comfort rating as a function of the rms six-degree-of-freedom aircraft motions during the maneuver. This ride-comfort model was exercised to examine various synthesized flight maneuvers.

Schoonover, W. E., Jr.↗

NASA NTRS1976

Analysis of pressure distortion testing

The development of a distortion methodology, method D, was documented, and its application to steady state and unsteady data was demonstrated. Three methodologies based upon DIDENT, a NASA-LeRC distortion methodology based upon the parallel compressor model, were investigated by applying them to a set of steady state data. The best formulation was then applied to an independent data set. The good correlation achieved with this data set showed that method E, one of the above methodologies, is a viable concept. Unsteady data were analyzed by using the method E methodology. This analysis pointed out that the method E sensitivities are functions of pressure defect level as well as corrected speed and pattern.

Koch, K. E.↗

NASA NTRS1975

Nuclear cardiograph and scintigraphy

Extensive advances in the technology of detectors, data analysis systems, and tracers used have resulted in greatly expanded applications of radioisotopes to the assessment of cardiac function and disease. The development of nuclear cardiology has proceeded along four lines: (1) radionuclide angiography, (2) myocardial perfusion imaging, (3) intracoronary microsphere imaging, and (4) regional myocardial blood flow determination using inert gases.

Mclaughlin, P.↗

NASA NTRS1979

Radar observation of known and unknown clear echoes

Target cross-section as a function of wavelength for known insects, known bird, and dot targets is presented. Tracking data using the time series analysis was tabulated for known birds. Examples were selected from these early works to give entomologists some indication of the types of information that are available by radar as well as examples of the different sources of clear-air radar backscatter.

Glover, K. M.↗

NASA NTRS1982

Thin film concentrator panel development

The development and testing of a rigid panel concept that utilizes a thin film reflective surface for application to a low-cost point-focusing solar concentrator is discussed. It is shown that a thin film reflective surface is acceptable for use on solar concentrators, including 1500 F applications. Additionally, it is shown that a formed steel sheet substrate is a good choice for concentrator panels. The panel has good optical properties, acceptable forming tolerances, environmentally resistant substrate and stiffeners, and adaptability to low to mass production rates. Computer simulations of the concentrator optics were run using the selected reflector panel design. Experimentally determined values for reflector surface specularity and reflectivity along with dimensional data were used in the analysis. The simulations provided intercept factor and net energy into the aperture as a function of aperture size for different surface errors and pointing errors. Point source and Sun source optical tests were also performed.

Zimmerman, D. K.↗

NASA NTRS1985

Development of non-linear finite element computer code

Recent work has shown that the use of separable symmetric functions of the principal stretches can adequately describe the response of certain propellant materials and, further, that a data reduction scheme gives a convenient way of obtaining the values of the functions from experimental data. Based on representation of the energy, a computational scheme was developed that allows finite element analysis of boundary value problems of arbitrary shape and loading. The computational procedure was implemental in a three-dimensional finite element code, TEXLESP-S, which is documented herein.

Becker, E. B.↗

NASA NTRS1988

An expert system for satellite and instrument data anomaly and fault isolation

A prototype Generic Payload Operations Control System (GPOCC) is being developed at the NASA Jet Propulsion Laboratory to provide a low-cost command and control processing center for science instruments and small payloads. The GPOCC supports the difficult transition from integration and test to flight operations. The prototype will incorporate four expert systems to perform telemetry, command, and mission planning functions as well as telecommunications scheduling. The first of these expert systems to be developed will perform telemetry data analysis and fault isolation, as well as propose corrective action. This Data Analysis Module (DAM) will monitor telemetry data and perform continual data monitoring and trend analysis based on a knowledge base and historic data archived on an optical disk storage device. The system maintains a continuous knowledge database of past system performance characteristics. The goal of the Data Analysis Module is to achieve consistent, dependable and validatable performance, to demonstrate thorough, reliable and fast reasoning, and to reduce the concentration demanded of flight analysis personnel.

Busse, Carl↗