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At least 217 records · Page 12

Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

Background . Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results . A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus. Each group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions . This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family.

59 BASIC BIOLOGICAL SCIENCES↗

Higher Efficiency HVAC Motors

The objective of this project was to design and build a cost competitive, more efficient heating, ventilation, and air conditioning (HVAC) motor than what is currently available on the market. Though different potential motor architectures among QMP’s primary technology platforms were investigated and evaluated, including through the building of numerous prototypes, the project ultimately focused on scaling up QM Power, Inc.’s (QMP) Q-Sync permanent magnet synchronous motors from available sub-fractional horsepower (HP) sizes for commercial refrigeration fan applications to larger fractional horsepower sizes appropriate for HVAC applications, and to add multi-speed functionality. The more specific goal became the research, design, development, and testing of a prototype 1/2 HP Q-Sync motor that has at least two operating speeds and 87% peak efficiency compared to incumbent electronically commutated motors (EC or ECM, also known as brushless direct current (DC) motors), the heretofore highest efficiency HVACR fan motor solution, at approximately 82% peak efficiency. The resulting motor prototype built achieved these goals, hitting 90% efficiency and .95 power factor at full load and speed, and 80% efficiency and .7 power factor at half speed. Q-Sync, developed in part through a DOE SBIR grant (Award # DE-SC0006311), is a novel, patented motor technology that improves on electronically commutated permanent magnet motors through an advanced electronic circuit technology. It allows a motor to “sync” with the alternating current (AC) power flow. It does so by eliminating the constant, wasteful power conversions from AC to DC and back to AC through the synthetic creation of a new AC wave on the primary circuit board (PCB) by a process called pulse width modulation (PWM; aka electronic commutation) that is incessantly required to sustain motor operation in an EC permanent magnet motor. The Q-Sync circuit improves the power factor of the motor by removing all failure prone capacitors from the power stage. Q-Sync’s simpler electronics also result in higher efficiency because it eliminates the power required by the PCB to perform the obviated power conversions and PWM processes after line synchronous operating speed is reached in the first 5 seconds of operation, after which the PWM circuits drop out and a much less energy intensive “pass through” circuit takes over, allowing the grid-supplied AC power to sustain the motor’s ongoing operation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Psychophysical evaluation of three-dimensional auditory displays

This report describes the progress made during the first year of a three-year cooperative research agreement (CRA NCC2-542). The CRA proposed a program of applied psychophysical research designed to determine the requirements and limitations of three-dimensional (3-D) auditory display systems. These displays present synthesized stimuli to a pilot or virtual workstation operator that evoke auditory images at predetermined positions in space. The images can be either stationary or moving. In previous years, we completed a number of studies that provided data on listeners' abilities to localize stationary sound sources with 3-D displays. the current focus is on the use of 3-D displays in 'natural' listening conditions, which include listeners' head movements, moving sources, multiple sources and 'echoic' sources. The results of our research on two of these topics, the role of head movements and the role of echoes and reflections, were reported in the most recent semi-annual progress report (Appendix A). In the period since the last progress report we have been studying a third topic, the localizability of moving sources. The results of this research are described.

Wightman, Frederic L.↗

Psychophysical Evaluation of Three-Dimensional Auditory Displays

This report describes the progress made during the second year of a three-year Cooperative Research Agreement. The CRA proposed a program of applied psychophysical research designed to determine the requirements and limitations of three-dimensional (3-D) auditory display systems. These displays present synthesized stimuli to a pilot or virtual workstation operator that evoke auditory images at predetermined positions in space. The images can be either stationary or moving. In previous years, we completed a number of studies that provided data on listeners' abilities to localize stationary sound sources with 3-D displays. The current focus is on the use of 3-D displays in 'natural' listening conditions, which include listeners'head movements, moving sources, multiple sources and 'echoic' sources. The results of our research on one of these topics, the localization of multiple sources, was reported in the most recent Semi-Annual Progress Report (Appendix A). That same progress report described work on two related topics, the influence of a listener's a-priori knowledge of source characteristics and the discriminability of real and virtual sources. In the period since the last Progress Report we have conducted several new studies to evaluate the effectiveness of a new and simpler method for measuring the HRTF's that are used to synthesize virtual sources and have expanded our studies of multiple sources. The results of this research are described below.

Wightman, Frederic L.↗

Psychophysical Evaluation of Three-Dimensional Auditory Displays

This report describes the process made during the first year of a three-year Cooperative Research Agreement (CRA NCC2-542). The CRA proposed a program of applied of psychophysical research designed to determine the requirements and limitations of three-dimensional (3-D) auditory display systems. These displays present synthesized stimuli to a pilot or virtual workstation operator that evoke auditory images at predetermined positions in space. The images can be either stationary or moving. In previous years. we completed a number of studies that provided data on listeners' abilities to localize stationary sound sources with 3-D displays. The current focus is on the use of 3-D displays in 'natural' listening conditions, which include listeners' head movements, moving sources, multiple sources and 'echoic' sources. The results of our research on two of these topics, the role of head movements and the role of echoes and reflections, were reported in the most recent Semi-Annual Pro-ress Report (Appendix A). In the period since the last Progress Report we have been studying a third topic, the localizability of moving sources. The results of this research are described. The fidelity of a virtual auditory display is critically dependent on precise measurement of the listener''s Head-Related Transfer Functions (HRTFs), which are used to produce the virtual auditory images. We continue to explore methods for improving our HRTF measurement technique. During this reporting period we compared HRTFs measured using our standard open-canal probe tube technique and HRTFs measured with the closed-canal insert microphones from the Crystal River Engineering Snapshot system.

Wightman, Frederic L.↗

PyBioNetFit

Systems biology models written in the BioNetGen language often contain parameters that must be fit based on experimental data. PyBioNetFit is a software tool designed to fit parameters of BioNetGen models. The user is expected to provide a BioNetGen model that contains unknown parameters, along with one or more text files containing experimental data. PyBioNetFit will perform a series of calls to the BioNetGen simulator using different parameter sets, to identify the parameter set that best fits the data. The parameter search is dictated by the user's choice of one of several metaheuristic optimization algorithms, including differential evolution, particle swarm optimization, scatter search, and simulated annealing. The software supports parallelized computing on multi-core computers and on computing clusters. We expect this software to be a useful tool for researchers designing BioNetGen models in collaboration with experimentalists.

Mitra, Eshan↗

Post-IOC space station: Models of operation and their implications for organizational behavior, performance and effectiveness

Issues of crew productivity during design work on space station are discussed. The crew productivity is defined almost exclusively in terms of human factors engineering and habitability design concerns. While such spatial environmental conditions are necessary to support crew performance and productivity, they are not sufficient to ensure high levels of crew performance and productivity on the post-Initial Operational Configurations (IOC) space station. The role of the organizational environment as a complement to the spatial environment for influencing crew performance in such isolated and confined work settings is examined. Three possible models of operation for post-IOC space station's organizational environment are identified and it is explained how they and space station's spatial environment will combine and interact to occasion patterns of crew behavior is suggested. A three phase program of research design: (1) identify patterns of crew behavior likely to be occasioned on post-IOC space station for each of the three models of operation; and (2) to determine proactive/preventative management strategies which could be adopted to maximize the emergence of preferred outcomes in crew behavior under each of the several spatial and organizational environment combinations.

Danford, S.↗

Neutron Absorber Considerations for the DOE Standardized Canister Powerpoint

The DOE Standardized SNF Canister will allow a broad range of DOE-managed fuels to be loaded, stored, transported, and disposed of while avoiding the need to re-open canisters after being sealed. A key safety function of the DOE Standardized SNF Canister is to ensure the material maintains a subcritical configuration for storage, transportation, and disposal. Researchers designed a basket made of a material which should ensure subcriticality (e.g. by geometry control and inclusion of neutron absorber) and be structurally sound. The basket material should resist the corrosive effects of a 10,000 year period in a breached container and still provide adequate neutronic isolation or degrade in a form which prevents a critical configuration of fissile material. This report summarizes the materials evaluated to ensure subcriticality of the DOE Standardized SNF Canister for credible disposal scenarios. Recommendations for future work include performing criticality evaluations using borated stainless steel for the basket material in the DOE Standardized SNF Canister and determining the solubility on boron’s corrosion products. If researchers determine the properties of borated stainless steel are insufficient, ANA needs to undergo more corrosion testing and continue the process to become an ASME code case for welded construction.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

Quantitative stable isotope probing (qSIP) estimates isotope tracer incorporation into DNA of individual microbes and can link microbial biodiversity and biogeochemistry in complex communities. As with any quantitative estimation technique, qSIP involves measurement error, and a fuller understanding of error, precision, and statistical power benefits qSIP experimental design and data interpretation. We used several qSIP data sets—from soil and seawater microbiomes—to evaluate how variance in isotope incorporation estimates depends on organism abundance and resolution of the density fractionation scheme. We assessed statistical power for replicated qSIP studies, plus sensitivity and specificity for unreplicated designs. As a taxon’s abundance increases, the variance of its weighted mean density declines. Nine fractions appear to be a reasonable trade-off between cost and precision for most qSIP applications. Increasing the number of density fractions beyond that reduces variance, although the magnitude of this benefit declines with additional fractions. Our analysis suggests that, if a taxon has an isotope enrichment of 10 atom% excess, there is a 60% chance that this will be detected as significantly different from zero (with alpha 0.1). With five replicates, isotope enrichment of 5 atom% could be detected with power (0.6) and alpha (0.1). Finally, we illustrate the importance of internal standards, which can help to calibrate per sample conversions of %GC to mean weighted density. These results should benefit researchers designing future SIP experiments and provide a useful reference for metagenomic SIP applications where both financial and computational limitations constrain experimental scope.

59 BASIC BIOLOGICAL SCIENCES↗

Brookfield Homes Passive House Performance Evaluation

In 2012-2013, IBACOS worked with a builder, Brookfield Homes in Denver, Colorado, to design and construct a Passive House certified model home. IBACOS used several modeling programs and calculation methods to complete the final design package along with Brookfield's architect KGA Studio. This design package included upgrades to the thermal enclosure, basement insulation, windows, and heating, ventilation, and air conditioning. Short-term performance testing in the Passive House was done during construction and after construction. Testing with a blower door indicated that whole-building air leakage to the outside was 324 CFM and 0.60 ACH50. The other two test homes had little short-term testing done post-construction by the local energy rater. IBACOS then monitored the energy consumption and whole-house comfort conditions of that occupied Passive House after one year of operation and compared the monitoring results to those for two other occupied test houses in the same area with similar square footage but slightly different floor plans. IBACOS also assisted the builder, Brookfield Homes, in researching design scenarios for Zero Energy Ready Home and ENERGY STAR acceptance levels. IBACOS also assisted Brookfield in conceptualizing product for Denver's Brighton Heights area. Brookfield was considering building to Zero Energy Ready Home standards in that location. IBACOS provided strategies that Brookfield may draw from in the event the builder chooses to pursue a Zero Energy Ready Home plan for that market.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Sputtered protective coatings for die casting dies

Three experimental research designs investigating candidate materials and processes involved in protective die surface coating procedures by sputter deposition, using ion beam technologies, are discussed. Various pre-test results show that none of the coatings remained completely intact for 15,000 test cycles. The longest lifetime was observed for coatings such as tungsten, platinum, and molybdenum which reduced thermal fatigue, but exhibited oxidation and suppressed crack initiation only as long as the coating did not fracture. Final test results confirmed earlier findings and coatings with Pt and W proved to be the candidate materials to be used on a die surface to increase die life. In the W-coated specimens, which remained intact on the surface after thermal fatigue testing, no oxidation was found under the coating, although a few cracks formed on the surface where the coating broke down. Further research is planned.

Mirtich, M. J.↗

The Making of a Self-Neglect Severity Scale

Research in elder self-neglect has lagged behind that of other forms of mistreatment, despite the fact that self-neglect is the most common allegation reported to Adult Protective Service agencies throughout the US. The lack of a gold-standard to measure self-neglect has hampered efforts to study this phenomenon. Researchers designed the Self-neglect Severity Scale (SSS) based on interviews with Adult Protective Service workers and a national expert panel. The SSS is based on observation and interview and is administered in the home to include an environmental assessment. It was piloted, extensively field tested and then revised. The CREST SSS was developed using survey data and consultation with experts in the field. This instrument utilizes observer ratings, interview responses, and assesses subjects physical and environmental domains. It also assesses functional status as it relates to health and safety issues. After field and pilot testing the SSS was finalized and is currently undergoing reliability and validity testing. The CREST SSS was developed as a state scale to provide a common language for describing cases of self-neglect. It is the first self-neglect severity scale available to researchers. If found to be both reliable and valid it can be used in future intervention studies.

Smith, Scott M.↗

Training the Powered-Lift Evaluation Pilot

This poster describes a project to prepare pilots for a study assessing novel aircraft automation concepts for electric Vertical Takeoff and Landing (eVTOL) aircraft using NASA’s Vertical Motion Simulator (VMS). By exploring the operational and learning challenges related to transitioning between forward flight and vertical landing, we seek to establish baselines of pilot workload and aircraft handling qualities across varying atmospheric conditions and automation states. The simulated eVTOL design differentiates flight control allocations as a function of airspeed across four speed ranges as the vehicle transitions between fully thrust-borne lift and wing-borne lift. As speed increases, side stick controls command: translational ground speeds, vertical and lateral acceleration, vertical rate, vertical flight path angle, and bank angle. This novel approach to flight control allocation creates a significant learning challenge for pilots. Since initial eVTOL aircraft may have limitations on hover capabilities, automation and flight guidance cues also vary with airspeed to provide efficient landing profiles while still providing cues suitable for cruise flight. The NASA team prepared the study pilots to follow these flight guidance cues along curved Required Navigation Performance (RNP) approaches and along 6o and 12o glide paths to energy-efficient assistive-hover landing and goarounds. The pre-VMS preparation sought to prepare pilots from diverse levels of experience and background. To do this, NASA researchers designed and developed a fixed-based, large field-ofview simulator with terrain, structures, and air traffic. With one day of combined classroom learning and skill development in the fixedbase simulator, pilots were largely able to fly the simulated eVTOL in the VMS with sufficient mastery to provide handling quality assessments using the Cooper-Harper Handling Qualities Rating and workload assessments through the Bedford Workload Scale.

AAM↗

NASA Remote Sensing Applications for Archaeology and Cultural Resources Management

NASA's Earth Science Mission Directorate recently completed the deployment of the Earth Observation System (EOS) which is a coordinated series of polar-orbiting and low inclination satellites for long-term global observations of the land surface, biosphere, solid Earth, atmosphere, and oceans. One of the many applications derived from EOS is the advancement of archaeological research and applications. Using satellites, manned and unmanned airborne platform, NASA scientists and their partners have conducted archaeological research using both active and passive sensors. The NASA Stennis Space Center (SSC) located in south Mississippi, near New Orleans, has been a leader in space archaeology since the mid-1970s. Remote sensing is useful in a wide range of archaeological research applications from landscape classification and predictive modeling to site discovery and mapping. Remote sensing technology and image analysis are currently undergoing a profound shift in emphasis from broad classification to detection, identification and condition of specific materials, both organic and inorganic. In the last few years, remote sensing platforms have grown increasingly capable and sophisticated. Sensors currently in use, including commercial instruments, offer significantly improved spatial and spectral resolutions. Paired with new techniques of image analysis, this technology provides for the direct detection of archaeological sites. As in all archaeological research, the application of remote sensing to archaeology requires a priori development of specific research designs and objectives. Initially targeted at broad archaeological issues, NASA space archaeology has progressed toward developing practical applications for cultural resources management (CRM). These efforts culminated with the Biloxi Workshop held by NASA and the University of Mississippi in 2002. The workshop and resulting publication specifically address the requirements of cultural resource managers through the use of remote sensing. In 2007, NASA awarded six competitively chosen projects in Space Archaeology through an open solicitation whose purpose, among several, was to addresses the potential benefits to modern society that can be derived through a better understanding of how past cultures succeeded or failed to adapt to local, regional, and global change. A further objective of NASA's space archaeology is the protection and preservation of cultural heritage sites while planning for the sustainable development of cultural resources. NASA s archaeological approach through remote sensing builds on traditional methods of aerial archaeology (i.e. crop marks) and utilizes advanced technologies for collecting and analyzing archaeological data from digital imagery. NASA s archaeological research and application projects using remote sensing have been conducted throughout the world. In North America, NASA has imaged prehistoric mound sites in Mississippi; prehistoric shell middens in Louisiana, Puebloan sites in New Mexico and more recently the sites associated with the Lewis and Clark Corps of Discovery Expedition (1804-1806). In Central America, NASA archaeologists have researched Mayan sites throughout the region, including the Yucatan and Costa Rica, as well as Olmec localities in Veracruz. Other data has been collected over Angkor, Cambodia, Giza in Egypt, the lost city of Ubar on the Arabian Peninsula.

Giardino, Marco J.↗

A Brief Description of My Projects

My internship was in the IDC which consist of a machine shop and an array of design space. During my tour I worked on a wide variety of projects some of which included design, research, machining and fabrication. I gained further knowledge on some machines that I have had prior experience on such as the lathe and Hurco CNC machines. The first thing we did was complete our checkout in the machine shop which went pretty well, since I was already familiar with most of the machines. I also did a couple of practice parts on some of the machines, I made a name block on the CNC machine and I also used the vertical milling machine to complete this project. One of the other projects that I did was machine a hammer with my initials with the use of the lathe and CNC machine, this project took much longer since I had to set up a cylindrical piece on the CNC machine. The first project that I began work on was the Systems Engineering & Management Advancement Program (SEPMAP) Hexacopter project and helped them to assemble and modify one of their particle capture doors on their boxes. After a while we ended up helping them make a hinge and holes to reduce the weight of their design. We helped the NASA Extreme Environment Mission Operations (NEEMO) team a bit with some of their name tags and assembly of some of their underwater parts. One of the more challenging projects was a rail that came in with a rather weirdly drawn part. The biggest project that I worked on was the solar array project. Which consisted of a variety of machining and 3D printing and it took me about 3 different times of re-designing to come up with a final prototype. Along with this project I also had to complete a project in which I had to modify a thermos. This was rather simple since I just had to draw up a part and print it out on the 3D printer. I also learned how to use Pro E/Creo parametric to design a square block and print it on the 3D Printer. All of these projects increased my experience on all of the machines and equipment that I used. I also got to tweak my design skills and better understand how to modify my designs and how to improve those specific designs.

Barnes, Tobin↗

Progress toward a universal biomedical data translator

Clinical, biomedical, and translational science has reached an inflection point in the breadth and diversity of available data and the potential impact of such data to improve human health and well-being. However, the data are often siloed, disorganized, and not broadly accessible due to discipline-specific differences in terminology and representation. To address these challenges, the Biomedical Data Translator Consortium has developed and tested a pilot knowledge graph-based “Translator” system capable of integrating existing biomedical data sets and “translating” those data into insights intended to augment human reasoning and accelerate translational science. Having demonstrated feasibility of the Translator system, the Translator program has since moved into development, and the Translator Consortium has made significant progress in the research, design, and implementation of an operational system. Herein, we describe the current system’s architecture, performance, and quality of results. We apply Translator to several real-world use cases developed in collaboration with subject-matter experts. Finally, we discuss the scientific and technical features of Translator and compare those features to other state-of-the-art, biomedical graph-based question-answering systems.

60 APPLIED LIFE SCIENCES↗

Probing Heterogeneity in Bovine Enamel Composition through Nanoscale Chemical Imaging using Atom Probe Tomography

Objective: The aim of this study was to determine the heterogeneity in chemical composition of bovine enamel using atom probe tomography, and thereby evaluate the suitability of bovine enamel as a substitute for human enamel in in vitro dental research. Design: Enamel samples from extracted bovine incisor teeth were first sectioned using a diamond saw and then milled into needle-like samples (<100 nm diameter) by focused ion beam (FIB) coupled with a scanning electron microscope (SEM). The samples were then analyzed in the atom probe to acquire three-dimensional (3D) images and quantify the atomic chemistry and distribution in bovine enamel. Results: For the first time, the atomic-level composition and clustering of major constituents and impurities within bovine enamel were determined and imaged. We discovered that the chemical composition of bovine enamel is spatially inhomogeneous at the atomic scale. The average bulk Ca/P ratio, ~1.4, was in agreement with previously reported literature values from alternative conventional methods. When assessed locally at the atomic scale, the Ca/P ratio varied between 1.1 and 2.03. We also discovered that the Mg impurities were significantly segregated throughout the enamel, and such clustering influenced the variation of Ca/P ratios. The increase in Mg concentrations, near the Mg clusters, correlated with increased Ca and decreased P concentrations. Conclusion: In conclusion, the presented findings of variability in local composition should be taken into account when interpreting dental research results from bovine enamel.

59 BASIC BIOLOGICAL SCIENCES↗

Hardware Development Process for Human Research Facility Applications

The simple goal of the Human Research Facility (HRF) is to conduct human research experiments on the International Space Station (ISS) astronauts during long-duration missions. This is accomplished by providing integration and operation of the necessary hardware and software capabilities. A typical hardware development flow consists of five stages: functional inputs and requirements definition, market research, design life cycle through hardware delivery, crew training, and mission support. The purpose of this presentation is to guide the audience through the early hardware development process: requirement definition through selecting a development path. Specific HRF equipment is used to illustrate the hardware development paths. The source of hardware requirements is the science community and HRF program. The HRF Science Working Group, consisting of SCientists from various medical disciplines, defined a basic set of equipment with functional requirements. This established the performance requirements of the hardware. HRF program requirements focus on making the hardware safe and operational in a space environment. This includes structural, thermal, human factors, and material requirements. Science and HRF program requirements are defined in a hardware requirements document which includes verification methods. Once the hardware is fabricated, requirements are verified by inspection, test, analysis, or demonstration. All data is compiled and reviewed to certify the hardware for flight. Obviously, the basis for all hardware development activities is requirement definition. Full and complete requirement definition is ideal prior to initiating the hardware development. However, this is generally not the case, but the hardware team typically has functional inputs as a guide. The first step is for engineers to conduct market research based on the functional inputs provided by scientists. CommerCially available products are evaluated against the science requirements as well as modifications needed to meet program requirements. Options are consolidated and the hardware development team reaches a hardware development decision point. Within budget and schedule constraints, the team must decide whether or not to complete the hardware as an in-house, subcontract with vendor, or commercial-off-the-shelf (COTS) development. An in-house development indicates NASA personnel or a contractor builds the hardware at a NASA site. A subcontract development is completed off-site by a commercial company. A COTS item is a vendor product available by ordering a specific part number. The team evaluates the pros and cons of each development path. For example, in-bouse developments utilize existing corporate knowledge regarding bow to build equipment for use in space. However, technical expertise would be required to fully understand the medical equipment capabilities, such as for an ultrasound system. It may require additional time and funding to gain the expertise that commercially exists. The major benefit of subcontracting a hardware development is the product is delivered as an end-item and commercial expertise is utilized. On the other hand, NASA has limited control over schedule delays. The final option of COTS or modified COTS equipment is a compromise between in-house and subcontracts. A vendor product may exist that meets all functional requirements but req uires in-house modifications for successful operation in a space environment. The HRF utilizes equipment developed using all of the paths described: inhouse, subcontract, and modified COTS.

Bauer, Liz↗