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At least 127 records · Page 7

Regulatory gene networks and the properties of the developmental process

Genomic instructions for development are encoded in arrays of regulatory DNA. These specify large networks of interactions among genes producing transcription factors and signaling components. The architecture of such networks both explains and predicts developmental phenomenology. Although network analysis is yet in its early stages, some fundamental commonalities are already emerging. Two such are the use of multigenic feedback loops to ensure the progressivity of developmental regulatory states and the prevalence of repressive regulatory interactions in spatial control processes. Gene regulatory networks make it possible to explain the process of development in causal terms and eventually will enable the redesign of developmental regulatory circuitry to achieve different outcomes.

Non-NASA Center↗

Where are the Data? Automating a Workflow for Carbon Storage Data Gap Analyses

This presentation demonstrates a spatial analysis workflow to assess data availability for the many components of geologic carbon storage technical viability. The workflow relies upon a knowledge-data framework that links the different components of GCS technical viability to the data types needed for evaluation. Using this contextual information, a combination of data science methods (e.g., natural language processing) and spatial analyses are applied to identify areas where sufficient data exists for a given component. The results are aggregated into maps illustrating data density and spatial gaps across all technical viability factors and data categories, as well as the individual component and category level for a more nuanced understanding. Presented at the FECM NETL Carbon Management Program Review Meeting 2024.

Creason, Christopher↗

Where are the Data? Automating a Workflow for Carbon Storage Data Gap Analyses

This presentation demonstrates a spatial analysis workflow to assess data availability for the many components of geologic carbon storage technical viability. The workflow relies upon a knowledge-data framework that links the different components of GCS technical viability to the data types needed for evaluation. Using this contextual information, a combination of data science methods (e.g., natural language processing) and spatial analyses are applied to identify areas where sufficient data exists for a given component. The results are aggregated into maps illustrating data density and spatial gaps across all technical viability factors and data categories, as well as the individual component and category level for a more nuanced understanding. Presented at the Geological Society of America Connects 2024 Annual Meeting in Anaheim, California, 22-25 September 2024.

Creason, Christopher↗

Multiscale geographically and temporally weighted regression (MGTWR): exploring the spatiotemporal heterogeneity of EV market adoption

As an innovative vehicle technology, electric vehicles are experiencing growing sales and have made significant inroads into the traditional automotive market in the United States and around the world. However, EV adoption rates vary significantly across space and over time, influenced by a complex interplay of socio-economic and infrastructural factors alongside federal and state policies. Here, this paper presents a comprehensive spatial–temporal investigation of EV market adoption within one city in the US, that of Chicago, utilizing Multiscale Geographically and Temporally Weighted Regression (MGTWR) alongside Multiscale Geographically Weighted Regression (MGWR). The aim is to unravel the spatial and temporal dynamics affecting EV adoption and to explore how the influence of various determinants of EV adoption, such as demographic factors and economic conditions, vary spatially. Moreover, by utilizing MGTWR, we provide insights into the evolution of these relationships over time, offering a predictive outlook on future EV market growth. Our findings, with an 86.6% prediction accuracy for EV market adoption, tailored policy measures to support accelerated EV adoption. Methodologically, this work advances MGWR frameworks by integrating temporal dynamics to examine nonstationary processes in spatially disaggregated contexts. These findings offer evidence–based guidance for policymakers, urban planners, and stakeholders in the automotive industry, supporting the transition toward a more sustainable and efficient transportation system.

EV Market Adoption↗

Multiscale spatial analysis of fracture nodes in two dimensions

Spatial arrangement of fractures as a function of scale is an important component of fracture quantification for inferential and predictive modeling. Available methods that analyze fracture spatial arrangement are based on one-dimensional spacing data; therefore, they are limited to semi-parallel fractures. Such methods cannot be applied to fracture networks in higher dimensions, particularly when fractures have different orientations. Here to characterize fracture arrangements in two dimensions, we propose using Ripley’s K-function, as a method of point pattern analysis, to quantify spatial arrangement of fracture nodes. Fracture nodes, such as barycenters, intersection points, and tips, are point-based representations of fracture locations and connectivity within the fracture network. We introduce formulations for isotropic as well as directional analyses of spatial arrangement. In addition, we derive formulations for edge correction in circular and rectangular study domains. Finally, we demonstrate applications of Ripley’s K-function on two natural fracture datasets. Our proposed method supports quantification and characterization of fracture spatial arrangements that allow practitioners to build representative models of fractures in the subsurface.

02 PETROLEUM↗

A novel statistical methodology for quantifying the spatial arrangements of axons in peripheral nerves

A thorough understanding of the neuroanatomy of peripheral nerves is required for a better insight into their function and the development of neuromodulation tools and strategies. In biophysical modeling, it is commonly assumed that the complex spatial arrangement of myelinated and unmyelinated axons in peripheral nerves is random, however, in reality the axonal organization is inhomogeneous and anisotropic. Present quantitative neuroanatomy methods analyze peripheral nerves in terms of the number of axons and the morphometric characteristics of the axons, such as area and diameter. In this study, we employed spatial statistics and point process models to describe the spatial arrangement of axons and Sinkhorn distances to compute the similarities between these arrangements (in terms of first- and second-order statistics) in various vagus and pelvic nerve cross-sections. We utilized high-resolution transmission electron microscopy (TEM) images that have been segmented using a custom-built high-throughput deep learning system based on a highly modified U-Net architecture. Our findings show a novel and innovative approach to quantifying similarities between spatial point patterns using metrics derived from the solution to the optimal transport problem. We also present a generalizable pipeline for quantitative analysis of peripheral nerve architecture. Our data demonstrate differences between male- and female-originating samples and similarities between the pelvic and abdominal vagus nerves.

59 BASIC BIOLOGICAL SCIENCES↗

Visual Orientation in Unfamiliar Gravito-Inertial Environments

The goal of this project is to better understand the process of spatial orientation and navigation in unfamiliar gravito-inertial environments, and ultimately to use this new information to develop effective countermeasures against the orientation and navigation problems experienced by astronauts. How do we know our location, orientation, and motion of our body with respect to the external environment ? On earth, gravity provides a convenient "down" cue. Large body rotations normally occur only in a horizontal plane. In space, the gravitational down cue is absent. When astronauts roll or pitch upside down, they must recognize where things are around them by a process of mental rotation which involves three dimensions, rather than just one. While working in unfamiliar situations they occasionally misinterpret visual cues and experience striking "visual reorientation illusions" (VRIs), in which the walls, ceiling, and floors of the spacecraft exchange subjective identities. VRIs cause disorientation, reaching errors, trigger attacks of space motion sickness, and potentially complicate emergency escape. MIR crewmembers report that 3D relationships between modules - particularly those with different visual verticals - are difficult to visualize, and so navigating through the node that connects them is not instinctive. Crew members learn routes, but their apparent lack of survey knowledge is a concern should fire, power loss, or depressurization limit visibility. Anecdotally, experience in mockups, parabolic flight, neutral buoyancy and virtual reality (VR) simulators helps. However, no techniques have been developed to quantify individual differences in orientation and navigation abilities, or the effectiveness of preflight visual. orientation training. Our understanding of the underlying physiology - for example how our sense of place and orientation is neurally coded in three dimensions in the limbic system of the brain - is incomplete. During the 16 months that this human and animal research project has been underway, we have obtained several results that are not only of basic research interest, but which have practical implications for the architecture and layout of spacecraft interiors and for the development of astronaut spatial orientation training countermeasures.

Oman, Charles M.↗

Quantitative modeling of soil genesis processes

For fine spatial scale simulation, a model is being developed to predict changes in properties over short-, meso-, and long-term time scales within horizons of a given soil profile. Processes that control these changes can be grouped into five major process clusters: (1) abiotic chemical reactions; (2) activities of organisms; (3) energy balance and water phase transitions; (4) hydrologic flows; and (5) particle redistribution. Landscape modeling of soil development is possible using digitized soil maps associated with quantitative soil attribute data in a geographic information system (GIS) framework to which simulation models are applied.

Levine, E. R.↗

Validating spatial structure in canopy water content using geostatistics

Heterogeneity in ecological phenomena are scale dependent and affect the hierarchical structure of image data. AVIRIS pixels average reflectance produced by complex absorption and scattering interactions between biogeochemical composition, canopy architecture, view and illumination angles, species distributions, and plant cover as well as other factors. These scales affect validation of pixel reflectance, typically performed by relating pixel spectra to ground measurements acquired at scales of 1m(exp 2) or less (e.g., field spectra, foilage and soil samples, etc.). As image analysis becomes more sophisticated, such as those for detection of canopy chemistry, better validation becomes a critical problem. This paper presents a methodology for bridging between point measurements and pixels using geostatistics. Geostatistics have been extensively used in geological or hydrogeolocial studies but have received little application in ecological studies. The key criteria for kriging estimation is that the phenomena varies in space and that an underlying controlling process produces spatial correlation between the measured data points. Ecological variation meets this requirement because communities vary along environmental gradients like soil moisture, nutrient availability, or topography.

Sanderson, E. W.↗

A Virtual Audio Guidance and Alert System for Commercial Aircraft Operations

Our work in virtual reality systems at NASA Ames Research Center includes the area of aurally-guided visual search, using specially-designed audio cues and spatial audio processing (also known as virtual or "3-D audio") techniques (Begault, 1994). Previous studies at Ames had revealed that use of 3-D audio for Traffic Collision Avoidance System (TCAS) advisories significantly reduced head-down time, compared to a head-down map display (0.5 sec advantage) or no display at all (2.2 sec advantage) (Begault, 1993, 1995; Begault & Pittman, 1994; see Wenzel, 1994, for an audio demo). Since the crew must keep their head up and looking out the window as much as possible when taxiing under low-visibility conditions, and the potential for "blunder" is increased under such conditions, it was sensible to evaluate the audio spatial cueing for a prototype audio ground collision avoidance warning (GCAW) system, and a 3-D audio guidance system. Results were favorable for GCAW, but not for the audio guidance system.

Begault, Durand R.↗

Pushing the Limits of Aquatic Remote Sensing: Synthetic Data and Deep Learning for Fast Inverse Emulation of A Coupled Ocean-Atmosphere Radiative Transfer Model

The inversion of electromagnetic information to physical and biological properties of the water column is a notoriously difficult problem, yet fundamental to our ability of understanding aquatic processes on large time and space scales. There is now a growing necessity to develop pragmatic approaches that allow timely and effective extrapolation of local processes, to spatially resolved global products, and to promote operational and sustainable resource policy management. This presentation will discuss research integrating advanced biological and radiative modeling, high-end computation, and machine learning to develop a portable global processor for simultaneous retrieval of atmosphere and water optics for diverse aquatic systems from the open and coastal ocean to optically extreme inland waters and harmful algal blooms. We will discuss some of the basic concepts behind the forward modeling approach including DEAP, the novel Distributed Equivalent Algal Populations model, for developing large spectral libraries of aquatic particle optics to aid in our ability to distinguish phytoplankton functional types (PFTs) and inorganic material, as well as other factors which enable comprehensive modeling from the benthos to top-of-atmosphere (TOA). This information is being used to understand how we can leverage next-generation deep learning methods for maximum information retrieval and rapid image processing, while also providing capabilities to identify minimum sensor spectral requirements necessary for certain aquatic applications. Further, I will touch on how we envision this research to enable the aquatic community for science discovery and how we are moving closer towards the capability for high-fidelity global analysis of aquatic ecosystems.

Jeremy Alan Kravitz↗

ORNL Second Target Station Project: Biological & Environmental Science Workshop

Recent advances in neutron sources and instrumentation have opened up many new opportunities for the application of neutron scattering techniques in the biological and environmental sciences. Neutrons enable studies of the structure and dynamics of biological and environmental samples with a particular sensitivity to light elements, such as hydrogen, which is a key component of biological and environmental samples. Studies using neutrons are complementary to X-rays and have the unique advantage of being non-destructive and highly-penetrating. Oak Ridge National Laboratory’s upcoming Spallation Neutron Source (SNS) Second Target Station (STS) will provide high brightness cold neutron sources that significantly advance the scientific capabilities of neutron scattering instruments. The STS will advance our understanding of biological and environmental processes across spatial and temporal scales. The capabilities will enhance our ability to discover, design, and develop new materials essential for advanced sustainable technologies to address society’s most pressing needs. This report summarizes the discussions and recommendations from a joint workshop held by the STS Project and the Biological and Environmental Systems Science Directorate (BESSD) in June 2022. The purpose of the workshop was to explore science opportunities and capabilities related to biological and environmental systems that could be incorporated into both current and future STS instrument designs, as well as additional instruments at the SNS First Target Station (FTS) and High Flux Isotope Reactor (HFIR). With six breakout sessions, each with two invited plenary speakers from other institutions, the participants discussed a wide range of topics relevant to biological and environmental research. Based on the input from participants, a number of recommendations on instrumentation, sample environments, complementary multi-modal methods, data processing and analysis and sample deuteration are provided in the report. The participants also identified science opportunities that are emerging from the planned instrument capabilities at STS. Selected recommendations and science opportunities are listed in the Executive Summary.

54 ENVIRONMENTAL SCIENCES↗

Synthetic Hyperspectral Data for Global Water Quality Algorithm Development

Eutrophication and increasing prevalence of potentially toxic algal blooms (cyanoHABs) among global inland water bodies have become a major ecological concern and require direct attention. There is now a growing necessity to develop pragmatic approaches that allow timely and effective extrapolation of local aquatic processes, to spatially resolved global products. Planned aquatic biogeochemistry remote sensing data products from hyperspectral imagers such as NASA’s Surface Biology and Geology (SBG) mission and relevant aquatic sensor sensitivity precursor airborne imaging spectrometer data provide unprecedented radiometric resolution and sensor sensitivity for characterizing complex aquatic ecosystems. However, scarcity of high-quality freshwater in-situ optical data hinders our capability to develop and validate robust retrieval algorithms. A state-of-the-art synthetic dataset of paired top-of-atmosphere, bottom-of-atmosphere, and optical and biogeophysical data was developed through radiative transfer modeling to simulate natural freshwater ecosystems. A synthetic or precursor dataset for SBG is being used to train robust machine learning models to derive water quality products pertinent to SBG mission objectives. The dataset is also used to show the potential of performing vigorous aquatic sensitivity studies and explored pathways for how best to optimize hyperspectral data for machine learning development. A processing pipeline and resultant global synthetic/precursor dataset for inland waters is presented to establish the innovation for water quality studies of inland waters globally. Optical Society of America Imaging and Applied Optics Congress, Hyperspectral Imaging and Sounding of the Environment (OSA HISE) Meeting, 19-23 July 2021, Virtual Meeting, https://www.osa.org/enus/meetings/osa_meetings/optical_sensors_and_sensing_congress/program/hyperspectral_imaging_and_sounding_of_the_environm/

Synthetic↗

SWIPE: Spectral Water Inversion Processor and Emulator

Degradation of Earth’s inland water resources due to anthropogenic perturbations and climate anomalies at both local and global scales continues to place human health at substantial risk. There is now a growing necessity to develop pragmatic approaches that allow timely and effective extrapolation of local processes, to spatially resolved global products, and to promote operational and sustainable resource policy management. This presentation will be discussing the progress made developing SWIPE: Spectral Water Inversion Processor and Emulator. SWIPE is a platform for advanced modeling of coastal and inland aquatic habitats. The goal is create a comprehensive and cohesive system to leverage recent advancements in computation and machine learning to develop a synthetic training ground for sensitivity studies and algorithm development. The four principal facets of SWIPE include: 1. Advanced two-layer coated sphere bio-optical modeling and GPU radiative transfer modeling, 2. Big Data involving massive synthetic spectral libraries of optical properties of various global aquatic particles, surface reflectance, and top-of-atmosphere reflectance, all at hyperspectral resolution leveraging high-end computing systems at NASA Ames Research Center, 3. Deep Learning for algorithm development for water quality inversion of concentrations of common biogeophysical variables as well as optics, full uncertainty characterization by water type, and forward emulation, and lastly, 4. Image Processing for application of developed retrieval algorithms for both hyperspectral and multispectral sensors with experimental corrections for global adjacency, noise, sunglint, and benthic reflectance. This presentation will demonstrate the Equivalent Algal Populations (EAP) two-layer coated sphere scattering model which has been used develop spectral libraries of hyperspectral inherent optical properties of roughly 80 species of phytoplankton, covering 15 different classes and nine taxonomic functional types. The EAP model was also used to derive spectral properties of 10 different non-algal particle functional types. Examples of how the SMART-G (Speed-up Monte-carlo Advanced Radiative Transfer using GPU) radiative transfer code is used to model optically complex aquatic signals will be presented and discussed in the context of creating a massive synthetic database which can leverage the full power of next generation machine learning techniques and high end computing for water quality inversion. We will discuss our active investigation in things like appropriate model architectures, dimensionality reduction techniques such as PCA and autoencoders, uncertainty quantification and abstaining, and which variables actually benefit most from hyperspectral information versus multispectral resolution. We are also curious about questions relating to cost/benefit analysis in terms of computation resources, neural network complexity, and data volumes. Answers to these questions will hopefully elaborate on cost efficiency for potential future sensor design considerations.

SWIPE↗

LL18-Signal Analysis-NDD2Ad (Final Report)

Under favorable circumstances, seismic waveforms corresponding to an ensemble of events related by a common, spatially-distributed process collectively exhibit a regular, signal-space geometry. When events in the ensemble have a common, or nearly common, source mechanism, this geometry is a distorted image of the distribution of events in the source region. The signal space image can be visualized using a relatively simple waveform alignment and projection operation. Ensemble waveform correlation measurements can be inverted to estimate the distribution of the events in the source region, up to an arbitrary rotation, reflection, and scaling with residual distortion. We demonstrate these concepts with synthetic waveforms and with observations of long-wall mining induced seismicity for which substantial ground truth information is available. Our experience with these data has implications for location, correlation detection and machine learning, and possible application to studies of repeating events in induced, volcanic, and glacial seismicity. Our results place limits on the widely-held assumption that waveform correlation is a useful measure of event separation. We suggest that the constraints on event separation need to be evaluated in the context of a population of related events, whose waveforms sample the signal space image of the source region. A better indicator of event separation is the length of the shortest path in signal space along the image.

58 GEOSCIENCES↗

WHONDRS Surface Water and Sediment Geochemistry and Organic Matter Characterization Data from Streams across HJ Andrews Experimental Forest, Oregon (v2)

This dataset supports a broader study developing conceptual models for river corridor critical zone processes across spatial scales and was generated in collaboration with the HJ Andrews River Corridor Critical Zone Workshop in 2025. The dataset provides surface water geochemistry (dissolved organic carbon, total dissolved nitrogen) from 48 sites across the HJ Andrews Experimental Forest, Oregon (https://andrewsforest.oregonstate.edu). Some of the sites have been impacted by the Holiday Farm Fire and the Lookout Fire in 2020 and 2023, respectively. Related data were collected as part of the workshop and will be published separately in collaboration with other workshop attendees and available at http://www.hydroshare.org/resource/b274c4a234bf4b12b7cb8a54a696c629. Related genomic data can be found on the National Center for Biotechnology Information (NCBI) under BioProject PRJNA1503030 (see critical details section below for more information). Additional related data collected in 2016 from a similar effort can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/3377027 and http://www.hydroshare.org/resource/ea6c0832885a46c3939e7bb22e48e754 and are described within https://doi.org/10.5194/essd-11-1-2019 (Ward et al., 2019). This data package was originally published in March 2026. It was updated in August 2026 (v2; new and modified files). See the change history section in the readme for more details. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) a folder of field photos, (2) a folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data, (3) a data checks report, (4) a folder of sample data, (5) file-level metadata, (6) data dictionary, (7) field metadata, (8) readme, (9) international generic sample number (IGSN) mapping file; and (10) field protocol. The sample data subfolder contains surface water and sediment (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data and averages, (2) total dissolved nitrogen data and averages, (3) methods codes, (4) FTICR-MS methods; and (5) a subfolder of 9.4 Tesla (9.4T) FTICR-MS data. This folder contains the CoreMS processed data and seven subfolders, thee containing .xml files for each sample type (sediment, surface water and blank samples), three containing the sediment CoreMS output files for each sample type (sediment, surface water and blank samples), and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .xml, .Rmd, .py, .cal, .json, .jpg, or .jpeg.

Biogeochemistry↗

Evaluating sulfurization as a blue carbon sink in a southern California salt marsh

Blue carbon ecosystems such as seagrass meadows, mangrove forests, and salt marshes are important carbon sinks that can store carbon for millennia. Recently, organic matter sulfurization and pyritization have been proposed as mechanisms of net carbon storage in blue carbon ecosystems. At our study site, organic sulfur that is resistant to acid hydrolysis (protokerogen) is an order of magnitude less abundant than pyrite sulfur, suggesting a dominance of pyritization over sulfurization. The C/N ratios and carbon isotope compositions suggest that nearly half of total organic carbon and ≥ 80% of protokerogen is composed of marsh plant material. Sediment protokerogen appears to be sulfurized based on its low δ 34 S values (− 10‰), abundance of disulfides, and higher S/C ratio (~ 1.0%) relative to potential biogenic sulfur sources. However, the interpretation of protokerogen δ 34 S values is complicated by the wide range in sulfur isotope compositions of marsh plants. Evidence for sulfurization occurs within the shallowest sediments across different vegetation zones, yielding consistent products, while pyritization appears to be more sensitive to alterations in sediment redox conditions. Based on organic sulfur and pyrite content, sulfurization may be a more spatially consistent process than pyritization, with implications for carbon storage. The relative abundance of pyrite and protokerogen organic sulfur indicates that pyritization is favored at our study site, but this is likely to vary across the spectrum of blue carbon ecosystems.

54 ENVIRONMENTAL SCIENCES↗