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At least 1,153 records · Page 64

Abundant raw material for cis-regulatory evolution in humans

Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (<13,000), in part because of an overrepresentation among the former in multiallelic tandem repeat variation, especially (AC)(n) dinucleotide microsatellites. The role of microsatellites in gene expression variation may provide a larger store of heritable phenotypic variation, and a more rapid mutational input of such variation, than has been realized. Finally, we outline the distinctive consequences of cis-regulatory variation for the genotype-phenotype relationship, including ubiquitous epistasis and genotype-by-environment interactions, as well as underappreciated modes of pleiotropy and overdominance. Ordinary small-scale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.

NASA Discipline Evolutionary Biology↗

A Mechanism For Solar Forcing of Climate: Did the Maunder Minimum Cause the Little Ice Age?

The mechanism we wish to demonstrate exploits chemical, radiative, and dynamical sensitivities in the stratosphere to affect the climate of the troposphere. The sun, while its variability in total radiative output over the course of the solar cycle is on the order of 0.1%, exhibits variability in the UV output on the order of 5%. We expect to show that a substantially decreased solar UV output lessened the heating of the Earth's stratosphere during the Maunder Minimum, through decreased radiative absorption by ozone and oxygen. These changes in stratospheric heating would lead to major changes in the stratospheric zonal wind pattern which would in turn affect the propagation characteristics of planetary-scale waves launched in the winter hemisphere. Until recently, there was no quantitative data to relate the changes in the stratosphere to those at the surface. There is now empirical evidence from the NCEP Reanalysis data that a definitive effect of the solar cycle on climate in the troposphere exists. Our recent work is summarized as follows (see complete list of publications in later part of this report).

Yung, Yuk L.↗

Modified Light Use Efficiency Model for Assessment of Carbon Sequestration in Grasslands of Kazakhstan: Combining Ground Biomass Data and Remote-sensing

A modified light use efficiency (LUE) model was tested in the grasslands of central Kazakhstan in terms of its ability to characterize spatial patterns and interannual dynamics of net primary production (NPP) at a regional scale. In this model, the LUE of the grassland biome (εn) was simulated from ground-based NPP measurements, absorbed photosynthetically active radiation (APAR) and meteorological observations using a new empirical approach. Using coarse-resolution satellite data from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS), monthly NPP was calculated from 1998 to 2008 over a large grassland region in Kazakhstan. The modelling results were verified against scaled up plot-level observations of grassland biomass and another available NPP data set derived from a field study in a similar grassland biome. The results indicated the reliability of productivity estimates produced by the model for regional monitoring of grassland NPP. The method for simulation of εn suggested in this study can be used in grassland regions where no carbon flux measurements are accessible.

Kazakhstan↗

Spatiotemporal Organization of Energy Release Events in the Quiet Solar Corona

Using data from the STEREO and SOHO spacecraft, we show that temporal organization of energy release events in the quiet solar corona is close to random, in contrast to the clustered behavior of flaring times in solar active regions. The locations of the quiet-Sun events follow the meso- and supergranulation pattern of the underling photosphere. Together with earlier reports of the scale-free event size statistics, our findings suggest that quiet solar regions responsible for bulk coronal heating operate in a driven self-organized critical state, possibly involving long-range Alfvenic interactions.

sun activity↗

On the Feasibility of Monitoring Carbon Monoxide in the Lower Troposphere from a Constellation of Northern Hemisphere Geostationary Satellites: Global Scale Assimilation Experiments (Part II)

This paper describes the second phase of an Observing System Simulation Experiment (OSSE) that utilizes the synthetic measurements from a constellation of satellites measuring atmospheric composition from geostationary (GEO) Earth orbit presented in part I of the study. Our OSSE is focused on carbon monoxide observations over North America, East Asia and Europe where most of the anthropogenic sources are located. Here we assess the impact of a potential GEO constellation on constraining northern hemisphere (NH) carbon monoxide (CO) using data assimilation. We show how cloud cover affects the GEO constellation data density with the largest cloud cover (i.e., lowest data density) occurring during Asian summer. We compare the modeled state of the atmosphere (Control Run), before CO data assimilation, with the known 'true' state of the atmosphere (Nature Run) and show that our setup provides realistic atmospheric CO fields and emission budgets. Overall, the Control Run underestimates CO concentrations in the northern hemisphere, especially in areas close to CO sources. Assimilation experiments show that constraining CO close to the main anthropogenic sources significantly reduces errors in NH CO compared to the Control Run. We assess the changes in error reduction when only single satellite instruments are available as compared to the full constellation. We find large differences in how measurements for each continental scale observation system affect the hemispherical improvement in long-range transport patterns, especially due to seasonal cloud cover. A GEO constellation will provide the most efficient constraint on NH CO during winter when CO lifetime is longer and increments from data assimilation associated with source regions are advected further around the globe.

Geo Stationary Constellation↗

Boreal Canopy Surfaces from Spaceborne Stereogrammetry

Surface elevation estimates from high resolution spaceborne image (HRSI) stereogrammetry are used to examine fine-scaled structure of boreal forest canopies. These data can depict detailed spatial patterns of vertical forest structure at remote sites across the circumpolar domain where these estimates would otherwise be unavailable. This work examines where these estimates are most effective at describing vertical forest structure to explain which canopy surfaces they represent. We evaluated the variation in canopy surface estimates captured from four general types of HRSI digital surface models (DSMs) across the full range of boreal canopy cover.

Paul M Montesano↗

3D Localization of Defects in Facility Inspection

Wind tunnels are crucial facilities that support the aerospace industry. However, these facilities are large, complex, and pose unique maintenance and inspection requirements. Manual inspections to identify defects such as cracks, missing fasteners, leaks, and foreign objects are important but labor and schedule intensive. Our goal is to utilize small Unmanned Aircraft Systems (sUAS) and computer vision-based analysis to automate the inspection of the interior and exterior of NASA’s critical wind tunnel facilities. We detect missing fasteners as our defect class, and detect existing fasteners to provide potential future missing fastener sites for preventative maintenance. These detections are done on both 2D raw images and in 3D space to provide a visual reference and real world location to facilitate repairs. A dataset was created consisting of images taken along a grid-like pattern of an interior tunnel section in the AEDC National Full-Scale Aerodynamics Complex (NFAC) at NASA Ames Research Center. Our method uses object detection to create image level bounding boxes of the fasteners and missing fasteners, then uses photogrammetry to create a mapping from 2D image locations to 3D real world locations. The image level bounding boxes and the 2D to 3D mapping are then combined to determine the 3D location of the defects. We describe the data collection, photogrammetry, and computer vision techniques used for object detection as well as a quantitative analysis of the method.

Small Unmanned Aircraft Systems (sUAS)↗

Durability of YSZ coated Ti2AlC in 1300°C high velocity burner rig tests

A thermal barrier coating system survived 500 h in cyclic burner rig tests at 1300°C, exceeding the life of all previous systems. An yttria stabilized zirconia (7YSZ) thermal barrier coating (TBC) was plasma sprayed on the oxidation resistant Ti2AlC MAX phase and tested in a jet fuel burner. No coating spallation or recession was observed, only a 2.4 mg/sq.cm mass gain due to typical cubic Al2O3 oxidation kinetics. The modest weight gain contrasted with large TBC spallation or oxide volatility losses that might occur under cyclic, high velocity (~100 m/s) burner conditions. The coating surface exhibited colonies of [111]flourite fiber-textured columns separated by craze crack patterns, but with no visible moisture attack. The thickness of the alumina scale under the YSZ face was >20 μm, more than twice that formed on TBC/superalloy systems at failure. TiO2 nodules, initially formed on the uncoated backside, were then removed as volatile hydroxides formed in high temperature, high velocity water vapor (~10%). Overall, the test indicated the exceptional stability of the YSZ/Ti2AlC system under turbine conditions, due in large part to good thermal expansion matching.

alumina, MAX phases, thermal barrier coatings (TBC↗

Boreal canopy surfaces from spaceborne stereogrammetry

Surface elevation estimates from high resolution spaceborne image (HRSI) stereogrammetry are used to examine fine-scaled structure of boreal forest canopies. These data can depict detailed spatial patterns of vertical forest structure at remote sites across the circumpolar domain where these estimates would otherwise be unavailable. This work examines where these estimates are most effective at describing vertical forest structure to explain which canopy surfaces they represent. We evaluated the variation in canopy surface estimates captured from four general types of HRSI digital surface models (DSMs) across the full range of boreal canopy cover. These DSMs, classified into 4 types by grouping them according to the acquisition's (1) sun elevation angle (low or high) and (2) seasonality-driven ground surface condition (snow presence/absence), vary with acquisition characteristics and the details of this variation continues to be studied. We explored some of this variation by comparing the distributions of differences in boreal canopy percentile heights derived from reference small footprint lidar in Tanana Valley, Alaska with canopy surface elevations derived from these 4 types of HRSI DSMs. We examined how canopy surface estimates from HRSI DSMs differ according to acquisition characteristics and canopy cover, and ultimately which canopy surfaces are represented in these DSMs. Our results help clarify which boreal canopy surfaces are representative of those captured with HRSI DSMs. They show that in the Tanana Valley (1) DSMs grouped by sun elevation angle and ground surface condition provide different surface estimates of boreal canopies; (2) the two DSM types that appear to most differently capture boreal forest canopy surfaces are DSMs from snow-free images acquired at sun elevation angles <30° (Low sun elev. & snow-free) and those with snow-cover at sun elevation angles ≥30° (High sun elev. & snow-free); (3) DSMs with snow most often do not capture upper canopy surfaces; (4) the “Low sun elev. & snow-free” DSMs resolve surfaces that are most representative of upper canopy surfaces (dense forests >60% cover, 70th–80th percentile heights); and (5) in the most dense forests (>80% cover) where canopy gaps are least likely to bias downward the average surface estimates, the snow-free DSM types are representative of 70th - 80th percentile heights (“Low sun elev. & snow-free”) and 60th–70th percentile heights (“High sun elev. & snow-free”). The combination of horizontal structure (canopy cover) and acquisition characteristics affect the boreal vertical structure (canopy surface height) estimates from spaceborne stereogrammetry. These effects should be considered when analyzing products derived from HRSI DSMs, and as part of a comprehensive approach to spaceborne remote sensing of circumpolar boreal forests.

forest structure↗

Impact of Anthropogenic Activity, Climate Change, and Urbanization on Wetland Habitat in the Platte River Basin​

The Platte River Basin (PRB) is a dynamic ecosystem where wetlands play a pivotal role as essential habitats for various flora and fauna, including local and migratory birds. It provides many crucial ecosystem services that benefit humans directly and indirectly. However, anthropogenic activity, climate change, and urbanization have resulted in decline in wildlife habitat, elevated flood risk, and wetland loss. To address this issue, NASA DEVELOP partnered with Audubon Great Plains (AGP) to address the vital habitats within urban areas to protect bird species, reduce flood hazards, and analyze the potential impact of future development on wetlands. We utilized remotely sensed data from Landsat 8 Operational Land Imager (OLI), Sentinel-2 Multispectral Instrument (MSI), and Sentinel-1 Synthetic Aperture Radar (SAR) to assess land use and land cover (LULC) change. Nighttime lights data from Suomi National Polar-orbiting Partnership (NPP) Visible Infrared Imaging Radiometer Suite (VIIRS) as well as NASA Socioeconomic Data and Applications Center (SEDAC) population data were also used as inputs to simulate urban growth potential up to 2050 using the open-source FUTure Urban-Regional Environment Simulation (FUTURES) model. A broad scale analysis across 13 focal cities showed varied changes in land use patterns across the PRB, with the most notable being a decrease in agricultural land coverage and an increase in vegetation and grassland coverage. We overlaid a flood extent map with the LULC classifications in Grand Island to identify possible restoration sites under AGP’s Urban Woods and Prairies Initiative. The results for two proposed scenarios showed that at least 51 counties out of 81 in the PRB would experience growth by year 2050. The first scenario (all wetlands are protected) showed that there will be no loss of wetlands by 2050. However, the second scenario (no wetlands are protected) showed a decrease in wetland area and loss of habitat for bird conservation. The results will help AGP to lead awareness workshops for communities about wetland protection and to form impactful conservation strategies in the future.​

Nancee Uniyal↗

Distributed Multi-GPU Community Detection on Exascale Computing Platforms

Community detection is a fundamental operation in graph mining, and by uncovering hidden structures and patterns within complex systems it helps solve fundamental problems pertaining to social networks, such as information diffusion, epidemics, and recommender systems. Scaling graph algorithms for massive networks becomes challenging on modern distributed-memory multi-GPU (Graphics Processing Unit) systems due to limitations such as irregular memory access patterns, load imbalances, higher communication-computation ratios, and cross-platform support. We present a novel algorithm HiPDPL-GPU (Distributed Parallel Louvain) to address these challenges. We conduct experiments involving different partitioning techniques to achieve an optimized performance of HiPDPL-GPU on the two largest supercomputers: Frontier and Summit. Remarkably, HiPDPL-GPU processes a graph with 4.2 billion edges in less than 3 minutes using 1024 GPUs. Qualitatively, the performance of HiPDPL-GPU is similar or better compared to other state-of-the-art CPU- and GPU-based implementations. While prior GPU implementations have predominantly employed CUDA, our first-of-its-kind implementation for community detection is cross-platform, accommodating both AMD and NVIDIA GPUs.

Sattar, Naw Safrin↗

Machine Learning Approaches to Predicting Induced Seismicity and Imaging Geothermal Reservoir Properties

This project developed machine learning (ML) methods, lab data sets, and field data to advance geothermal exploration and geothermal energy production. The work had three focus areas. One involved the development of ML methods to use microearthquakes (MEQs) for imaging geothermal reservoir properties and improving subsurface characterization – most importantly the evolution of permeability within the evolving reservoir. This part of the work included development of ML approaches for automated MEQ location, focal mechanism determination and identification of earthquake precursors. The second area focused on using MEQ signals generated by geothermal exploration and production to predict the relationship between fluid injection and seismicity. Here, we extended to reservoir scale our success in using ML to predict laboratory earthquakes and fault zone stress state. The third focus area was on lab experiments. Here, we developed new ML models for lab earthquake prediction and identification of precursors to failure to improve earthquake forecasting and early warning in geothermal settings. Major outcomes of our work include ML models that learn from MEQ signals during geothermal exploration and production to predict induced seismicity. MEQs occur naturally in connection with drilling and energy production. We developed ML methods to use the seismic waves from these events to characterize the elastic, hydraulic and poromechanical properties of reservoirs. Our work illuminated fracture geometry and the evolution of fracture permeability by incorporating seismic coda wave analysis and ML methods to relate fluid injection and seismicity. We significantly expanded laboratory earthquake prediction to include methods that use both passive measurements of microearthquakes within the lab fault zones and also active source acoustic measurements of fault zone elastic properties. These methods can now predict fault zone stress state, time to failure and the magnitude of lab earthquakes. Our work showed that repetitive stick- slip failure events during frictional sliding (the lab equivalent of earthquakes) are preceded by a cascade of micro-failure events that radiate energy in a manner that foretells unstable failure – manifest as laboratory MEQs. We documented a mapping between fracture properties and statistical attributes of elastic radiation. We extended existing works to geothermal reservoir scale and developed ML methods to determine reservoir permeability, fracture properties, and their evolution during geothermal energy production. An attractive feature of ML algorithms is their ability to handle big datasets and reveal patterns and correlations that may remain invisible to conventional analyses. Our work connected data from field, laboratory and intermediate scales to study permeability, stress, strength, fracture stiffness and geometry. At the field scale we used data from the Newberry Volcano field site, UtahFORGE, EGS Collab, and also the Bedretto underground research lab in Switzerland. These data sets are bridging the gap between the lab scale, theory, and reservoir scale. Our work produced plain language summaries to improve public understanding of DOE research. We also developed openly distributed ML and seismicity datasets for use by all researchers and we published connections between induced seismicity in geothermal areas and reservoir properties including permeability, fracture properties, and stress state. Our models are designed for the large data sets of induced seismicity typically associated with geothermal sites. We produced labeled event catalogs and used them on geothermal data to assess how ML can facilitate geothermal production and exploration. All datasets are available on the GDR Productivity: The project produced 32 publications in peer reviewed journals (two are in review). It supported the work of 6 PhD students, 40 conference presentations, 6 keynote talks at national meetings, and mentoring and professional development for 4 postdoctoral fellows.

15 GEOTHERMAL ENERGY↗

Chapter 19B - Antenna Radiation Patterns

Modern civil and military aircraft are equipped with a variety of communication devices, radio navigation equipment, and air traffic control systems. For all of these devices appropriate antennas must be available to transmit and receive the signals. As a result, as many as 30 antennas, and sometimes even more, are mounted around today's aircraft. For this reason, it is necessary to know the capabilities of the receiving/transmitting equipment on board. These capabilities are driven by the antenna characteristics. Therefore, coverage, shading, and beam pointing pattern data are necessary for optimum electronic coverage. The aircraft antenna has to convert the available power density of the electromagnetic field to an electric voltage at its connector. This voltage level must be sufficiently high to operate the connected equipment. The reciprocity principle states that it makes no difference if the antenna is receiving or transmitting. For the certification of the aircraft antennas it must be proven that the antennas are at least generating the minimum receiver input voltage which is required for each radio service. The prime condition is, of course, that the specified field power densities of the different radio navigation and communication services are available. An important property of a radio frequency link is the electro-magnetic field intensity at every point in space for a given output power of the antenna. As the propagation of radio frequency waves in free space is well known, the spatial distribution of the field intensity needs only be measured at one spatial sphere around the antenna. The information is usually given as distributions along the circumference of flat sections through this sphere: each of these is called an ARP. Several ARPs are usually required to describe the complete spatial antenna pattern of an antenna. In addition to mathematical modeling, measurements on sub-scale models, and static measurements on full size models or aircraft on the ground, dynamic measurements on aircraft in flight play the most important role in the aircraft antenna testing and certification. [19B-1] The shape of an ARP, for one given frequency, is determined by the shape of the antenna and the shape and material of the surface it is mounted on. As the directly transmitted waves interfere with waves reflected by the aircraft skin with its complex geometry, and the surface material parameters are only roughly known, it is not possible to predict the ARP with the required accuracy. In ground measurements the earth's surface also acts as a reflector thereby causing the ground ARP to be different from the in-flight ARP. As the in-flight ARP is the ARP we are actually interested in it becomes clear that it is necessary to conduct in-flight ARP measurements. The Flight Test Engineer must be aware of the needs of the specialists who are establishing the test program for measuring antenna patterns and radar cross sections. These tests will require special test equipment and dedicated flights to obtain the data that they require. This Section provides an introduction to the principles of determining antenna patterns and the flight techniques for determining both antenna patterns and radar cross section. Reference 19B-1 provides detailed information.

Helmut Bothe↗

DyG-DPCD: A Distributed Parallel Community Detection Algorithm for Large-Scale Dynamic Graphs

Dynamic (Temporal) graphs capture the valuable evolution of real-world systems, from the continuously evolving patterns of social interactions and genetic pathways to the dynamic fluctuations of economic forces. Detecting communities for such evolving networks poses unique challenges. Detecting and analyzing the evolution of communities within dynamic graphs unlocks valuable insights into the underlying structural and temporal patterns of real-world systems. However, the sheer volume of modern graph data and the inherent complexity of the temporal dimension pose significant challenges to scalable community detection algorithms. Addressing this gap, our work explores the limited landscape of scalable distributed-memory parallel methods specifically designed for dynamic network community detection. We propose a novel parallel algorithm, DyG-DPCD (Dynamic Graph Distributed Parallel Community Detection), to detect communities in dynamic networks using the Message Passing Interface (MPI) framework. We present a vertex-centric approach, allowing us to detect communities through local optimization. Furthermore, we enhance our baseline algorithm by incorporating three heuristics, which improve the algorithm’s performance significantly while maintaining the quality of the solutions. We demonstrate the efficiency of our algorithm by experimenting on several real-world large-scale networks with hundreds of millions of edges spanning diverse domains. Notably, DyG-DPCD achieves speedups between 25× and 30× for large networks that we experimented on using NERSC compute nodes. In conclusion, our algorithm outperforms the STINGER parallel re-agglomeration algorithm by 30×.

97 MATHEMATICS AND COMPUTING↗

Riverine dissolved organic matter transformations increase with watershed area, water residence time, and Damköhler numbers in nested watersheds

Abstract Quantifying the relative influence of factors and processes controlling riverine ecosystem function is essential to predicting future conditions under global change. Dissolved organic matter (DOM) is a fundamental component of riverine ecosystems that fuels microbial food webs, influences nutrient and light availability, and represents a significant carbon flux globally. The heterogeneous nature of DOM molecular composition and its propensity for interaction (i.e., functional diversity) can characterize riverine ecosystem function across spatiotemporal scales. To investigate fundamental drivers of DOM diversity, we collected seasonal water samples from 42 nested locations within five watersheds spanning multiple watershed sizes (~ 5 to 30,000 km 2 ) across the United States. Patterns in DOM molecular richness, aromaticity, relative abundance of N-containing formulas, and putative biochemical transformations derived from high-resolution mass spectrometry were assessed across gradients of explanatory variables associated with watershed characteristics (e.g., watershed area, water residence time, land cover). We found that putative biochemical transformations were more strongly related to explanatory variables across watersheds than common bulk DOM parameters and that watershed area, surface water residence time and derived Damköhler numbers representing DOM reactivity timescales were strong predictors of DOM diversity. The data also indicate that catchment-specific land cover factors can significantly influence DOM diversity in diverging directions. Overall, the results highlight the importance of considering water residence time and land cover when interpreting longitudinal patterns in DOM chemistry and the continued challenge of identifying generalizable drivers that are transferable across watershed and regional scales for application in Earth system models. This work also introduces a Findable Accessible Interoperable Reusable (FAIR) dataset (> 300 samples) to the community for future syntheses.

54 ENVIRONMENTAL SCIENCES↗

Airborne antenna polarization study for the microwave landing system

The feasibility of the microwave landing system (MLS) airborne antenna pattern coverage requirements are investigated for a large commercial aircraft using a single omnidirectional antenna. Omnidirectional antennas having vertical and horizontal polarizations were evaluated at several different station locations on a one-eleventh scale model Boeing 737 aircraft. The results obtained during this experimental program are presented which include principal plane antenna patterns and complete volumetric coverage plots.

Gilreath, M. C.↗

Modulated spectral activity (MSA) - Implications for planetary radio sources

The properties of the Jovian and Saturnian MSA, modulation patterns within the normally diffuse nonthermal radio emission that are characterized by distinctive banded structures of enhanced intensity fluctuations in frequency over time scales of minutes to tens of minutes, are discussed. Although Jovian and Saturnian MSA are both normally observed in the 0.2-1.3-MHz frequency range, similar pattern have been noted in Jovian decametric emission above 30 MHz. The MSA properties are used to constrain the possible source mechanism.

Thieman, James R.↗

A comparison of the overall and broadband noise characteristics of full-scale and model helicopter rotors.

The broadband noise generated by full-scale and model rotors is compared in terms of spectral content and the dependence on tip speed and rotor thrust/pitch angle. Low frequency broadband noise and high frequency broadband noise are studied separately and blade 'scaling' effects are outlined. The degree of agreement between measurements and theoretical and semi-empirical prediction methods is reviewed together with the directionality patterns. The parameters relating to the overall noise are also discussed. It is shown that in general good agreement is obtained between the full-scale and model rotors when considering spectral content and the dependency of the noise levels on tip speed and thrust. The scaling factors usually considered applicable to the low frequency broadband noise do not, however, appear to apply to either the model or full scale rotors.

Leverton, J. W.↗