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DOE OSTI2023

Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing

ABSTRACT Targeted amplicon sequencing is widely used in microbial ecology studies. However, sequencing artifacts and amplification biases are of great concern. To identify sources of these artifacts, a systematic analysis was performed using mock communities comprised of 16S rRNA genes from 33 bacterial strains. Our results indicated that while sequencing errors were generally isolated to low-abundance operational taxonomic units, chimeric sequences were a major source of artifacts. Singleton and doubleton sequences were primarily chimeras. Formation of chimeric sequences was significantly correlated with the GC content of the targeted sequences. Low-GC-content mock community members exhibited lower rates of chimeric sequence formation. GC content also had a large impact on sequence recovery. The quantitative capacity was notably limited, with substantial recovery variations and weak correlation between anticipated and observed strain abundances. The mock community strains with higher GC content had higher recovery rates than strains with lower GC content. Amplification bias was also observed due to the differences in primer affinity. A two-step PCR strategy reduced the number of chimeric sequences by half. In addition, comparative analyses based on the mock communities showed that several widely used sequence processing pipelines/methods, including DADA2, Deblur, UCLUST, UNOISE, and UPARSE, had different advantages and disadvantages in artifact removal and rare species detection. These results are important for improving sequencing quality and reliability and developing new algorithms to process targeted amplicon sequences. IMPORTANCE Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Synchronous Machine Governor Upgrade

Conventional generation sources play a critical role in the stability and reliability of the electrical grid, particularly as we transition towards more renewable energy sources. To understand and accurately emulate their behavior for optimizing grid operations and ensuring seamless integration with renewable technologies, it is essential to better emulate the grid- and plant-level impacts of conventional generation sources, such as natural gas (NG) driven heat recovery steam generators (HRSGs) and combustion turbines (CTs). Therefore, a governor model is developed in a programmable logic controller (PLC) to investigate the performance of the conventional generator under various dynamic operating conditions and to identify the impact on grid stability in a controlled environment. The governor model aims to enable the hardware-in-the-loop (HIL) based emulation of these conventional generation sources using the existing 2 MVA synchronous machine/generator that is driven by a flexible 2.5 MW variable speed drive. This setup will allow us to replicate the dynamic characteristics and response behaviors of NG-driven HRSGs and CTs. The controls for the emulated conventional plants follow the industry standard and are adjustable, ensuring they accurately reflect the operational capabilities and limitations of real-world systems. These controls include load-following capabilities, ramp rates, startup and shutdown sequences, and emissions characteristics. By incorporating these adjustable controls, we aim to capture the nuanced impacts of conventional generation, such as their ability to provide ancillary services like frequency regulation, voltage support, and spinning reserve. In this report, we simulate two types of dynamic operations: grid-connected and islanding. For each dynamic operation, representative starting sequences are tested, including turbine purge, ignition, speed ramping up, generator excitation and synchronizing, and breaker close. The HIL based tests provides insights for field deployment, specifically the high-fidelity governor model provides results to predict the potential stability and reliability risk and suggest possible integration measures (e.g., generation and load balancing, tuning of governor control parameters). Ultimately, this enhanced emulation capability will be integrated into our Advanced Research on Integrated Energy Systems (ARIES), enabling us to conduct comprehensive studies on the interactions between conventional and renewable energy sources. By better understanding these interactions, we can develop strategies to optimize the overall performance and reliability of the grid. This will support the deployment of advanced grid management techniques, such as demand response, grid-forming inverters, and energy storage systems. The main contributions are summarized as follows: (1) This report introduces a PLC-based governor model for gas turbines. This model accurately simulates the dynamic behavior of conventional generation sources under various operational scenarios; (2) The model is integrated with an HIL testbed that includes a 2.5 MW variable speed drive and a 2 MVA synchronous machine. This setup enables realistic, real-time emulation of conventional power plants, particularly NG driven HRSGs and CTs; (3) The developed model is adaptable to various gas turbine configurations and allows for precise control over parameters such as MW ramp rates. This flexibility makes it a valuable tool for future research and industry collaboration; and (4) By incorporating the model into the National Renewable Energy Laboratory's Advanced Research on Integrated Energy Systems, the report lays the groundwork for future studies on interactions between conventional and renewable energy sources, enhancing the ability to develop advanced grid management strategies.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Investigating the Linear Thermal Expansion of Additively Manufactured Multi-Material Joining between Invar and Steel

This work investigated the linear thermal expansion properties of a multi-material specimen fabricated with Invar M93 and A36 steel. A sequence of tests was performed to investigate the viability of additively manufactured Invar M93 for lowering the coefficient of thermal expansion (CTE) in multi-material part tooling. Invar beads were additively manufactured on a steel base plate using a fiber laser system, and samples were taken from the steel, Invar, and the interface between the two materials. The CTE of the samples was measured between 40 °C and 150 °C using a thermomechanical analyzer, and the elemental composition was studied with energy dispersive X-ray spectroscopy. The CTE of samples taken from the steel and the interface remained comparable to that of A36 steel; however, deviations between the thermal expansion values were prevalent due to element diffusion in and around the heat-affected zone. The CTEs measured from the Invar bead were lower than those from the other sections with the largest and smallest thermal expansion values being 10.40 μm/m-K and 2.09 μm/m-K. In each of the sections, the largest CTE was measured from samples taken from the end of the weld beads. An additional test was performed to measure the aggregate expansion of multi-material tools. Invar beads were welded on an A36 steel plate. The invar was machined, and the sample was heated in an oven from 40 °C and 160 °C. Strain gauges were placed on the surface of the part and were used to analyze how the combined thermal expansions of the invar and steel would affect the thermal expansion on the surface of a tool. There were small deviations between the expansion values measured by gauges placed in different orientations, and the elongation of the sample was greatest along the dimension containing a larger percentage of steel. On average, the expansion of the machined Invar surface was 42% less than the expansion of the steel surface. The results of this work demonstrate that additively manufactured Invar can be utilized to decrease the CTE for multi-material part tooling.

36 MATERIALS SCIENCE↗

NASA NTRS1978

Premix fuels study applicable to duct burner conditions for a variable cycle engine

Emission levels and performance of a premixing Jet-A/air duct burner were measured at reference conditions representative of take-off and cruise for a variable cycle engine. In a parametric variation sequence of tests, data were obtained at inlet temperatures of 400, 500 and 600K at equivalence ratios varying from 0.9 to the lean stability limit. Ignition was achieved at all the reference conditions although the CO levels were very high. Significant nonuniformity across the combustor was observed for the emissions at the take-off condition. At a reference Mach number of 0.117 and an inlet temperature of 600K, corresponding to a simulated cruise condition, the NOx emission level was approximately 1 gm/kg-fuel.

Venkataramani, K. S.↗

NASA NTRS1982

Modeling stiffness loss in boron/aluminum below the fatigue limit

Boron/aluminum can develop significant internal matrix cracking when fatigued. These matrix cracks can result in a 40 percent secant modulus loss in some laminates, even when fatigued below the fatigue limit. It is shown that the same amount of fatigue damage will develop during stress or strain-controlled tests. Stacking sequence has little influence on secant modulus loss. The secant modulus loss in unidirectional composites is small, whereas the losses are substantial in laminates containing off-axis plies. A simple analysis is presented that predicts unnotched laminate secant modulus loss due to fatigue. The analysis is based upon the elastic modulus and Poisson's ratio of the fiber and matrix, fiber volume fraction, fiber orientations, and the cyclic-hardened yield stress of the matrix material. Excellent agreement was achieved between model predictions and experimental results. With this model, designers can project the material stiffness loss for design load or strain levels and assess the feasibility of its use in stiffness-critical parts.

Johnson, W. S.↗

NASA NTRS1983

Modeling stiffness loss in boron/aluminum laminates below the fatigue limit

Johnson, W. S.↗

NASA NTRS1986

The RANDOM computer program: A linear congruential random number generator

The RANDOM Computer Program is a FORTRAN program for generating random number sequences and testing linear congruential random number generators (LCGs). The linear congruential form of random number generator is discussed, and the selection of parameters of an LCG for a microcomputer described. This document describes the following: (1) The RANDOM Computer Program; (2) RANDOM.MOD, the computer code needed to implement an LCG in a FORTRAN program; and (3) The RANCYCLE and the ARITH Computer Programs that provide computational assistance in the selection of parameters for an LCG. The RANDOM, RANCYCLE, and ARITH Computer Programs are written in Microsoft FORTRAN for the IBM PC microcomputer and its compatibles. With only minor modifications, the RANDOM Computer Program and its LCG can be run on most micromputers or mainframe computers.

Miles, R. F., Jr.↗

NASA NTRS1985

Reasoning about procedural knowledge

A crucial aspect of automated reasoning about space operations is that knowledge of the problem domain is often procedural in nature - that is, the knowledge is often in the form of sequences of actions or procedures for achieving given goals or reacting to certain situations. In this paper a system is described that explicitly represents and reasons about procedural knowledge. The knowledge representation used is sufficiently rich to describe the effects of arbitrary sequences of tests and actions, and the inference mechanism provides a means for directly using this knowledge to reach desired operational goals. Furthermore, the representation has a declarative semantics that provides for incremental changes to the system, rich explanatory capabilities, and verifiability. The approach also provides a mechanism for reasoning about the use of this knowledge, thus enabling the system to choose effectively between alternative courses of action.

Georgeff, M. P.↗

NASA NTRS1988

Tests Of Amorphous-Silicon Photovoltaic Modules

Progress in identification of strengths and weaknesses of amorphous-silicon technology detailed. Report describes achievements in testing reliability of solar-power modules made of amorphous-silicon photovoltaic cells. Based on investigation of modules made by U.S. manufacturers. Modules subjected to field tests, to accelerated-aging tests in laboratory, and to standard sequence of qualification tests developed for modules of crystalline-silicon cells.

Ross, Ronald G., Jr.↗

NASA NTRS1990

Beam Stop For High-Power Lasers

Graphite/aluminum plate absorbs most of light. Beam stop fits on standard optical mounting fixture. Graphite plate thick enough to absorb incident laser beam but thin enough to transfer heat quickly to heat sink. Device used for variety of blocking purposes. For example, blocks laser beam after it passes through experimental setup, or at each stage of setup so stages checked and tested in sequence. Negligible reflectance of device is valuable safety feature, protecting both users and equipment from reflections.

Mcdermid, Iain S.↗

NASA NTRS1990

Kalman filter based range estimation for autonomous navigation using imaging sensors

Rotorcraft operating in high-threat environments fly close to the surface of the earth to utilize surrounding terrain, vegetation, or man-made objects to minimize the risk of being detected by the enemy. Two basic requirements for obstacle avoidance are detection and range estimation of the object from the current rotorcraft position. There are many approaches to the estimation of range using a sequence of images. The approach used in this analysis differes from previous methods in two significant ways: an attempt is not made to estimate the rotorcraft's motion from the images; and the interest lies in recursive algorithms. The rotorcraft parameters are assumed to be computed using an onboard inertial navigation system. Given a sequence of images, using image-object differential equations, a Kalman filter (Sridhar and Phatak, 1988) can be used to estimate both the relative coordinates and the earth coordinates of the objects on the ground. The Kalman filter can also be used in a predictive mode to track features in the images, leading to a significant reduction of search effort in the feature extraction step of the algorithm. The purpose is to summarize early results obtained in extending the Kalman filter for use with actual image sequences. The experience gained from the application of this algorithm to real images is very valuable and is a necessary step before proceeding to the estimation of range during low-altitude curvilinear flight. A simple recursive method is presented to estimate range to objects using a sequence of images. The method produces good range estimates using real images in a laboratory set up and needs to be evaluated further using several different image sequences to test its robustness. The feature generation part of the algorithm requires further refinement on the strategies to limit the number of features (Sridhar and Phatak, 1989). The extension of the work reported here to curvilinear flight may require the use of the extended Kalman filter.

Sridhar, Banavar↗

NASA NTRS1991

A powered lift experiment for CFD validation

The transitional flight characteristics of a geometrically simplified STOVL aircraft configuration were measured in the NASA Ames 7- by 10-Foot Wind Tunnel. The experiment is the first in a sequence of tests designed to provide detailed data for evaluating the capability of computational fluid dynamics methods to predict the important flow parameters for powered lift. The model consists of a 60-deg delta wing planform with two circular high-pressure air jets located in a blended fuselage. The measured flows have a maximum freestream Mach number of 0.2. The flow is sonic and at ambient temperature in both jets. The data presented include forces and moments measured using an internal balance, pressures measured at the 281 surface pressure ports, and jet pressures and temperatures. Measurements of the flow are also made in the tunnel test section upstream and downstream of the model and at the jet exists to provide boundary conditions for the planned computations.

Roth, Karlin R.↗

NASA NTRS1991

Description of the PMAD DC test bed architecture and integration sequence

NASA-Lewis is responsible for the development, fabrication, and assembly of the electric power system (EPS) for the Space Station Freedom (SSF). The SSF power system is radically different from previous spacecraft power systems in both the size and complexity of the system. Unlike past spacecraft power system the SSF EPS will grow and be maintained on orbit and must be flexible to meet changing user power needs. The SSF power system is also unique in comparison with terrestrial power systems because it is dominated by power electronic converters which regulate and control the power. Although spacecraft historically have used power converters for regulation they typically involved only a single series regulating element. The SSF EPS involves multiple regulating elements, two or more in series, prior to the load. These unique system features required the construction of a testbed which would allow the development of spacecraft power system technology. A description is provided of the Power Management and Distribution (PMAD) DC Testbed which was assembled to support the design and early evaluation of the SSF EPS. A description of the integration process used in the assembly sequence is also given along with a description of the support facility.

Beach, R. F.↗

NASA NTRS1991

Description of the PMAD DC test bed architecture and integration sequence

NASA-LEWIS is responsible for the development, fabrication, and assembly of the electric power system (EPS) for the Space Station Freedom (SSF). The SSF power system is radically different from previous spacecraft power systems in both the size and complexity of the system. Unlike past spacecraft power systems, the SSF EPS will grow and be maintained on orbit and must be flexible to meet challenging user power needs. The SSF power system is also unique in comparison with terrestrial power systems because it is dominated by power electronic converters which regulate and control the power. A description is provided of the Power Management and Distribution DC Testbed which was assembled to support the design and early evaluation of the SSF EPS. A description of the integration process used in the assembly sequence is also given along with a description of the support facility.

Beach, R. F.↗

NASA NTRS2007

Thermal-Mechanical Testing of Hypersonic Vehicle Structures

A viewgraph presentation describing thermal-mechanical tests on the structures of hypersonic vehicles is shown. The topics include: 1) U.S. Laboratories for Hot Structures Testing; 2) NASA Dryden Flight Loads Laboratory; 3) Hot Structures Test Programs; 4) Typical Sequence for Hot Structures Testing; 5) Current Hot Structures Testing; and 6) Concluding Remarks.

Hudson, Larry↗

NASA NTRS2010

Injecting Errors for Testing Built-In Test Software

Two algorithms have been conceived to enable automated, thorough testing of Built-in test (BIT) software. The first algorithm applies to BIT routines that define pass/fail criteria based on values of data read from such hardware devices as memories, input ports, or registers. This algorithm simulates effects of errors in a device under test by (1) intercepting data from the device and (2) performing AND operations between the data and the data mask specific to the device. This operation yields values not expected by the BIT routine. This algorithm entails very small, permanent instrumentation of the software under test (SUT) for performing the AND operations. The second algorithm applies to BIT programs that provide services to users application programs via commands or callable interfaces and requires a capability for test-driver software to read and write the memory used in execution of the SUT. This algorithm identifies all SUT code execution addresses where errors are to be injected, then temporarily replaces the code at those addresses with small test code sequences to inject latent severe errors, then determines whether, as desired, the SUT detects the errors and recovers

Gender, Thomas K.↗

NASA NTRS1998

Spread Spectrum Receiver Electromagnetic Interference (EMI) Test Guide

The objective of this test guide is to document appropriate unit level test methods and techniques for the performance of EMI testing of Direct Sequence (DS) spread spectrum receivers. Consideration of EMI test methods tailored for spread spectrum receivers utilizing frequency spreading, techniques other than direct sequence (such as frequency hopping, frequency chirping, and various hybrid methods) is beyond the scope of this test guide development program and is not addressed as part of this document EMI test requirements for NASA programs are primarily developed based on the requirements contained in MIL-STD-46 1 D (or earlier revisions of MIL-STD-46 1). The corresponding test method guidelines for the MIL-STD-461 D tests are provided in MIL-STD-462D. These test methods are well documented with the exception of the receiver antenna port susceptibility tests (intermodulation, cross modulation, and rejection of undesired signals) which must be tailored to the specific type of receiver that is being tested. Thus, test methods addressed in this guide consist only of antenna port tests designed to evaluate receiver susceptibility characteristics. MIL-STD-462D should be referred for guidance pertaining to test methods for EMI tests other than the antenna port tests. The scope of this test guide includes: (1) a discussion of generic DS receiver performance characteristics; (2) a summary of S-band TDRSS receiver operation; (3) a discussion of DS receiver EMI susceptibility mechanisms and characteristics; (4) a summary of military standard test guidelines; (5) recommended test approach and methods; and (6) general conclusions and recommendations for future studies in the area of spread spectrum receiver testing.

Wheeler, M. L.↗

NASA NTRS1993

Experimental investigation of an RNA sequence space

Modern rRNAs are the historic consequence of an ongoing evolutionary exploration of a sequence space. These extant sequences belong to a special subset of the sequence space that is comprised only of those primary sequences that can validly perform the biological function(s) required of the particular RNA. If it were possible to readily identify all such valid sequences, stochastic predictions could be made about the relative likelihood of various evolutionary pathways available to an RNA. Herein an experimental system which can assess whether a particular sequence is likely to have validity as a eubacterial 5S rRNA is described. A total of ten naturally occurring, and hence known to be valid, sequences and two point mutants of unknown validity were used to test the usefulness of the approach. Nine of the ten valid sequences tested positive whereas both mutants tested as clearly defective. The tenth valid sequence gave results that would be interpreted as reflecting a borderline status were the answer not known. These results demonstrate that it is possible to experimentally determine which sequences in local regions of the sequence space are potentially valid 5S rRNAs.

Lee, Youn-Hyung↗