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  • 1
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    A comprehensive comparison of general RNA-RNA interaction prediction methods (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-21
    Description: RNA–RNA interactions are fast emerging as a major functional component in many newly discovered non-coding RNAs. Basepairing is believed to be a major contributor to the stability of these intermolecular interactions, much like intramolecular basepairs formed in RNA secondary structure. As such, using algorithms similar to those for predicting RNA secondary structure, computational methods have been recently developed for the prediction of RNA–RNA interactions. We provide the first comprehensive comparison comprising 14 methods that predict general intermolecular basepairs. To evaluate these, we compile an extensive data set of 54 experimentally confirmed fungal snoRNA–rRNA interactions and 102 bacterial sRNA–mRNA interactions. We test the performance accuracy of all methods, evaluating the effects of tool settings, sequence length, and multiple sequence alignment usage and quality. Our results show that—unlike for RNA secondary structure prediction—the overall best performing tools are non-comparative energy-based tools utilizing accessibility information that predict short interactions on this data set. Furthermore, we find that maintaining high accuracy across biologically different data sets and increasing input lengths remains a huge challenge, causing implications for de novo transcriptome-wide searches. Finally, we make our interaction data set publicly available for future development and benchmarking efforts.
    Keywords: Nucleic acid structure, RNA characterisation and manipulation, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Marine Boundary Layer Cloud Property Retrievals from High-Resolution ASTER Observations: Case Studies and Comparison with Terra MODIS (2016)
    In:  Other Sources
    Details
    Publication Date: 2019-07-13
    Description: 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.
    Keywords: Earth Resources and Remote Sensing
    Type: GSFC-E-DAA-TN43376 , Atmospheric Measurement Techniques (ISSN 1867-1381) (e-ISSN 1867-8548); 9; 12; 5869-5894
    Format: text
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  • 3
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    Retrieval of Ice Cloud Properties Using an Optimal Estimation Algorithm and MODIS Infrared Observations: 2. Retrieval Evaluation (2016)
    In:  Other Sources
    Details
    Publication Date: 2019-07-13
    Description: An infrared-based optimal estimation (OE-IR) algorithm for retrieving ice cloud properties is evaluated. Specifically, the implementation of the algorithm with MODerate resolution Imaging Spectroradiometer (MODIS) observations is assessed in comparison with the operational retrieval products from MODIS on the Aqua satellite (MYD06), Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP), and the Imaging Infrared Radiometer (IIR); the latter two instruments fly on the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) satellite in the Afternoon Constellation (A-Train) with Aqua. The results show that OE-IR cloud optical thickness (tau) and effective radius (r(sub eff)) retrievals perform best for ice clouds having 0.5 〈 tau〈 7 and r(sub eff) 〈 50microns. For global ice clouds, the averaged retrieval uncertainties of tau and r(sub eff) are 19% and 33%, respectively. For optically thick ice clouds with tau larger than 10, however, the tau and r(sub eff) retrieval uncertainties can exceed 30% and 50%, respectively. For ice cloud top height (h), the averaged global uncertainty is 0.48km. Relatively large h uncertainty (e.g., 〉 1km) occurs for tau 〈 0.5. Analysis of 1month of the OE-IR retrievals shows large tau and r(sub eff) uncertainties in storm track regions and the southern oceans where convective clouds are frequently observed, as well as in high-latitude regions where temperature differences between the surface and cloud top are more ambiguous. Generally, comparisons between the OE-IR and the operational products show consistent tau and h retrievals. However, obvious differences between the OE-IR and the MODIS Collection 6 r(sub eff) are found.
    Keywords: Earth Resources and Remote Sensing
    Type: GSFC-E-DAA-TN66617 , GSFC-E-DAA-TN41908 , Journal of Geophysical Research: Atmospheres (ISSN 2169-897X); 121; 10; 5827–5845
    Format: text
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  • 4
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    Drought Rapidly Diminishes the Large Net CO2 Uptake in 2011 Over Semi-Arid Australia (2016)
    In:  Other Sources
    Details
    Publication Date: 2019-07-13
    Description: Each year, terrestrial ecosystems absorb more than a quarter of the anthropogenic carbon emissions, termed as land carbon sink. An exceptionally large land carbon sink anomaly was recorded in 2011, of which more than half was attributed to Australia. However, the persistence and spatially attribution of this carbon sink remain largely unknown. Here we conducted an observation-based study to characterize the Australian land carbon sink through the novel coupling of satellite retrievals of atmospheric CO2 and photosynthesis and in-situ flux tower measures. We show the 2010-11 carbon sink was primarily ascribed to savannas and grasslands. When all biomes were normalized by rainfall, shrublands however, were most efficient in absorbing carbon. We found the 2010-11 net CO2 uptake was highly transient with rapid dissipation through drought. The size of the 2010-11 carbon sink over Australia (0.97 Pg) was reduced to 0.48 Pg in 2011-12, and was nearly eliminated in 2012-13 (0.08 Pg). We further report evidence of an earlier 2000-01 large net CO2 uptake, demonstrating a repetitive nature of this land carbon sink. Given a significant increasing trend in extreme wet year precipitation over Australia, we suggest that carbon sink episodes will exert greater future impacts on global carbon cycle.
    Keywords: Earth Resources and Remote Sensing
    Type: GSFC-E-DAA-TN39056 , Scientific Reports (e-ISSN 2045-2322); 6; 37747
    Format: text
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  • 5
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    Cirrus Heterogeneity Effects on Cloud Optical Properties Retrieved with an Optimal Estimation Method from MODIS VIS to TIR Channels. (2016)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: This study presents preliminary results on the effect of cirrus heterogeneities on top-of-atmosphere (TOA) simulated radiances or reflectances for MODIS channels centered at 0.86, 2.21, 8.56, 11.01 and 12.03 micrometers , and on cloud optical properties retrieved with a research-level optimal estimation method (OEM). Synthetic cirrus cloud fields are generated using a 3D cloud generator (3DCLOUD) and radiances/reflectances are simulated using a 3D radiative transfer code (3DMCPOL). We find significant differences between the heterogeneity effects on either visible and near-infrared (VNIR) or thermal infrared (TIR) radiances. However, when both wavelength ranges are combined, heterogeneity effects are dominated by the VNIR horizontal radiative transport effect. As a result, small optical thicknesses are overestimated and large ones are underestimated. Retrieved effective diameter are found to be slightly affected, contrarily to retrievals using TIR channels only.
    Keywords: Earth Resources and Remote Sensing
    Type: GSFC-E-DAA-TN37465 , International Radiation Symposium (IRS 2016); Apr 16, 2016 - Apr 22, 2016; Auckland; New Zealand
    Format: application/pdf
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  • 6
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    Modis Collection 6 Shortwave-Derived Cloud Phase Classification Algorithm and Comparisons with CALIOP (2016)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: Cloud thermodynamic phase (e.g., ice, liquid) classification is an important first step for cloud retrievals from passive sensors such as MODIS (Moderate-Resolution Imaging Spectroradiometer). Because ice and liquid phase clouds have very different scattering and absorbing properties, an incorrect cloud phase decision can lead to substantial errors in the cloud optical and microphysical property products such as cloud optical thickness or effective particle radius. Furthermore, it is well established that ice and liquid clouds have different impacts on the Earth's energy budget and hydrological cycle, thus accurately monitoring the spatial and temporal distribution of these clouds is of continued importance. For MODIS Collection 6 (C6), the shortwave-derived cloud thermodynamic phase algorithm used by the optical and microphysical property retrievals has been completely rewritten to improve the phase discrimination skill for a variety of cloudy scenes (e.g., thin/thick clouds, over ocean/land/desert/snow/ice surface, etc). To evaluate the performance of the C6 cloud phase algorithm, extensive granule-level and global comparisons have been conducted against the heritage C5 algorithm and CALIOP. A wholesale improvement is seen for C6 compared to C5.
    Keywords: Earth Resources and Remote Sensing
    Type: GSFC-E-DAA-TN41877 , Atmospheric Measurement Techniques (ISSN 1867-1381) (e-ISSN 1867-8548); 9; 4; 1587-1599
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