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At least 1,297 records · Page 72

The UNO Aviation Monograph Series: The Airline Quality Rating 1997

The Airline Quality Rating (AQR) was developed and first announced in early 1991 as an objective method of comparing airline performance on combined multiple factors important to consumers. Development history and calculation details for the AQR rating system are detailed in The Airline Quality Rating 1991 issued in April, 1991, by the National Institute for Aviation Research at Wichita State University. This current report, Airline Rating 1997, contains monthly Airline Quality Rating scores for 1996. Additional copies are available by contacting Wichita State University or the University of Nebraska at Omaha. The Airline Quality Rating (AQR) 1997 is a summary of a month-by-month quality ratings for the nine major domestic U.S. airlines operating during 1996. Using the Airline Quality Rating system and monthly performance data for each airline for the calendar year of 1996, individual and comparative ratings are reported. This research monograph contains a brief summary of the AQR methodology, detailed data and charts that track comparative quality for major domestic airlines across the 12 month period of 1996, and industry average results. Also comparative Airline Quality Rating data for 1991 through 1995 are included to provide a longer term view of quality in the industry.

Bowen, Brent D.↗

Designing Agent Collectives For Systems With Markovian Dynamics

The "Collective Intelligence" (COIN) framework concerns the design of collectives of agents so that as those agents strive to maximize their individual utility functions, their interaction causes a provided "world" utility function concerning the entire collective to be also maximized. Here we show how to extend that framework to scenarios having Markovian dynamics when no re-evolution of the system from counter-factual initial conditions (an often expensive calculation) is permitted. Our approach transforms the (time-extended) argument of each agent's utility function before evaluating that function. This transformation has benefits in scenarios not involving Markovian dynamics, in particular scenarios where not all of the arguments of an agent's utility function are observable. We investigate this transformation in simulations involving both linear and quadratic (nonlinear) dynamics. In addition, we find that a certain subset of these transformations, which result in utilities that have low "opacity (analogous to having high signal to noise) but are not "factored" (analogous to not being incentive compatible), reliably improve performance over that arising with factored utilities. We also present a Taylor Series method for the fully general nonlinear case.

Wolpert, David H.↗

Calculation of Supersonic Combustion Using Implicit Schemes

One of the technology goals of NASA for advanced space transportation is to develop highly efficient propulsion systems to reduce the cost of payload for space missions. Developments of rockets for the second generation Reusable Launch Vehicle (RLV) in the past several years have been focused on low-cost versions of conventional engines. However, recent changes in the Integrated Space Transportation Program to build a crew transportation vehicle to extend the life of the Space Shuttle fleet might suggest that air-breathing rockets could reemerge as a possible propulsion system for the third generation RLV to replace the Space Shuttle after 2015. The weight of the oxygen tank exceeds thirty percent of the total weight of the Space Shuttle at launch while the payload is only one percent of the total weight. The air-breathing rocket propulsion systems, which consume oxygen in the air, offer clear advantages by making vehicles lighter and more efficient. Experience in the National Aerospace Plane Program in the late 1980s indicates that scramjet engines can achieve high specific impulse for low hypersonic vehicle speeds. Whether taking a form of Rocket Based Combined Cycle (RBCC) or Turbine Based Combined Cycle (TBCC), the scramjet is an essential mode of operation for air-breathing rockets. It is well known that fuel-air mixing and rapid combustion are of crucial importance for the success of scramjet engines since the spreading rate of the supersonic mixing layer decreases as the Mach number increases. A factored form of the Gauss-Seidel relaxation method has been widely used in hypersonic flow research since its first application to non-equilibrium flows. However, difficulties in stability and convergence have been encountered when there is strong interaction between fluid motion and chemical reaction, such as multiple fuel injection problems. The present paper reports the results from investigation of the effect of modifications to the original algorithm on the performance for multiple injectors.

Yoon, Seokkwan↗

Designing Agent Collectives For Systems With Markovian Dynamics

The Collective Intelligence (COIN) framework concerns the design of collectives of agents so that as those agents strive to maximize their individual utility functions, their interaction causes a provided world utility function concerning the entire collective to be also maximized. Here we show how to extend that framework to scenarios having Markovian dynamics when no re-evolution of the system from counter-factual initial conditions (an often expensive calculation) is permitted. Our approach transforms the (time-extended) argument of each agent's utility function before evaluating that function. This transformation has benefits in scenarios not involving Markovian dynamics of an agent's utility function are observable. We investigate this transformation in simulations involving both hear and quadratic (nonlinear) dynamics. In addition, we find that a certain subset of these transformations, which result in utilities that have low opacity (analogous to having high signal to noise) but are not factored (analogous to not being incentive compatible), reliably improve performance over that arising with factored utilities. We also present a Taylor Series method for the fully general nonlinear case.

Wolpert, David H.↗

High-precision Non-Contact Measurement of Creep of Ultra-High Temperature Materials for Aerospace

For high-temperature applications (greater than 2,000 C) such as solid rocket motors, hypersonic aircraft, nuclear electric/thermal propulsion for spacecraft, and more efficient jet engines, creep becomes one of the most important design factors to be considered. Conventional creep-testing methods, where the specimen and test apparatus are in contact with each other, are limited to temperatures approximately 1,700 C. Development of alloys for higher-temperature applications is limited by the availability of testing methods at temperatures above 2000 C. Development of alloys for applications requiring a long service life at temperatures as low as 1500 C, such as the next generation of jet turbine superalloys, is limited by the difficulty of accelerated testing at temperatures above 1700 C. For these reasons, a new, non-contact creep-measurement technique is needed for higher temperature applications. A new non-contact method for creep measurements of ultra-high-temperature metals and ceramics has been developed and validated. Using the electrostatic levitation (ESL) facility at NASA Marshall Space Flight Center, a spherical sample is rotated quickly enough to cause creep deformation due to centrifugal acceleration. Very accurate measurement of the deformed shape through digital image analysis allows the stress exponent n to be determined very precisely from a single test, rather than from numerous conventional tests. Validation tests on single-crystal niobium spheres showed excellent agreement with conventional tests at 1985 C; however the non-contact method provides much greater precision while using only about 40 milligrams of material. This method is being applied to materials including metals and ceramics for non-eroding throats in solid rockets and next-generation superalloys for turbine engines. Recent advances in the method and the current state of these new measurements will be presented.

Rogers, Jan R.↗

Analysis of International Space Station Materials on MISSE-3 and MISSE-4

For high-temperature applications (> 2,000 C) such as solid rocket motors, hypersonic aircraft, nuclear electric/thermal propulsion for spacecraft, and more efficient jet engines, creep becomes one of the most important design factors to be considered. Conventional creep-testing methods, where the specimen and test apparatus are in contact with each other, are limited to temperatures ~1,700 deg. C. Development of alloys for higher-temperature applications is limited by the availability of testing methods at temperatures above 2000 C. Development of alloys for applications requiring a long service life at temperatures as low as 1500 C, such as the next generation of jet turbine superalloys, is limited by the difficulty of accelerated testing at temperatures above 1700 0c. For these reasons, a new, non-contact creep-measurement technique is needed for higher temperature applications. A new non-contact method for creep measurements of ultra-high-temperature metals and ceramics has been developed and validated. Using the electrostatic levitation (ESL) facility at NASA Marshall Space Flight Center, a spherical sample is rotated quickly enough to cause creep deformation due to centrifugal acceleration. Very accurate measurement of the deformed shape through digital image analysis allows the stress exponent n to be determined very precisely from a single test, rather than from numerous conventional tests. Validation tests on single-crystal niobium spheres showed excellent agreement with conventional tests at 1985 C; however the non-contact method provides much greater precision while using only about 40 milligrams of material. This method is being applied to materials including metals and ceramics for noneroding throats in solid rockets and next-generation superalloys for turbine engines. Recent advances in the method and the current state of these new measurements will be presented.

Finckenor, Miria M.↗

Addressing Human System Risks to Future Space Exploration

NASA is contemplating future human exploration missions to destinations beyond low Earth orbit, including the Moon, deep-space asteroids, and Mars. While we have learned much about protecting crew health and performance during orbital space flight over the past half-century, the challenges of these future missions far exceed those within our current experience base. To ensure success in these missions, we have developed a Human System Risk Board (HSRB) to identify, quantify, and develop mitigation plans for the extraordinary risks associated with each potential mission scenario. The HSRB comprises research, technology, and operations experts in medicine, physiology, psychology, human factors, radiation, toxicology, microbiology, pharmacology, and food sciences. Methods: Owing to the wide range of potential mission characteristics, we first identified the hazards to human health and performance common to all exploration missions: altered gravity, isolation/confinement, increased radiation, distance from Earth, and hostile/closed environment. Each hazard leads to a set of risks to crew health and/or performance. For example the radiation hazard leads to risks of acute radiation syndrome, central nervous system dysfunction, soft tissue degeneration, and carcinogenesis. Some of these risks (e.g., acute radiation syndrome) could affect crew health or performance during the mission, while others (e.g., carcinogenesis) would more likely affect the crewmember well after the mission ends. We next defined a set of design reference missions (DRM) that would span the range of exploration missions currently under consideration. In addition to standard (6-month) and long-duration (1-year) missions in low Earth orbit (LEO), these DRM include deep space sortie missions of 1 month duration, lunar orbital and landing missions of 1 year duration, deep space journey and asteroid landing missions of 1 year duration, and Mars orbital and landing missions of 3 years duration. We then assessed the likelihood and consequences of each risk against each DRM, using three levels of likelihood (Low: less than or equal to 0.1%; Medium: 0.1%–1.0%; High: greater than or equal to 1.0%) and four levels of consequence ranging from Very Low (temporary or insignificant) to High (death, loss of mission, or significant reduction to length or quality of life). Quantitative evidence from clinical, operational, and research sources were used whenever available. Qualitative evidence was used when quantitative evidence was unavailable. Expert opinion was used whenever insufficient evidence was available. Results: A set of 30 risks emerged that will require further mitigation efforts before being accepted by the Agency. The likelihood by consequence risk assessment process provided a means of prioritizing among the risks identified. For each of the high priority risks, a plan was developed to perform research, technology, or standards development thought necessary to provide suitable reduction of likelihood or consequence to allow agency acceptance. Conclusion: The HSRB process has successfully identified a complete set of risks to human space travelers on planned exploration missions based on the best evidence available today. Risk mitigation plans have been established for the highest priority risks. Each risk will be reassessed annually to track the progress of our risk mitigation efforts.

Paloski, W. H.↗

Development, Verification and Validation of Enclosure Radiation Capabilities in the CHarring Ablator Response (CHAR) Code

With the recent development of multi-dimensional thermal protection system (TPS) material response codes including the capabilities to account for radiative heating is a requirement. This paper presents the recent efforts to implement such capabilities in the CHarring Ablator Response (CHAR) code developed at NASA's Johnson Space Center. This work also describes the different numerical methods implemented in the code to compute view factors for radiation problems involving multiple surfaces. Furthermore, verification and validation of the code's radiation capabilities are demonstrated by comparing solutions to analytical results, to other codes, and to radiant test data.

Salazar, Giovanni↗

Refined Use of Satellite Aerosol Optical Depth Snapshots to Constrain Biomass Burning Emissions in the GOCART Model

Simulations of biomass burning (BB) emissions in global chemistry and aerosol transport models depend on external inventories, which provide location and strength of burning aerosol sources. Our previous work (Petrenko et al., 2012) shows that satellite snapshots of aerosol optical depth (AOD) near the emitted smoke plume can be used to constrain model-simulated AOD, and effectively, the assumed source strength. We now refine the satellite-snapshot method and investigate applying simple multiplicative emission correction factors for the widely used Global Fire Emission Database version 3 (GFEDv3) emission inventory can achieve regional-scale consistency between MODIS AOD snapshots and the Goddard Chemistry Aerosol Radiation and Transport (GOCART) model. The model and satellite AOD are compared over a set of more than 900 BB cases observed by the MODIS instrument during the 2004, and 2006-2008 biomass burning seasons. The AOD comparison presented here shows that regional discrepancies between the model and satellite are diverse around the globe yet quite consistent within most ecosystems. Additional analysis of including small fire emission correction shows the complimentary nature of correcting for source strength and adding missing sources, and also indicates that in some regions other factors may be significant in explaining model-satellite discrepancies. This work sets the stage for a larger intercomparison within the Aerosol Inter-comparisons between Observations and Models (AeroCom) multi-model biomass burning experiment. We discuss here some of the other possible factors affecting the remaining discrepancies between model simulations and observations, but await comparisons with other AeroCom models to draw further conclusions.

aerosol optical depth↗

Rapid Aero Modeling for Urban Air Mobility Aircraft in Computational Experiments

Rapid Aero Modeling (RAM) applied to computational testing, RAM-C, is an approach to efficiently and automatically obtain aerodynamic models during computational investigations. RAM-C is designed to estimate models appropriate for flight dynamics studies and simulations. The approach responds to a demand for experimental efficiency and model fidelity that has increased with growing aircraft complexity and aerodynamic nonlinearities associated with hybrid and electric vertical takeoff and landing (eVTOL) aircraft. In an Urban Air Mobility (UAM) transportation system, it is expected that aircraft will embrace many features from both airplanes and rotorcraft. These vehicles present many more factors than conventional aircraft which can lead to increased computational costs and missed key factor interactions when applying traditional testing and modeling methods. RAM-C provides feedback loops around computational codes to rapidly guide testing toward aerodynamic models meeting user-defined fidelity goals. It combines and extends concepts from design of experiment theory and aircraft system identification theory that allow the user the freedom to choose, in advance of the test, a specific level of fidelity in terms of prediction error. RAM-C only collects enough data required to meet the user-specified prediction error requirements thus saving computational time and resources. The overall achievable fidelity of the final model also depends on the accuracy of the test facility, or in this case, the computational modeling approach. Previous studies to support development of the RAM-T process were conducted in wind tunnel tests to assess potential metrics, algorithms, and procedures. This paper presents results from the next steps taken and tests conducted for the development of RAM-C technology and highlights some of the unique features of RAM applied eVTOL configurations in a computational study.

Aerodynamics↗

Performance of NOAA-20 VIIRS Solar Diffuser and Solar Diffuser Stability Monitor

Visible Infrared Imaging Radiometer Suite (VIIRS) radiometrically calibrates its reflective solar bands (RSBs) primarily through a sunlit onboard solar diffuser (SD). The sunlit SD provides a known radiance under the condition that the absolute product of the SD screen transmittance and the bidirectional reflectance distribution function (BRDF) along the SD-to-telescope direction is accurately known. The BRDF changes due to solar exposure. The change, referred to as the H-factor, is monitored by the onboard SD stability monitor (SDSM). The accuracy of the retrieved H-factor propagates to the retrieved F-factor which corrects the scene spectral radiance. High accuracy of the retrieved H-factor relies on high accuracies in the SDSM screen relative effective transmittance and the relative product of the SD screen effective transmittance and the BRDF at the mission start, and a high SDSM detector signal-to-noise ratio (SNR). This article briefly reviews the algorithms used for the NOAA-20 (N20) VIIRS RSB on-orbit radiometric calibration. Additionally, we show the performance of the N20 VIIRS SDSM, giving the SDSM detector SNRs and the SDSM detector gain temporal changes. We develop a model for the SNRs. The model shows that the decreased SNRs in time are due to the detector gain decreases. We also show the N20 VIIRS SD on-orbit performance, measured by the retrieved H-factor and the estimated standard deviation of its error. The H-factor for the telescope view is obtained from the H-factor for the SDSM view, multiplied by an H-factor angular dependence term. We use an innovative method to determine the angular dependence, using the dependence obtained for the Suomi National Polar-orbiting Partnership (SNPP) VIIRS.

VIIRS↗

Investigating seasonal ENSO forecast amplitude calibration for GEOS-S2S-2

The GEOS-S2S-2 is a global coupled model and assimilation system, encompassing many aspects of the Earth climate system. This project looked at seasonal (nine-month) ensemble forecasts, over the period from 1982 through the present. We explored and validated a forecast amplitude correction technique used by the North American Multi-Model Ensemble (NMME), of which GEOS is a member, for Niño3.4 sea-surface temperature (SST) anomaly predictions. The method relies on deriving a set of correction factors based on the standard deviations of hindcast and observed SST anomalies. This algorithm was implemented at the Global Modeling and Assimilation Office (GMAO) and applied to the GEOS-S2S-2 Niño 3.4 hindcasts. In general, the correction reduced the forecast amplitude. This improved the quality of the forecasts when measured by the root mean square error (RMSE) of the ensemble mean forecast. RMSE decreased for most initialization months and forecast leads. The correction had a larger impact on seasons with strong El Niño-Southern Oscillation (ENSO) events than neutral seasons. The effects of the correction on the ensemble characteristics were also examined, and a variation of the algorithm was proposed that preserves the ensemble spread. The outcome of this project is a tool that can be used to calibrate GEOS-S2S-2 ENSO forecasts and potentially improve the precision of multi-model El Niño outlooks.

ENSO↗

RF Characterization of a Photocurable PEDOT:PSS:PEGDA Conductive Biomaterial for 3D-Printing Implantable Antennas

In this work, we demonstrate photocurable PEDOT:PSS:PEGDA biomaterial as a promising candidate for intracorporeal 3D printing. Intracorporeal 3D printing offers a less invasive method which offer flexibility to tailor the form factor of printed structures. Previous work has demonstrated the feasibility of a robotic probe to 3D-print biological tissues intracorporeally via a minor incision. This same probe could also 3D-print implantable antennas as long as a suitable conductive material is identified in terms of conductivity, biocompatibility, and ability to cure at room/body temperature for safety purposes. We assess the frequency-dependent conductivity of this biomaterial and explore the Radio-Frequency (RF) performance of resulting antennas operating in free-space and inside tissue-emulating phantoms. Results show that PEDOT:PSS biomaterial with 21% and 30% PEGDA content exhibit a conductivity of ~10 4 S/m up to 5 GHz, suitable for wireless implants. Comparing the two, 21% PEGDA content exhibits poorer curing abilities, while 30% PEGDA exhibits slightly lower conductivity. Measurements for 2.4 GHz free-space dipoles conducted in an anechoic chamber reveal only ~0.8 dB and ~1 dB lower gain for PEDOT:PSS:21%PEGDA and PEDOT:PSS:30%PEGDA biomaterial, respectively, as compared to their copper counterpart. For a 5 mm-deep implanted patch antenna, these two biomaterials exhibit 3.05 dB and 3.84 dB higher transmission loss than copper, respectively. If deemed necessary, this performance degradation can be overcome by increasing the overall antenna size since the printing process is now minimally invasive and miniaturization requirements can be relaxed.

3D-printing↗

Improved Spectral and Angular Characterization of Libya-4 and Dome-C for consistent MODIS and VIIRS Radiometric Scaling

The NASA CERES observed SW and LW fluxes are utilized by the climate community for monitoring the Earth’s energy imbalance and for climate model validation. To facilitate seamless flux and cloud properties across MODIS, VIIRS, and geostationary (GEO) imagers the CERES project intercalibrates the imagers directly comparing the coincident ray-matched analogous channel radiances. For CERES edition 4 products, the MODIS, VIIRS and GEO imagers were radiometrically scaled to the Aqua-MODIS C5 calibration reference. There are no direct comparison opportunities between NPP and NOAA20 VIIRS, since they are positioned a half an orbit apart. The previous usage of Aqua-MODIS as a transfer radiometer is coming to an end, since the Aqua orbit is slowly drifting towards the terminator and will be deorbited in 2026. The CERES project will utilize the Libya-4 and Dome-C invariant targets to radiometrically scale between MODIS and VIIRS reflective solar bands. The Libya-4 and Dome-C Earth invariant targets will be characterized by the repeat cycle angular configuration. The target spectral band adjustment factors (SBAF) will be derived using EMIT and DESIS hyper-spectral observations onboard the ISS and will be compared with the existing SCIAMACHY, GOME-2, and Hyperion SBAFs. The DESIS and EMIT SBAF approach can incorporate the future CLARREO CPF SI traceable hyper-spectral measurements allowing the targets to be referenced to an absolute calibration reference. Utilizing the BRDF and atmospheric corrected characterization of one sensor with another will provide the scaling factors. Consistent scaling factors between the two invariant target validates the method.

David R. Doelling↗

Visual, Optical and Replica Inspections: Surface Preparation of 650 MHz NB Cavity for PIP-II Linac

Surface preparation of niobium superconducting RF cavities is a critical step for achieving good RF performance under the superconducting state. Surface defect, roughness, and contamination affect the accelerating gradient and quality factor of the cavities. We report surface inspection methods used to control the surface processing of 650 MHz cavities designated for the pre-production and prototype cryomodules for PIP-II linac. The cavity surface was routinely inspected visually, with an optical camera, and by microscopic scanning of surface replicas. This article covers details on the surface inspection methods and surface polishing process used to repair the surface.

43 PARTICLE ACCELERATORS↗

Methods for making polypeptides including d-amino acids

A method of making a polypeptide including one or more D-amino acids is provided. The method includes combining a ribosome with protein translation factors including (1) a template encoding the polypeptide, wherein the template encoding the polypeptide includes one or more codons which have been recoded to accept a tRNA attached to a D-amino acid, (2) a plurality of L-amino acids and a plurality of corresponding tRNAs, (3) a plurality of D-amino acids and their corresponding aminoacyl tRNA synthetase or a plurality of tRNAs ligated with a D-amino acid, and (4) elongation factor P in a concentration of 2 to 20 micromolar, wherein translation of the template encoding the polypeptide occurs to produce the polypeptide including one or more D-amino acids.

Church, George M.↗

Effect of Heat Treatment on Microstructure and Mechanical Property of 316L Stainless Steel Produced by Laser Powder Bed Fusion

The advanced non-light water reactor designs (Gen IV reactors), including molten salt/ very high temperature/ sodium-cooled and lead-cooled fast reactors, typically operate at higher temperatures and more extreme radiation conditions than light water reactors. An intrinsic part of the deployment and progress of Gen IV reactor designs is selecting the most suitable structural material for a specific application. Additive manufacturing (AM), a fairly new process of making physical, three-dimensional objects from a computer design file, is going to completely change the way of design, build and certify nuclear systems. It offers a range of opportunities to produce complex geometries from existing materials, offers new routes for processing of previously difficult to process materials, allows for design of new high-performance materials, and finally facilitates hybridization of dissimilar materials. This emerging technology has successfully produced cars, wind turbine blade molds and even live cells. It could also open up big opportunities for the nuclear industry to quickly deploy technologies at a fraction of the cost. So far, AM techniques have been preliminarily applied in the field of nuclear reactors, including the classical parts such as the pressure vessel of a small reactor with 508-III steel, the bottom nozzle of a fuel assembly with 304L steel, the fuel cladding with zirconium alloy and the integrated impeller of a pump and the multi-channel valve body with 316L steel [6,7]. The AM applications for operating nuclear reactors started in auxiliary plant components and have slowly migrated to metallic reactors and core components, but many of these are not safety critical components. Although many parts used for nuclear reactors have been fabricated by AM techniques, practical applications in engineering are still a long way off due to the uncertainty factors focused on the processing, material properties, analysis methods and application standards, which feeds the safety and life-cycle of the nuclear reactor. Due to rapid, repeated heating and cooling during production, a high dislocation density was present in the AM material. This microstructure feature is unstable at elevated temperature while high temperature is one of the typical operation environments for nuclear reactors. Thus, it is important to understand the thermal effect on the microstructure of AM material. The objectives of this study are to investigate the effect of heat treatment on the microstructure and mechanical properties of 316L stainless steel produced by laser powder bed fusion additive manufacturing, and to determine an appropriate heat treatment practice that will be applied to the lightweight AM lattice-structured material with the same chemistry. The heat treatment study consisted of annealing the samples at a temperature range of 800 to 1200 oC with a 50 oC increment for different times (1-24 hours), followed by vacuum or air cooling. Microstructural characterization was carried out by Scanning Electron Microscope (SEM). Grain size and crystallographic orientation were investigated by Electron Backscatter Diffraction (EBSD). Vickers hardness tests with a 0.5 kg load were employed to determine the hardness of samples after different heat treatments. After heat treatment, the random crystallographic orientation was preserved, and the volume fraction of high-angle grain boundaries (grain boundary misorientation =15 oC) remained the same. The dislocation density decreased with annealing temperature due to recovery. The fine subgrain structures in the as-printed specimen were quite stable up to 1200 oC. Minimal recrystallization was observed up to 1200 oC. Recrystallization initiated only after 8.5 hours at 1200 oC. The SEM images did not show obvious dependence of microstructure on cooling rate. The hardness of the specimens decreased with increasing annealing temperature as a result of the decrease in dislocation density. It is interesting to note that the AM material showed very similar hardness to the wrought material when annealing at similar temperature, although the microstructures are very different. Annealing at 1050 oC for 1 hour followed by air cooling was selected as the heat treatment procedure for the lattice designed lightweight AM 316L material.

36 MATERIALS SCIENCE↗

Identifying strengths and weaknesses of methods for computational network inference from single-cell RNA-seq data

Single-cell RNA-sequencing (scRNA-seq) offers unparalleled insight into the transcriptional programs of different cellular states by measuring the transcriptome of thousands of individual cells. An emerging problem in the analysis of scRNA-seq is the inference of transcriptional gene regulatory networks and a number of methods with different learning frameworks have been developed to address this problem. Here, we present an expanded benchmarking study of eleven recent network inference methods on seven published scRNA-seq datasets in human, mouse, and yeast considering different types of gold standard networks and evaluation metrics. We evaluate methods based on their computing requirements as well as on their ability to recover the network structure. We find that, while most methods have a modest recovery of experimentally derived interactions based on global metrics such as Area Under the Precision Recall curve, methods are able to capture targets of regulators that are relevant to the system under study. Among the top performing methods that use only expression were SCENIC, PIDC, MERLIN or Correlation. Addition of prior biological knowledge and the estimation of transcription factor activities resulted in the best overall performance with the Inferelator and MERLIN methods that use prior knowledge outperforming methods that use expression alone. We found that imputation for network inference did not improve network inference accuracy and could be detrimental. Comparisons of inferred networks for comparable bulk conditions showed that the networks inferred from scRNA-seq datasets are often better or at par with the networks inferred from bulk datasets. Our analysis should be beneficial in selecting methods for network inference. At the same time, this highlights the need for improved methods and better gold standards for regulatory network inference from scRNAseq datasets.

59 BASIC BIOLOGICAL SCIENCES↗