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NASA NTRS2016

Marine Boundary Layer Cloud Property Retrievals from High-Resolution ASTER Observations: Case Studies and Comparison with Terra MODIS

A research-level retrieval algorithm for cloud optical and microphysical properties is developed for the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) aboard the Terra satellite. It is based on the operational MODIS algorithm. This paper documents the technical details of this algorithm and evaluates the retrievals for selected marine boundary layer cloud scenes through comparisons with the operational MODIS Data Collection 6 (C6) cloud product. The newly developed, ASTERspecific cloud masking algorithm is evaluated through comparison with an independent algorithm reported in Zhao and Di Girolamo (2006). To validate and evaluate the cloud optical thickness (tau) and cloud effective radius (r(sub eff)) from ASTER, the high-spatial-resolution ASTER observations are first aggregated to the same 1000m resolution as MODIS. Subsequently, tau(sub aA) and r(sub eff, aA) retrieved from the aggregated ASTER radiances are compared with the collocated MODIS retrievals. For overcast pixels, the two data sets agree very well with Pearson's product-moment correlation coefficients of R greater than 0.970. However, for partially cloudy pixels there are significant differences between r(sub eff, aA) and the MODIS results which can exceed 10 micrometers. Moreover, it is shown that the numerous delicate cloud structures in the example marine boundary layer scenes, resolved by the high-resolution ASTER retrievals, are smoothed by the MODIS observations. The overall good agreement between the research-level ASTER results and the operational MODIS C6 products proves the feasibility of MODIS-like retrievals from ASTER reflectance measurements and provides the basis for future studies concerning the scale dependency of satellite observations and three-dimensional radiative effects.

marine boundary layer↗

NASA NTRS2017

Remote Sensing of Crystal Shapes in Ice Clouds

Ice crystals in clouds exist in a virtually limitless variation of geometries. The most basic shapes of ice crystals are columnar or plate-like hexagonal prisms with aspect ratios determined by relative humidity and temperature. However, crystals in ice clouds generally display more complex structures owing to aggregation, riming and growth histories through varying temperature and humidity regimes. Crystal shape is relevant for cloud evolution as it affects microphysical properties such as fall speeds and aggregation efficiency. Furthermore, the scattering properties of ice crystals are affected by their general shape, as well as by microscopic features such as surface roughness, impurities and internal structure. To improve the representation of ice clouds in climate models, increased understanding of the global variation of crystal shape and how it relates to, e.g., location, cloud temperature and atmospheric state is crucial. Here, the remote sensing of ice crystal macroscale and microscale structure from airborne and space-based lidar depolarization observations and multi-directional measurements of total and polarized reflectances is reviewed. In addition, a brief overview is given of in situ and laboratory observations of ice crystal shape as well as the optical properties of ice crystals that serve as foundations for the remote sensing approaches. Lidar depolarization is generally found to increase with increasing cloud height and to vary with latitude. Although this variation is generally linked to the variation of ice crystal shape, the interpretation of the depolarization remains largely qualitative and more research is needed before quantitative conclusions about ice shape can be deduced. The angular variation of total and polarized reflectances of ice clouds has been analyzed by numerous studies in order to infer information about ice crystal shapes from them. From these studies it is apparent that pristine crystals with smooth surfaces are generally inconsistent with the data and thus crystal impurity, distortion or surface roughness is prevalent. However, conclusions about the dominating ice shapes are often inconclusive and contradictory and are highly dependent on the limited selection of shapes included in the investigations. Since ice crystal optical properties are mostly determined by the aspect ratios of the crystal components and their microscale structure, it is advised that remote sensing applications focus on the variation of these ice shape characteristics, rather than on the macroscale shape or habit. Recent studies use databases with nearly continuous ranges of crystal component aspect ratio and-or roughness levels to infer the variation of ice crystal shape from satellite and airborne remote sensing measurements. Here, the rationale and results of varying strategies for the remote sensing of ice crystal shape are reviewed. Observed systematic variations of ice crystal geometry with location, cloud height and atmospheric state suggested by the data are discussed. Finally, a prospective is given on the future of the remote sensing of ice cloud particle shapes.

clouds↗

NASA NTRS2016

Comet Dust: The Diversity of Primitive Particles and Implications

Comet dust is primitive and shows significant diversity. Our knowledge of the properties of primitive particles has expanded significantly through microscale investigations of cosmic dust samples (IDPs and AMMs) and of comet dust samples (Stardust and Rosetta's COSIMA), as well as through remote sensing (spectroscopy and imaging) via Spitzer and via spacecraft encounters with 103P/Hartley 2 and 67P/Churyumov-Gerasimenko. Microscale investigations show that comet dust and cosmic dust are particles of unequilibrated materials, including aggregates of materials unequilibrated at submicron scales. We call unequilibrated materials "primitive" and we deduce they were incorporated into ice-‐rich (H2O-, CO2-, and CO-ice) parent bodies that remained cold, i.e., into comets, because of the lack of aqueous or thermal alteration since particle aggregation; yet some Stardust olivines suggest mild thermal metamorphism. Primitive particles exhibit a diverse range of: structure and typology; size and size distribution of constituents; concentration and form of carbonaceous and organic matter; D-, N-, and O- isotopic enhancements over solar; Mg-, Fe-contentsof thesilicate minerals; the compositions and concentrations of sulfides, and of less abundant mineral species such as chondrules, CAIs and carbonates. The unifomity within a group of samples points to: aerodynamic sorting of particles and/or particle constituents; the inclusion of a limited range of oxygen fugacities; the inclusion or exclusion of chondrules; a selection of organics. The properites of primitive particles imply there were disk processes that resulted in different comets having particular selections of primitive materials. The diversity of primitive particles has implications for the diversity of materials in the protoplanetary disk present at the time and in the region where the comets formed.

Comet dust is primitive and shows significant dive↗

NASA NTRS2017

Development of Multi-Sensor Global Cloud and Radiance Composites for DSCOVR EPIC Imager with Subpixel Definition

The Deep Space Climate Observatory (DSCOVR) enables analysis of the daytime Earth radiation budget via the onboard Earth Polychromatic Imaging Camera (EPIC) and National Institute of Standards and Technology Advanced Radiometer (NISTAR). EPIC delivers adequate spatial resolution imagery but only in shortwave bands (317-780 nm), while NISTAR measures the top-of-atmosphere (TOA) whole-disk radiance in shortwave and longwave broadband windows. Accurate calculation of albedo and outgoing longwave flux requires a high-resolution scene identification such as the radiance observations and cloud properties retrievals from low earth orbit (LEO, including NASA Terra and Aqua MODIS, Suomi-NPP VIIRS, and NOAA AVHRR) and geosynchronous (GEO, including GOES east and west, METEOSAT, INSAT-3D, MTSAT-2, and Himawari-8) satellite imagers. The cloud properties are derived using the Clouds and the Earth's Radiant Energy System (CERES) mission Cloud Subsystem group algorithms. These properties have to be co-located with EPIC pixels to provide the scene identification and to select anisotropic directional models (ADMs), which are then used to adjust the NISTAR-measured radiance and subsequently obtain the global daytime shortwave and longwave fluxes. This work presents an algorithm for optimal merging of selected radiance and cloud property parameters derived from multiple satellite imagers to obtain seamless global hourly composites at 5-km resolution. Selection of satellite data for each 5-km pixel is based on an aggregated rating that incorporates five parameters: nominal satellite resolution, pixel time relative to the EPIC time, viewing zenith angle, distance from day/night terminator, and probability of sun glint. To provide a smoother transition in the merged output, in regions where candidate pixel data from two satellite sources have comparable aggregated rating, the selection decision is defined by the cumulative function of the normal distribution so that abrupt changes in the visual appearance of the composite data are avoided. Higher spatial accuracy in the composite product is achieved by using the inverse mapping with gradient search during reprojection and bicubic interpolation for pixel resampling.

Khlopenkov, Konstantin V.↗

NASA NTRS2018

Particle Size Distributions in Chondritic Meteorites: Evidence for Pre-Planetesimal Histories

Magnesium-rich silicate chondrules and calcium-, aluminum-rich refractory inclusions (CAIs) are fundamental components of primitive chondritic meteorites. It has been suggested that concentration of these early-formed particles by nebular sorting processes may lead to accretion of planetesimals, the planetary bodies that represent the building blocks of the terrestrial planets. In this case, the size distributions of the particles may constrain the accretion process. Here we present new particle size distribution data for Northwest Africa 5717, a primitive ordinary chondrite (ungrouped 3.05) and the well-known carbonaceous chondrite Allende (CV3). Instead of the relatively narrow size distributions obtained in previous studies (Ebel et al., 2016; Friedrich et al., 2015; Paque and Cuzzi, 1997, and references therein), we observed broad size distributions for all particle types in both meteorites. Detailed microscopic image analysis of Allende shows differences in the size distributions of chondrule subtypes, but collectively these subpopulations comprise a composite "chondrule" size distribution that is similar to the broad size distribution found for CAIs. Also, we find accretionary 'dust' rims on only a subset (approximately 15-20 percent) of the chondrules contained in Allende, which indicates that subpopulations of chondrules experienced distinct histories prior to planetary accretion. For the rimmed subset, we find positive correlation between rim thickness and chondrule size. The remarkable similarity between the size distributions of various subgroups of particles, both with and without fine grained rims, implies a common size sorting process. Chondrite classification schemes, astrophysical disk models that predict a narrow chondrule size population and/or a common localized formation event, and conventional particle analysis methods must all be critically reevaluated. We support the idea that distinct "lithologies" in NWA 5717 are nebular aggregates of chondrules. If greater than or equal to centimeter-sized aggregates of chondrules can form it will have implications for planet formation and suggests the sticking stage is where the preferential size physics is operating.

chondritic meteorites↗

NASA NTRS2018

Light Microscopy Module Biophysics - 4 (LMM-B4)

Compare incorporation of protein aggregates into growing protein crystals on ISS (International Space Station) and on Earth. Measure growth rates in 1g (1 gravity) versus microgravity (micro-g) for different size aggregates of proteins. Compare the defect density and crystal quality via fluorescent-based atomic force microscopy and X-ray diffraction quality of crystals grown at different rates in a 1g environment.

Penn, Benjamin G.↗

NASA NTRS2017

Sensitivity Analysis Method to Address User Disparities in the Analytic Hierarchy Process

Decision makers often face complex problems, which can seldom be addressed well without the use of structured analytical models. Mathematical models have been developed to streamline and facilitate decision making activities, and among these, the Analytic Hierarchy Process (AHP) constitutes one of the most utilized multi-criteria decision analysis methods. While AHP has been thoroughly researched and applied, the method still shows limitations in terms of addressing user profile disparities. A novel sensitivity analysis method based on local partial derivatives is presented here to address these limitations. This new methodology informs AHP users of which pairwise comparisons most impact the derived weights and the ranking of alternatives. The method can also be applied to decision processes that require the aggregation of results obtained by several users, as it highlights which individuals most critically impact the aggregated group results while also enabling to focus on inputs that drive the final ordering of alternatives. An aerospace design and engineering example that requires group decision making is presented to demonstrate and validate the proposed methodology.

Marie Ivanco↗

NASA NTRS2018

Microphysical Properties of Tropical Tropopause Layer Cirrus

Pervasive cirrus clouds in the tropical tropopause layer (TTL) play an important role in determining the composition of stratospheric air through dehydration of tropospheric air entering the stratosphere. This dehydration affects Earth's energy budget and climate, yet uncertainties remain regarding the microphysical processes that govern TTL cirrus. TTL cirrus were sampled with the NASA Global Hawk UAV for over 30 hr in the Western Pacific in 2014 during the Airborne Tropical TRopopause EXperiment. In situ measurements by a Fast Cloud Droplet Probe and Hawkeye probe (combination Fast Cloud Droplet Probe, Two‐Dimensional Stereo optical array probe, and Cloud Particle Imager) provided particle concentrations and sizing between 1‐ and 1,280‐μm diameter and high resolution images for habit identification. We present the variability in ice concentrations, size distributions, and habits as functions of temperature, altitude, and time since convective influence. Observed ice particles were predominantly small and quasi‐spheroidal in shape, with the percentage of quasi‐spheroids increasing with decreasing temperature. In comparison to the large fraction of the population consisting of quasi‐spheroids, faceted habits (columns, plates, rosettes, and budding rosettes) constituted a smaller percentage of the overall population and exhibited the opposite correlation with temperature. The trend of higher percentages of faceted crystals occurring at warmer temperatures may be due to diffusional growth or aggregation as particles descend through cloud, and/or the more rapid diffusional growth rate at warmer temperatures. Sampling was typically well away from deep convection, however, and very few aggregates were observed, so the trend of higher percentages of faceted habits is likely attributable to diffusional growth.

Woods, Sarah↗

NASA NTRS2019

Using Graph Coloring to Compute Total Derivatives More Efficiently in OpenMDAO

When they are applicable, gradient based optimization algorithms are the most efficient way to solve design optimization problems. Although gradient based methods are generally efficient, they can be made significantly more so through the usage of analytic techniques to compute the necessary total derivatives. The traditional forward (direct) and reverse (adjoint) analytic techniques have computational costs that scale linearly with the number of design variables and the number of constraints, respectively. In this work, we present an application of a graph coloring algorithm to the analytic techniques for computing total derivative Jacobians in order to achieve much better computational scaling than the pure analytic methods can provide alone. A detailed theoretical explanation of how coloring algorithms interact with analytic derivative methods is presented that illustrates specific types of sparsity patterns that must be present in total derivative Jacobians in order for this coloring technique to be effective. The new technique has been implemented as a feature in the OpenMDAO framework and the implementation is demonstrated on two example problems. The performance on the example problems up to 50% reduction in compute cost for optimizations with bi-directional coloring compared to traditional constraint aggregation. Additionally, the results show how coloring technique alleviates some of the numerical difficulties that constraint aggregation can cause, leading to the ability to solve larger problems. It is expected that the new method will have wide applicability to multidisciplinary optimization problems, and that its availability in OpenMDAO will offer significant computational savings for users without the need for them to implement the coloring algorithm themselves.

Trajectory↗

NASA NTRS2015

Human Factors Assessment of Disturbances to Scheduled Performance-Based Navigation Arrival Operations

The introduction of Performance-Based Navigation (PBN) specifications to air traffic management has resulted in many benefits during nominal operations, including shorter flight paths, reduced fuel costs, and improved terminal area arrival rates. However, these benefits become less noticeable during off-nominal operations where aircraft are routinely interrupted from staying on PBN procedures due to disturbances such as missed approaches. This human-in-the-loop (HITL) study used multiple types of disturbance events to perturb the arrival schedule. Perturbed schedules were managed with different types of schedule adjustments, including a condition with no adjustments. The study collected data on a host of dependent variables, including human factors measures on controller workload and system performance measures such as schedule nonconformance (nc). Initial analyses showed strong correlations between aggregated controller workload and aggregated nc, as well as benefits of both automatic and manual schedule adjustments for increasing system performance, such as reduced PBN procedure interruptions. The goal of this paper is to further test these initial findings. The results indicated that an increase in schedule nonconformance correlated with an increase in controller workload at specific time intervals, and automated schedule adjustments consistently reduced controller workload associated with nonconformance.

Human factors↗

NASA NTRS2019

Surface Height and Sea Ice Freeboard of the Arctic Ocean from ICESat-2: Characteristics and Early Results

We present the first winter season of surface height and sea ice freeboards of the Arctic Ocean from the new ICESat-2 (IS-2) mission. The Advanced Topographic Laser Altimeter System (ATLAS) onboard has six photon-counting beams for surface profiling with a 10-kHz pulse-rate (inter-pulse distance ~0.7m) and footprints of ~17m. Geolocated heights assigned to individual photons scattered from the surface allow significant flexibility in the construction of height distributions used in surface finding. For IS-2 sea ice products, a fixed 150-photon aggregate is used to control height precision and obtain better along-track resolution over high reflectance surfaces. Quasi-specular returns in openings as narrow as ~27m, crucial for freeboard calculations, are resolved. The fixed photon aggregate results in unique variable along-track resolutions and non-uniform sampling (17m x 27m to 17m x 200m for the strong beams) of the surface. The six profiling beams – three pairs separated by 3.3 km with a strong and weak beam in each pair – provide correlated statistics at regional length scales for assessment of beam-to-beam retrieval consistency and accuracy. Analysis shows along-track height precisions of ~2cm, and agreement in the monthly freeboard distributions across the strong beams to 1-2cm. In this paper, we describe briefly the approaches used in surface height and freeboard retrievals from ATLAS photon clouds, and detail the key features of these along-track sea ice products, focusing on the first release of data collected over the Arctic Ocean, which spans the period between October 14, 2018 – the start of data collection – and the end of March 2019.

R Kwok↗

NASA NTRS2020

Mg Isotopic Compositions of Fine-Grained Ca-Al-Rich Inclusions from Reduced CV3 Chondrites and Implications on the Timescale of Nebular Condensation

Fine-grained Ca-Al-rich inclusions (FGIs) in carbonaceous chondrites are interpreted as aggregates of nebular gas-solid condensates that escaped significant melting [1]. Recent Al-Mg isotopic studies of small FGIs (<200 µm in size) from pristine CO3 chondrites have revealed significant variations in initial 26Al/27Al ratio, (26Al/27Al)(sub 0), spanning from 5.73×10(exp ˗5) to 8×10(exp ˗6) [2,3]. Importantly, [3] found a main CAI population characterized by (26Al/27Al)(sub 0) = 5.4×10(exp ˗5) that likely record the onset of dust condensation and initial coagulation events, followed by multiple thermal events over an extended time period. Thus far, a small number of large FGIs from CV3 chondrites have been analyzed, showing a narrower range of ( 26Al/27Al)(sub 0) = 5.27×10(exp ˗5) to 3.35×10(exp ˗5) [4-6], similar to those inferred from coarse-grained, igneous CAIs (CGIs) from CV3 chondrites [7]. These observed different ratios may raise a question if large FGIs in CV3 chondrites record a time interval from primary direct condensation of refractory solids to their aggregation and growth into larger inclusions. In this study, we present Al-Mg isotopic compositions of FGIs from reduced CV3 chondrites to better constrain their formation timescale relative to smaller FGIs in CO3 chondrites, as well as to CGIs in CV3 chondrites. This isotopic study is coordinated with a microstructural study to elucidate the origin and nature of FGIs in the petrologic and mineralogical context.

Han, J.↗

NASA NTRS2020

Two-Year Cosmology Large Angular Scale Surveyor (CLASS) Observations: 40GHz Telescope Pointing, Beam Profile, Window Function, and Polarization Performance

The Cosmology Large Angular Scale Surveyor (CLASS) is a telescope array that observes the cosmic microwave background (CMB) over 75% of the sky from the Atacama Desert, Chile, at frequency bands centered near 40, 90, 150, and 220 GHz. CLASS measures the large angular scale (1°~< θ >=90°) CMB polarization to constrain the tensor-to-scalar ratio at the r ∼ 0.01 level and the optical depth to last scattering to the sample variance limit. This paper presents the optical characterization of the 40 GHz telescope during its ﬁrst observation era, from 2016 September to 2018 February. High signal-to-noise observations of the Moon establish the pointing and beam calibration. The telescope boresight pointing variation is <0°. 023 (<1.6% of the beam’s full width at half maximum (FWHM)). We estimate beam parameters per detector and in aggregate, as in the CMB survey maps. The aggregate beam has an FWHM of 1°.579 ± 0°.001 and a solid angle of 838 ± 6 μsr, consistent with physical optics simulations. The corresponding beam window function has a sub-percent error per multipole at ℓ < 200. An extended 90° beam map reveals no signiﬁcant far sidelobes. The observed Moon polarization shows that the instrument polarization angles are consistent with the optical model and that the temperature-to-polarization leakage fraction is <10(exp −4) (95% C.L.). We ﬁnd that the Moon-based results are consistent with measurements of M42, RCW 38, and Tau A from CLASS’s CMB survey data. In particular, Tau A measurements establish degree- level precision for instrument polarization angles.

Xu, Zhilei↗

NASA NTRS2020

Linkage among Ice Crystal Microphysics, Mesoscale Dynamics and Cloud and Precipitation Structures Revealed By Collocated Microwave Radiometer and Multi-Frequency Radar Observations

Ice clouds and falling snow are ubiquitous globally and play important roles in the Earth’s radiation budget and precipitation processes. Ice particle microphysical properties (e.g., size, habit and orientation) are not only influenced by ambient environment’s dynamic and thermodynamic conditions, but also intimately connect to the cloud radiative effects and particle fall speeds, which therefore impact up to the future climate projection and down to the details of the surface precipitation (e.g., onset-time, location, type and strength). Our previous work revealed that high-frequency Polarimetric radiance Difference (PD) from passive microwave sensors is a good indicator of the bulk aspect ratio of horizontally oriented ice particles that are often occur inside anvil clouds and/or stratiform precipitations. In this current work, we further investigate the dynamic/thermodynamic mechanisms and cloud/precipitation structures associated with ice-phase microphysics corresponding to different PD signals. In order to do so, collocated CloudSat radar (W-band) and Global Precipitation Measurement Dual-frequency Precipitation Radar (GPM-DPR, Ku/Ka bands) observations as well as European Centre for Medium-Range Weather Forecasts (ECMWF) atmosphere background profiles are grouped according to the magnitude of PD for only stratiform precipitation and/or anvil cloud scenes. We found that horizontally-oriented snow aggregates or large snow particles are likely the major contributor to the high-PD signals at 166 GHz, while low-PD magnitudes can be attributed to small cloud ice, randomly oriented snow aggregates, riming snow or super-cooled water. Further, high (low) PD scenes are found to be associated with stronger (weaker) wind shear and higher (lower) ambient humidity, both of which help promote (prohibit) the growth of frozen particles and the organization of convective systems. An ensemble of squall line cases is studied at the end to demonstrate that the PD asymmetry in the leading and trailing edges of the deep convection line is closely tied to the anvil cloud and stratiform precipitation layers respectively, suggesting the potential usefulness of PD as a proxy of stratiform/convective precipitation flag, as well as a proxy of convection life stage.

Ice crystal microphysics↗

NASA NTRSDate not supplied

Evaluation of Correction Methods for NASA GeneLab Transcriptomic Datasets

Conducting space biology experiments aboard the International Space Station, particularly those utilizing complex model organisms like mice, is expensive and difficult due to limited crew availability, hardware, and space. As a result, sample numbers from these studies are low, reducing the statistical power of any one experiment. Aggregating spaceflight datasets serves as a method to increase sample numbers, allowing for novel insights through bioinformatic analysis of ‘omics data from merged datasets. However, aggregating datasets can introduce unwanted variation including 1) differences in sample handling, processing, and sequencing platforms between datasets (technical variation) as well as 2) differences in experimental design between datasets such as sex or age of the model organism used. In the present study, NASA GeneLab-hosted RNAseq datasets from rodent liver tissues were used to evaluate several statistical methods to correct for this unwanted variation through two approaches, reference-based and standard. The following correction algorithms were applied with (reference-based) and/or without (standard) considering Universal Mouse RNA Reference samples: ComBat and ComBat_seq from the SVA package, median polish, empirical Bayes, and ANOVA-based algorithms from the MBatch package, and negative binomial regression normalization in the DESeq2 package. For each approach, after the correction algorithm was applied, differential gene expression (DGE) analysis of flight and ground control samples was performed with the combined data. The robustness of each tool was evaluated using BatchQC, to determine statistical differences between datasets before and after correction, Principal Component Analysis, to evaluate global gene expression in samples before and after correction, and by comparing DGE analysis of individual datasets and combined datasets before and after correction. The results showed that the reference-based approach introduced several additional (and likely artificial) DEGs when compared with the standard approach. Thus, the most robust standard correction will be implemented in the GeneLab Visualization 2.0 platform when datasets are combined.

GeneLab, RNA-seq, Batch Correction↗

NASA NTRSDate not supplied

Evaluation of Correction Methods for NASA GeneLab Transcriptomic Datasets

Conducting space biology experiments aboard the International Space Station, particularly those utilizing complex model organisms like mice, is expensive and difficult due to limited crew availability, hardware, and space. As a result, sample numbers from these studies are low, reducing the statistical power of any one experiment. Aggregating spaceflight datasets serves as a method to increase sample numbers, allowing for novel insights through bioinformatic analysis of ‘omics data from merged datasets. However, aggregating datasets can introduce unwanted variation including 1) differences in sample handling, processing, and sequencing platforms between datasets (technical variation) as well as 2) differences in experimental design between datasets. In the present study, NASA GeneLab-hosted RNAseq datasets from mouse liver tissues were used to evaluate several statistical methods to correct for this unwanted variation through two approaches, reference-based and standard. The following correction algorithms were applied with (reference-based) and/or without (standard) considering Universal Mouse RNA Reference samples: ComBat and ComBat_seq from the SVA package, median polish, empirical Bayes, and ANOVA-based algorithms from the MBatch package, and negative binomial regression normalization in the DESeq2 package. For each approach, after the correction algorithm was applied, differential gene expression (DGE) analysis of flight and ground control samples was performed with the combined data. The robustness of each tool was evaluated using BatchQC to determine statistical differences between datasets before and after correction, Principal Component Analysis to evaluate global gene expression in samples before and after correction, and by comparing DGE analysis of individual datasets and combined datasets before and after correction. The results showed that the reference-based approach introduced several additional (and likely artificial) DEGs when compared with the respective standard approach. Of the methods tested, standard ComBat and DESeq2 were identified as the most robust correction methods for combining spaceflight mouse liver RNAseq datasets hosted on GeneLab.

GeneLab↗

NASA NTRSDate not supplied

Combining RNA-SEQ Datasets from NASA GENELAB: An Evaluation of Correction Methods

Background: Conducting space biology experiments aboard the International Space Station, particularly those utilizing complex model organisms like mice, is expensive and difficult due to limited crew availability, hardware, and space. As a result, sample numbers from these studies are low, reducing the statistical power of any one experiment. Aggregating spaceflight datasets serves as a method to increase sample numbers, allowing for novel insights through bioinformatic analysis of ‘omics data from merged datasets. However, aggregating datasets can introduce unwanted variation including 1) differences in sample handling, processing, and sequencing platforms between datasets (technical variation) as well as 2) differences in experimental design between datasets. Methods: In the present study, NASA GeneLab-hosted RNAseq datasets from mouse liver tissues were used to evaluate several statistical methods to correct for this unwanted variation through two approaches, reference-based and standard. The following correction algorithms were applied with (reference-based) and/or without (standard) considering Universal Mouse RNA Reference samples: ComBat and ComBat_seq from the SVA package, the median polish, empirical Bayes, and ANOVA-based algorithms from the MBatch package, and negative binomial regression normalization in the DESeq2 package. For each approach, after the correction algorithm was applied, differential gene expression (DGE) analysis of flight and ground control samples was performed with the combined data. The robustness of each tool was evaluated using BatchQC to determine statistical differences between datasets before and after correction, Principal Component Analysis to evaluate global gene expression in samples before and after correction, and by comparing DGE analysis of individual datasets and combined datasets before and after correction. Results: The results showed that the reference-based approach introduced several additional (and likely artificial) differentially expressed genes when compared with the respective standard approach. Conclusions: Of the methods tested, standard ComBat_seq and DESeq2 were identified as the most robust correction methods for combining spaceflight mouse liver RNAseq datasets hosted on GeneLab.

Finsam Samson↗

NASA NTRS2021

Exploring uncertainties in global crop yield projections in a large ensemble of crop models and CMIP5 and CMIP6 climate scenarios

Concerns over climate change are motivated in large part because of their impact on human society. Assessing the effect of that uncertainty on specific potential impacts is demanding, since it requires a systematic survey over both climate and impacts models. We provide a comprehensive evaluation of uncertainty in projected crop yields for maize, spring and winter wheat, rice, and soybean, using a suite of nine crop models and up to 45 CMIP5 and 34 CMIP6 climate projections for three different forcing scenarios. To make this task computationally tractable, we use a new set of statistical crop model emulators. We find that climate and crop models contribute about equally to overall uncertainty. While the ranges of yield uncertainties under CMIP5 and CMIP6 projections are similar, median impact in aggregate total caloric production is typically more negative for the CMIP6 projections (+1% to −19%) than for CMIP5 (+5% to −13%). In the first half of the 21st century and for individual crops is the spread across crop models typically wider than that across climate models, but we find distinct differences between crops: globally, wheat and maize uncertainties are dominated by the crop models, but soybean and rice are more sensitive to the climate projections. Climate models with very similar global mean warming can lead to very different aggregate impacts so that climate model uncertainties remain a significant contributor to agricultural impacts uncertainty. These results show the utility of large-ensemble methods that allow comprehensively evaluating factors affecting crop yields or other impacts under climate change. The crop model ensemble used here is unbalanced and pulls the assumption that all projections are equally plausible into question. Better methods for consistent model testing, also at the level of individual processes, will have to be developed and applied by the crop modeling community.

crop yield projections↗