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NASA NTRSDate not supplied

Transcriptomics-based Machine Learning (ML) Analysis Predicts Space-Exposed Murine Livers

NASA has employed high-throughput molecular assays to identify sub-cellular changes impacting human physiology during spaceflight. Machine learning (ML) methods hold the promise to improve our ability to identify important signals within highly dimensional molecular data. However, the inherent limitation of study subject numbers within a spaceflight mission minimizes the utility of ML approaches. To overcome the sample power limitations, data from multiple spaceflight missions must be aggregated while appropriately addressing intra- and inter-study variabilities. Here we describe an approach to log transform, scale and normalize data from six heterogeneous, mouse liver derived transcriptomics datasets (ntotal=137) which enabled ML-methods to perform well (AUC ≥ 0.87) in classifying spaceflown vs ground control animals rather than mission-of-origin. Concordance was found between liver-specific biological processes identified from harmonized ML-based analysis and study-by-study classical omics analysis. This work demonstrates the feasibility of applying ML methods on integrated, heterogeneous datasets of small sample size.

Machine Learning↗

NASA NTRS2021

Geometric calibration of the Multi-Angle Imager for Aerosols (MAIA)

The Multi-Angle Imager for Aerosols (MAIA) instrument is currently scheduled for launch into polar Earth orbitin 2022. MAIA uses a single camera on a 2-axis gimbal for multi-angle viewing. The camera focal plane consistsof one visible and one SWIR detector, comprising a total of 14 wavelength channels from the UV to SWIR.Three of the channels are polarimetric to enhance the camera's sensitivity to airborne particle type. The MAIAtelescope is a standard four-mirror anastigmat and has signi?cant distortion of the ?eld-of-view. Each channelin the camera comprises one or two rows of pixels, and each row has a total of 1216 pixels. This talk will reviewthe tests undertaken to measure pixel positions in the focal plane with respect to their corresponding angles inobject space, i.e. the pointing angle of each pixel. This measurement is necessary to achieve good geo-locationof ground control points, a precursor to the successful registration of the 14 channels to each other.

Bruegge, Carol J.↗

NASA NTRSDate not supplied

Optimizing Single Nuclei Sequencing of Brain Samples From Space Flown Mice Across Age and Strain

The NASA GeneLab Sample Processing Laboratory offers high-throughput sequencing services to NASA-funded space biology researchers. Space biology studies have specific challenges such as low sample numbers, introducing susceptibility to batch effects from sample handling. These issues are compounded by complex protocols such as single-nuclei isolation and sequencing, which has recently become an attractive methodology for assessing the cellular diversity within spaceflight samples. High quality single-nuclei sequencing requires reproducible protocols to dissociate tissue and generate clean suspension of intact single nuclei. Producing single-nuclei suspension from brain tissue is particularly challenging due to cell type heterogeneity and the myelin sheath that carries over into the nuclei suspension as debris. Current procedures tend to be time consuming and sometimes include steps that can alter gene expression and create cell-type bias. Commercially available nuclei isolation kits, such as the 10X Genomics nuclei isolation kit, offers a streamlined way to process samples for nuclei isolation, thereby minimizing batch effects and enabling reproducibility. In this study, we report on the performance of the 10X Genomics nuclei isolation kit and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit to generate sequencing libraries from space-flown mouse brain samples. Single nuclei sequencing was performed on frozen mouse brain tissue from two spaceflight missions, Rodent Research-10 (RR-10) and RR Reference Mission-2 (RRRM-2). RR-10 mice were female B6129SF2/J, euthanized at 18-19 weeks whereas RRRM-2 mice were female C57BL/6NTac, euthanized at 20 or 37 weeks. Sequencing data was processed using standard GeneLab data processing pipelines. We report evaluation of the performance of the 10X Genomics nuclei isolation kit for spaceflight samples from mouse brain, and evaluation of reproducibility across different mouse strains and age groups. We also report preliminary scientific results including cell type inference, cell clustering, and differentially expressed genes and pathways between spaceflight and ground control samples.

RR-10↗

NASA NTRSDate not supplied

NASA GeneLab Multi-study Visualization Portal

NASA GeneLab has helped advance the field of Space Biology by providing a public repository where researchers can store, share, analyze and visualize the results of space flight related omics experiments. The GeneLab data visualization portal allows any user, regardless of bioinformatics knowledge or access to computational resources, to interact with the experimental data, draw their own conclusions, and gain insights about the effects of space on living systems. These tools help democratize scientific research and foster the NASA Open Science initiative. The new multi-study feature of the GeneLab visualization platform allows users to mine study metadata from RNA sequencing (RNA-seq) experiments to identify samples of interest by filtering datasets based on organism, tissue, assay technology type, and/or factor. Once samples are selected from multiple datasets, users can combine and normalize the sample data, then utilize the visualization displays, including Principal Component Analysis (PCA) plots, to assess sample distributions. Finally, users can perform differential gene expression analysis on the combined data and visualize the results through PCA plots, Volcano plots, Pair plots, Heatmap, Ideogram and Gene Set Enrichment Analysis. All user-generated results and visualizations will be available for download. Here, we present a biological study using samples from multiple GeneLab RNA-seq datasets and analyzed using the multi-study visualization platform to demonstrate inter- and intra-study variability, as well as commonly differentially expressed genes between spaceflight and ground control conditions across datasets. This new feature opens a wide range of possibilities and opportunities for further development including combining other assay technology types and integration with batch effect correction techniques and machine learning applications. Overall, this tool allows users to increase the statistical power of individual experiments, validate hypothesis, identify patterns, and opens the door to new and exciting research.

space biology↗

NASA NTRS2023

Uncovering Unique Molecular Adaptations in the Arabidopsis Thaliana Cvi-0 Ecotype

This research proposal aims to investigate the unique molecular adaptations exhibited by Arabidopsis Thaliana, specifically focusing on the Cape Verde Islands (Cvi-0) ecotype, in response to microgravity conditions. The study examines data from NASA’s Open Science Data Repository and applies a multifaceted RNAseq analysis pipeline using tools in the UseGalaxy.org open platform. Through transcriptomic analysis, differential gene expression patterns were identified in Cvi-0, revealing an absence of heat shock protein (HSP) upregulation and an upregulation of Rubisco Activase (RCA) and chloroplast-related pathways. To test the hypothesis that these adaptations may contribute to Cvi-0’s increased adaptability in microgravity, a three-fold experimental design is proposed. Four experimental groups will be cultivated under simulated microgravity and ground control conditions, including Cvi-0, Col-0, and genetically modified Col-0 with silenced HSP genes, and genetically modified Col-0 with upregulated RCA gene. Growth parameters will be measured to assess plant resilience, and RNA sequencing will provide transcriptomic data for pathway analysis. Anticipated outcomes include improved markers of plant health (mass, growth, etc.) of Cvi-0 in simulated microgravity and enhanced resilience in genetically altered Col-0 variants, providing insights into potential mechanisms of adaptation. This research would bear significance for space agriculture, nutrition for extended space missions, and sustainable terrestrial crop enhancement. Moreover, the insights gained could reshape crop engineering on Earth, enhancing robustness to climate induced stresses and bolstering global food security. The proposal’s trajectory blends scientific curiosity with practical applicability, forging a path towards sustainable food production and improving human exploration beyond our planet.

GL4HS↗

NASA NTRSDate not supplied

Somatic Mutation in Mice on the International Space Station (ISS): Guanine Substitution Suggests Link to Cancer Risk

We conducted comprehensive analysis of single nucleotide somatic mutations in mice exposed to microgravity and other factors aboard the International Space Station (ISS), using data archived in GeneLab. Animals in the experimental cohort consisted of mice that spent 37 days on the ISS within the Rodent Habitat. Ground control animals consisted of mice of identical age, sex, strain, in a terrestrial Rodent Habitat controlled for temperature, humidity and carbon dioxide levels, to match ISS conditions as closely as possible. RNA extracted from eye, liver, skeletal muscle, and kidney tissue specimens was subjected to next-generation sequencing to acquire primary data. Our analysis employed cutting-edge software developed at NASA Ames Research Center, executed on the NASA Ames Supercomputer and on another high-performance computer, for accurate variant calling of single point mutations. ISS-flown mice exhibited a notably heightened level of somatic mutation compared to control mice. The degree of somatic mutation correlated with the degree of gene expression across the four tissue types, i.e., the greatest rate of mutation accumulation was seen in highly expressed genes. We discovered that guanine substitutions were the most common type of somatic mutation. This observation is consistent with the hypothesis that DNA mutation events stem from reactive oxygen/nitrogen/chlorine species-mediated guanine oxidation induced by the spaceflight environment. Since guanine oxidation is a prominent feature of the DNA mutation landscape that accompanies malignant transformation, our findings suggest a possible link between the spaceflight environment and cancer risk that is independent of radiation carcinogenesis.

ISS↗

NASA NTRS2023

Kankakee Water Resources: Monitoring Temperature and Vegetation to Detect River Flow Impediments at Energy Intake Structures

In recent years, unpredictable grassing events have occurred at the Dresden Generating Station, located on the Kankakee River in northern Illinois. Grassing events are characterized by large mats of aquatic vegetation that accumulate downstream, resulting in the clogging of water intake structures and leading to major disruptions in power generation. Currently, employees at the Dresden Generating Station are responsible for reactively responding to each grassing event individually. This project, in partnership with Constellation Nuclear and the United States Geological Survey (USGS), assessed the feasibility of using Earth observations (Landsat 9 OLI-2, Landsat 8 OLI, Sentinel-2 MSI, DOVE PlanetScope, WorldView-3, and GPM IMERG) to detect floating aquatic vegetation within the Kankakee River and identify predictive factors that trigger grassing events, as doing so will provide the Dresden Generating Station the ability to anticipate future grassing events and enhance general hydrologic modeling efforts held by the USGS. The results of this study illustrated that, while aquatic vegetation can be detected by satellites with up to moderate spatial resolution (30 m), temporal resolution is a major limiting factor for tracking movements in floating aquatic vegetation and identifying predictive measures for these events. In addition, correlation results suggest a possible negative relationship between grassing events and river discharge (-0.875 correlation coefficient). In the future, pairing these results with ground control surveys and sensors with higher temporal capabilities would allow our project partners to predict and proactively address future grassing events, ensuring the reliable operation of the Dresden Generating Station.

Marisa Smedsrud↗

NASA NTRS2024

Vertiport Management from Simulation to Flight: Continued Human Factors Assessment of Vertiport Operations

The Urban Air Mobility concept envisions a new future for transportation in urban environments, primarily focused around vertiport operations. A vertiport refers to an identifiable ground or elevated area used for the vertical takeoff and landing of an aircraft. One critical role within vertiport operations that has been proposed but is under-researched is the vertiport manager. The vertiport manager is expected to manage the ground-to-air operations at the vertiport, but their precise responsibilities, tasks, and challenges are currently undefined. The High Density Vertiplex Subproject at NASA is responsible for developing and testing technologies, concepts, and architectures that will support the infrastructure needed for terminal environments around vertiports. Our previous work investigated ground control station operators performing simulated and live flight operations within a remote operations environment. In the current study, we extended from our previous work to explore the role of a vertiport manager. Specifically, we investigated five participants serving as a vertiport manager across both simulated and live flight operations. We performed multiple knowledge elicitation techniques, a thematic content analysis of qualitative data, and naturalistic observations to create a list of insights, design and training recommendations, and a simplified cognitive task diagram of the vertiport manager’s primary task. Findings from this study are discussed within the context of the current debate on the degree to which this role should be automated. A third alternative is suggested to allow a human vertiport manager to be successful by teaming with increasingly autonomous systems, designing the role to improve safety and efficiency of Urban Air Mobility operations.

AAM↗

NASA NTRSDate not supplied

Human-Autonomy Teaming Assistant to Support Small Uncrewed Aircraft Systems for Wildland Firefighting Operations

An exploratory human-in-the-loop simulation was conducted to investigate and characterize a Human-Autonomy Teaming (HAT) Assistant to support a remote operator of multiple small Uncrewed Aircraft Systems (sUAS) using a ground control station (GCS) in the context of a wildland fire surveillance mission. Operator performance using the GCS with the HAT Assistant (Assisted Mode) was compared to operator performance using the GCS without the HAT Assistant (Unassisted Mode) during two types of contingency-event scenarios (Low and High Complexity). In the Assisted Mode, the HAT Assistant provided updates to the level of risk to the mission along with recommendations for risk mitigation, which were not provided in the Unassisted Mode. No significant differences in objective performance and subjective ratings of workload, situation awareness, and trust in automation between the Assisted and Unassisted Modes were detected, however there were indications that participants preferred the Assisted GCS over the Unassisted GCS and directions for further development were explored. Additional work is necessary to further refine the HAT Assistant and better characterize its effects on remote operator performance while managing multiple sUAS assets. Future work is recommended to optimize the implementation of an assistant to support operator performance during different missions and across vehicle classes.

Human-Autonomy Teaming↗

NASA NTRS2024

Vertiport Management from Simulation to Flight: Continued Human Factors Assessment of Vertiport Operations

AAM↗

NASA NTRSDate not supplied

Creating Benchmark Data for Artificial Intelligence and Machine Learning Space Biology Research

To identify an appropriate AI/ML approach for a specific problem, the best practice is to measure algorithm performance through the benchmarking process. A scientific benchmark consists of an AI-ready dataset and a reference implementation on a specific scientific question. The NASA Science Mission Directorate (SMD) has started the “Benchmark Initiative for AI/ML to create scientific benchmark datasets in three applications: 1) scientific benchmarking, which finds the best algorithm for a specific problem; 2) application benchmarking, which measures algorithm performance against a set of parameters; and 3) system benchmarking, which evaluates performance of hardware and software architecture. Currently, there are no standardized datasets available to benchmark AI/ML algorithms in the domain of space biology. In this work, we constructed two AI/ML-ready biological datasets from experiments in space-flown mice: cellular imaging and RNA-seq. First, radiation-exposed immune cells harbor DNA damage foci that can be fluorescently marked to visualize the amount of damage following exposure to ionizing radiation. However, such large datasets are difficult to analyze visually, due to imaging inconsistencies and human bias, and classical image processing approaches can fail on imaging artifacts. AI/ML are therefore exciting alternative, providing the speed of machines and the accuracy of humans. We have made this dataset available at https://registry.opendata.aws/bps_microscopy/. Second, high-throughput nucleic acid sequencing (DNA-seq, RNA-seq) has become widespread in biomedical research due to the growing availability and affordability of these assays. However, most sequencing datasets suffer from high dimensionality and low sample count. In this work, we used a generative adversarial network to synthesize a standardized, AI-ready, publicly available benchmark dataset for space biology RNA-seq data with sufficient space-flown and ground control mouse liver samples from NASA GeneLab. This dataset is available at https://registry.opendata.aws/bps_rnaseq/. These datasets are now fully open the Space Biology community to test their favorite AI/ML approaches.

James Casaletto↗

NASA NTRSDate not supplied

High Density Vertiplex: Scalable Autonomous Operations Prototype Assessment Simulation

Urban Air Mobility (UAM) is a rapidly growing topic within the field of aviation because of the impact a refined ecosystem and uncrewed aerial vehicles could have on modern society, such as urban air mobility, cargo, and emergency transport. Before the UAM concept can be actualized, research is needed to understand how to integrate these new classes of vehicles and operations into the National Airspace System. One under-researched but critical piece of infrastructure required for UAM operations is Vertiport operations. Vertiports are the envisioned takeoff and landing locations for these uncrewed aerial vehicles. To accommodate the high use of the vertiport, new technologies and roles will be required for optimal use. At NASA, the High Density Vertiplex sub-project targets research into vertiports. The High Density Vertiplex team created an Urban Air Mobility ecosystem to test and evaluate different concepts and tools used to support higher density operations at vertiports. Part of the test and evaluation included the Prototype Assessment Operations simulation of highdensity operations around a vertiport to study vertiport management and vertiport operations. The research team also evaluated how the prototype Urban Air Mobility ecosystem supported fleet managers, ground control station operators, and vertiport managers in execution of nominal and off-nominal high-density operations. Results from this simulation provided insight regarding UAM ecosystem research and development and vertiport automation systems.

Small Uncrewed Aerial Vehicle (sUAS)↗

NASA NTRSDate not supplied

High Density Vertiplex: Scalable Autonomous Operations Prototype Assessment Simulation

Urban Air Mobility is a rapidly growing topic within the field of aviation because of the impact a refined ecosystem and uncrewed aerial vehicles could have on modern society, such as urban air, cargo, and emergency transport. Before the UAM concept can be actualized, research is needed to understand how to integrate these new classes of vehicles and operations into the National Airspace System. One under-researched but critical piece of infrastructure required for UAM operations is Vertiport operations. Vertiports are the envisioned takeoff and landing locations for these uncrewed aerial vehicles. To accommodate the high use of the vertiport, new technologies and roles will be required for optimal use. At NASA, the High Density Vertiplex sub-project targets research into vertiports. The High Density Vertiplex team created their own Advanced Air Mobility ecosystem to test and evaluate different concepts and tools used to support higher density operations at vertiports. Part of the test and evaluation included the Prototype Assessment Operations simulation of high-density operations around a vertiport to study vertiport management and vertiport operations. The research team also evaluated how their simulated Urban Air Mobility ecosystem supported fleet managers, ground control station operators, and vertiport managers in execution of nominal and off-nominal high-density operations. Takeaways from this simulation helped the team evaluate well how the users of the ecosystem were able to use the components of the ecosystem to complete Urban Air Mobility missions.

Small Uncrewed Aerial Vehicle (sUAS)↗

NASA NTRSDate not supplied

Advancing Autonomy in Distributed Space Systems: Insights From on-Orbit Testing with the Starling 1.0 Mission

Autonomous decision-making is crucial for enhancing mission effectiveness in Distributed Space Systems (DSS), particularly in multi-spacecraft operations where communication constraints and mission complexity pose challenges. The Distributed Spacecraft Autonomy (DSA) team at NASA’s Ames Research Center is advancing autonomy in DSS through five key technical areas: distributed resource and task management, reactive operations, system modeling and simulation, human-swarm interaction, and ad hoc network communications. The DSA experiment onboard the Starling 1.0 Mission showcases collaborative resource allocation for multi-point science data collection with four small spacecraft. Autonomy in decision-making is highlighted as a crucial factor for multi-spacecraft missions, enabling spacecraft to operate independently, reducing reliance on ground control. This capability is particularly significant for future deep-space missions, where communication delays and limited data transmission capacity make traditional command and control approaches impractical. This demonstration focuses on a GPS Channel Selection Experiment, leveraging emergent capabilities like "shared sampling" and "simultaneous sampling" to optimize channel selection across the spacecraft swarm. The experiment aims to capture ionospheric phenomena such as the Equatorial Ionization Anomaly and Polar Patches. The DSA system's autonomous reconfiguration ability is showcased, emphasizing its adaptability to natural phenomena without significant integration efforts. The GPS Channel Selection Experiment utilizes a dual-band GPS receiver to estimate plasma density in the ionosphere. Explorative and exploitative channel selections are employed based on the nature of observed phenomena. The performance of DSA algorithms is evaluated in terms of optimal channel allocations and responsiveness to changes in observed features. The DSA Flight Software utilizes the Core Flight System (cFS) framework, ensuring compatibility with the Starling 1.0 flight mission software. DSA showcases results from RTI’s Connext DDS Micro communication middleware, enabling message routing over the Ad-Hoc Network of Starling 1.0. This paper provides a comprehensive overview of the DSA experiment's initial results, emphasizing the advancements in autonomy for Distributed Space Systems and the successful collaboration with the Starling 1.0 mission.

Caleb Ashmore Adams↗

NASA NTRSDate not supplied

Human-Autonomy Teaming Assistant to Support Small Uncrewed Aircraft Systems for Wildland Firefighting Operations

Human-Autonomy Teaming↗

NASA NTRS2024

High Density Vertiplex - Scalable Autonomous Operations - Flight Test Report

This Technical Memorandum describes the approach taken within the High Density Vertiplex Project to perform rapid prototyping and assessment of the UAM Ecosystem including representative: Onboard Autonomous Systems, Ground Control and Fleet Management Systems, Airspace Management Systems, and Vertiport Automation Systems (VAS). Small Uncrewed Aerial Systems (sUAS) were employed as effective low risk and inexpensive surrogates for larger proposed UAM aircraft to accelerate the prototyping effort, ensure safety, greatly mitigate costs, and accelerate progress. Flight testing performed included multivehicle operations where usability Human Factors (HF) data was collected on the operators.

Jacob Schaefer↗

NASA NTRSDate not supplied

Transcriptomic Analysis of ISS Crewmembers’ Peripheral Blood Mononuclear Cells Reveals Homeostatic Regulations in Space

The impact of spaceflight on the immune system has been investigated for decades. Studies conducted in cell models, animals and humans suggest that the spaceflight environment affects the innate and acquired immune systems, as the ability to recognize antigens, defend against foreign invaders, and orchestrate repair is significantly hindered. However, the molecular mechanisms behind spaceflight-induced immune dysregulations are still unclear. In this study, blood from eleven (11) International Space Station (ISS) crewmembers was collected before, during and after long duration space missions, as well as from 11 matched ground control subjects. Transcriptomic analysis was performed in isolated peripheral blood mononuclear cells (PBMCs) using the RNA-sequencing technique. In comparison to the blood samples collected from the crewmembers pre-flight, a total of ~1000 genes were found to be upregulated and ~1000 genes downregulated in PBMC collected between 4 and 6 months after they were in space. The most significantly DEGs (differentially expressed genes) include activation of RUBCNL which is an autophagy enhancer and inhibition of GRASP which regulates cell trafficking. Genes involved in cell adhesion, cell cycle progression and other functions were also dysregulated. Pathway analysis of the DEGs indicates mitochondria dysfunction, particularly reduced ATP production in the electron transport chain. Other pathways impacted by spaceflight include glycolysis, autophagy and inflammatory response. Our results suggest that, in space, blood cells may have also experienced energy depletion and reduced metabolism. Consequently, the cells may become autophagic, which is a known homeostatic mechanism for blood cells to become quiescent, but to stay alive. Further analysis of the data shows recovery of the crewmembers after mission and potential differential responses between genders to the space environment. Our data potentially explains some of the physiological changes that have been observed in space such as mitochondria dysfunction, inhibition of T cell activation and telomere lengthening. Comparison of our results with other transcriptomics studies of ISS crewmembers’ blood cells will also be presented.

Maria Moreno Villanueva↗

NASA NTRSDate not supplied

High School Citizen Scientists Use AI/ML to Predict Intra-Ocular Pressure From Gene Expression Data for Spaceflown Mice

Artificial Intelligence (AI) and Machine Learning (ML) have increasingly become pivotal in biological and biomedical research, largely due to the culture of open data sharing and its associated benefits. The methodologies inherent in AI/ML are particularly adept at identifying and forecasting biological phenotypes from the vast amounts of data generated by next-generation sequencing technologies. These techniques offer substantial promise for advancing research in space biosciences and for the development of automated systems for monitoring space health. Nevertheless, there are crucial aspects to consider when training, validating, and testing machine learning models in both biological research and clinical contexts. It is essential that Open Science principles, including data sharing and the availability of open-source code, are complemented by high-quality, publicly accessible training resources. These resources should focus on best practices and include modules based on real-world scientific cases and data to ensure that future AI/ML practitioners gain practical experience with genuine problems. Addressing this knowledge gap, we have designed, developed, and delivered both interactive and self-paced training programs for citizen scientists worldwide, enabling them to utilize AI/ML for space biology research. This initiative was made possible through generous funding from a Transformation to Open Science Training grant. The interactive training sessions, conducted this summer, utilized AI/ML techniques to analyze data from the Open Science Data Repository, specifically targeting the effects of spaceflight on ocular structure and function. The dataset OSD-583, from the Rodent Research 9 mission, provides experimental data detailing the ocular responses of mice subjected to a 35-day spaceflight, compared with ground control counterparts. Using OSD-583 as observational data, our summer training participants applied AI/ML methods to predict intraocular pressure from RNA-seq data and identify the genes most predictive of the observed responses. Further analysis through pathway enrichment and gene set enrichment revealed that these genes are involved in molecular and cellular processes contributing to retinal degeneration.

James Casaletto↗