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All sourcesNASA NTRSDOE OSTI
NASA NTRS2016

GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data

The GeneLab project is a science initiative to maximize the scientific return of omics data collected from spaceflight and from ground simulations of microgravity and radiation experiments, supported by a data system for a public bioinformatics repository and collaborative analysis tools for these data. The mission of GeneLab is to maximize the utilization of the valuable biological research resources aboard the ISS by collecting genomic, transcriptomic, proteomic and metabolomic (so-called omics) data to enable the exploration of the molecular network responses of terrestrial biology to space environments using a systems biology approach. All GeneLab data are made available to a worldwide network of researchers through its open-access data system. GeneLab is currently being developed by NASA to support Open Science biomedical research in order to enable the human exploration of space and improve life on earth. Open access to Phase 1 of the GeneLab Data Systems (GLDS) was implemented in April 2015. Download volumes have grown steadily, mirroring the growth in curated space biology research data sets (61 as of June 2016), now exceeding 10 TB/month, with over 10,000 file downloads since the start of Phase 1. For the period April 2015 to May 2016, most frequently downloaded were data from studies of Mus musculus (39) followed closely by Arabidopsis thaliana (30), with the remaining downloads roughly equally split across 12 other organisms (each 10 of total downloads). GLDS Phase 2 is focusing on interoperability, supporting data federation, including integrated search capabilities, of GLDS-housed data sets with external data sources, such as gene expression data from NIHNCBIs Gene Expression Omnibus (GEO), proteomic data from EBIs PRIDE system, and metagenomic data from Argonne National Laboratory's MG-RAST. GEO and MG-RAST employ specifications for investigation metadata that are different from those used by the GLDS and PRIDE (e.g., ISA-Tab). The GLDS Phase 2 system will implement a Google-like, full-text search engine using a Service-Oriented Architecture by utilizing publicly available RESTful web services Application Programming Interfaces (e.g., GEO Entrez Programming Utilities) and a Common Metadata Model (CMM) in order to accommodate the different metadata formats between the heterogeneous bioinformatics databases. GLDS Phase 2 completion with fully implemented capabilities will be made available to the general public in September 2017.

Space Biology↗
NASA NTRS1995

NASA space life sciences research and education support program

USRA's Division of Space Life Sciences (DSLS) was established in 1983 as the Division of Space Biomedicine to facilitate participation of the university community in biomedical research programs at the NASA Johnson Space Center (JSC). The DSLS is currently housed in the Center for Advanced Space Studies (CASS), sharing quarters with the Division of Educational Programs and the Lunar and Planetary Institute. The DSLS provides visiting scientists for the Johnson Space Center; organizes conferences, workshops, meetings, and seminars; and, through subcontracts with outside institutions, supports NASA-related research at more than 25 such entities. The DSLS has considerable experience providing visiting scientists, experts, and consultants to work in concert with NASA Life Sciences researchers to define research missions and goals and to perform a wide variety of research administration and program management tasks. The basic objectives of this contract have been to stimulate, encourage, and assist research and education in the NASA life sciences. Scientists and experts from a number of academic and research institutions in this country and abroad have been recruited to support NASA's need to find a solution to human physiological problems associated with living and working in space and on extraterrestrial bodies in the solar system.

Jones, Terri K.↗
NASA NTRS2015

Flying Through the Ages: Rodent Research for Human Health

As humans, we evolved, developed, grew, and now function in a continuous 1-gravity environment. Habitation in space poses unique challenges to human cells and organ systems. Biomedical research with rodents (primarily mice and rats) can help to both unravel molecular, cellular and physiologic mechanisms relevant to humans and test candidate interventions that mitigate adverse effects of space on humans, such as muscle atrophy, bone loss and cardiovascular deconditioning. One favored hypothesis that may explain the detrimental effects of spaceflight on humans is that reduced mechanical loading in microgravity accelerates aging. Rodents provide a relevant model system to study this problem as they age 40 times faster than humans. Now scientists from both public and commercial sectors conduct rodent experiments on the ISS using a new capability developed primarily at ARC. Results from the maiden voyage of the Rodent Research Project on the ISS reveal that long duration effects of spaceflight appear far different than short duration effects. Thus, Rodent Research missions on the ISS usher in a new era for exploration and biological discovery in space.

Globus, Ruth↗
NASA NTRS1987

Life sciences report 1987

Highlighted here are the major research efforts of the NASA Life Sciences Division during the past year. Topics covered include remote health care delivery in space, space biomedical research, gravitational biology, biospherics (studying planet Earth), the NASA Closed Ecological Life Support System (CELSS), exobiology, flight programs, international cooperation, and education programs.

Source record↗
NASA NTRS2000

Food and nutrition in space: application to human health

The National Aeronautics and Space Administration begins the new millennium with the hope of expanding human space exploration beyond Earth's orbit. These extended-duration missions (3-5 years) require an in-depth assessment of the critical risks (referred to as "show stoppers") to humans when exposed to the remote environment and reduced gravity conditions for such long periods of time. Food, and the nutrition it provides, is paramount to crew health. For short-duration spaceflight (30 days), the nutrient requirements pertaining to physiological adaptations are likely to be satisfied without significant impact on crew performance or health. However, prolonged exposure to reduced gravity, or microgravity, and isolation may alter human nutrient requirements as well as increase the psychosocial role of food/meals in daily activities. An outline of critical questions and related research needs in the area of food and nutrition has been drafted (1) at NASA JSC with the help of the National Space Biomedical Research Institute (http://www.nsbri.org). The research areas outlined in this plan will directly impact the success of extended-duration human space missions. Findings from this research will have direct applications to human health issues faced here on Earth.

NASA Discipline Regulatory Physiology↗
NASA NTRS2008

Periodontal Probe Improves Exams, Alleviates Pain

Dentists, comedian Bill Cosby memorably mused, tell you not to pick your teeth with any sharp metal object. Then you sit in their chair, and the first thing they grab is an iron hook!" Conventional periodontal probing is indeed invasive, uncomfortable for the patient, and the results can vary greatly between dentists and even for repeated measurements by the same dentist. It is a necessary procedure, though, as periodontal disease is the most common dental disease, involving the loss of teeth by the gradual destruction of ligaments that hold teeth in their sockets in the jawbone. The disease usually results from an increased concentration of bacteria in the pocket, or sulcus, between the gums and teeth. These bacteria produce acids and other byproducts, which enlarge the sulcus by eroding the gums and the periodontal ligaments. The sulcus normally has a depth of 1 to 2 millimeters, but in patients with early stages of periodontal disease, it has a depth of 3 to 5 millimeters. By measuring the depth of the sulcus, periodontists can have a good assessment of the disease s progress. Presently, there are no reliable clinical indicators of periodontal disease activity, and the best available diagnostic aid, periodontal probing, can only measure what has already been lost. A method for detecting small increments of periodontal ligament breakdown would permit earlier diagnosis and intervention with less costly and time-consuming therapy, while overcoming the problems associated with conventional probing. The painful, conventional method for probing may be destined for the archives of dental history, thanks to the development of ultrasound probing technologies. The roots of ultrasound probes are in an ultrasound-based time-of-flight technique routinely used to measure material thickness and length in the Nondestructive Evaluation Sciences Laboratory at Langley Research Center. The primary applications of that technology have been for corrosion detection and bolt tension measurements (Spinoff 2005). This ultrasound measurement system was adapted to the Periodontal Structures Mapping System, invented at Langley by John A. Companion, under the supervision of Dr. Joseph S. Heyman. Support of the research and development that led to this invention was provided by NASA s Technology Applications Engineering Program and by the Naval Institute for Dental and Biomedical Research, in Great Lakes, Illinois.

Source record↗
DOE OSTI2026

From Rules to Reasoning: A Survey of Large Language Model-Based Approaches to Scientific Hypothesis and Idea Generation

Scientific hypothesis generation represents a fundamental challenge in contemporary research due to exponentially expanding literature volumes and increasing disciplinary specialization. Large language models (LLMs) have emerged as transformative tools for automated scientific discovery, moving beyond traditional rule-based and literature-mining approaches. Four paradigmatic approaches define current LLM-driven hypothesis generation: direct prompting and fine-tuning methods, knowledge-enhanced frameworks integrating retrieval-augmented generation (RAG), multi-agent collaborative systems simulating research teams, and reasoning-focused approaches implementing cognitive architectures. Domain-specific applications demonstrate statistical equivalence to human expert performance in social psychology, experimental validation in biomedical research, and near-expert quality in astronomy. Evaluation methodologies encompass human expert assessment, LLM-as-judge frameworks, and comprehensive benchmarking systems. Technical challenges include hallucination management, knowledge integration limitations, and balancing novelty with feasibility. Future directions emphasize hybrid neural-symbolic architectures and sophisticated human-AI collaboration models for responsible scientific discovery acceleration.

AI-driven discovery↗
NASA NTRS2004

Balanced Expertise Distribution in Remote Ultrasound Imaging Aboard The International Space Station (ISS)

Astronaut training for ISS operations usually ensures independent performance. With small crew size same crews also conduct all science work onboard. With diverse backgrounds, a good "match" between the existing and required skills can only be anecdotal. Furthermore, full proficiency in most of the complex tasks can be attained only through long training and practice, which may not be justified and may be impossible given the scarcity of training time. To enable a number of operational and science advancements, authors have developed a new approach to expertise distribution in time and among the space and ground personnel. Methods: As part of NASA Operational Ultrasound Project (1998-2003) and the NASA-solicited experiment "Advanced Diagnostic Ultrasound in Microgravity-ADUM" (P.I. -S.D., ongoing), the authors have created a "Balanced Expertise Distribution" approach to perform complex ultrasound imaging tasks on ISS for both operational and science use. The four components of expertise are a) any pre-existing pertinent expertise; b) limited preflight training c) adaptive onboard proficiency enhancement tools; d) real-time ' guidance from the ground. Throughout the pre-flight training and flight time preceding the experiments, the four components are shaped in a dynamic fashion to meet in an optimum combination during the experiment sessions. Results: Procedure validation sessions and feasibility studies have given encouraging results. While several successful real-time remote guidance sessions have been conducted on ISS, Expedition 8 is the first to use an "on-orbit proficiency enhancement" tool. Conclusions: In spite of severely limited training time, daring peer-reviewed research and operational enhancements are feasible through a balanced distribution of expertise in time, as well as among the crewmembers and ground personnel. This approach shows great promise for biomedical research, but may be applicable for other areas of micro gravity-based science

Sargsyan, Ashot↗
NASA NTRS1974

Applications of aerospace technology in biology and medicine

The results of the medically related activities of the NASA Application Team Program at the Research Triangle Institute are presented. The RTI team, a multidisciplinary team of scientists and engineers, acted as an information and technology interface between NASA and individuals, institutions, and agencies involved in biomedical research and clinical medicine. The Team has identified 40 new problems for investigation, has accomplished 7 technology applications, 6 potential technology application, 4 impacts, has closed 54 old problems, and has a total of 47 problems under active investigation.

Brown, J. N.↗
NASA NTRS2010

Human Research Program Exploration Medical Capability

NASA s Human Research Program (HRP) conducts and coordinates research projects that provide human health and performance countermeasures, knowledge, technologies, and tools to enable safe, reliable, and productive human space exploration. The Program is divided into 6 major elements, which a) Provide the Program s knowledge and capabilities to conduct research, addressing the human health and performance risks. b) Advance the readiness levels of technology and countermeasures to the point of transfer to the customer programs and organizations. The National Space Biomedical Research Institute (NSBRI) is a partner with the HRP in developing a successful research program. 3

Barsten, Kristina↗
NASA NTRS1972

Mass spectrometry.

Review of the current state of mass spectrometry, indicating its unique importance for advanced scientific research. Mass spectrometry applications in computer techniques, gas chromatography, ion cyclotron resonance, molecular fragmentation and ionization, and isotope labeling are covered. Details are given on mass spectrometry applications in bio-organic chemistry and biomedical research. As the subjects of these applications are indicated alkaloids, carbohydrates, lipids, terpenes, quinones, nucleic acid components, peptides, antibiotics, and human and animal metabolisms. Particular attention is given to the mass spectra of organo-inorganic compounds, inorganic mass spectrometry, surface phenomena such as secondary ion and electron emission, and elemental and isotope analysis. Further topics include mass spectrometry in organic geochemistry, applications in geochronology and cosmochemistry, and organic mass spectrometry.

Burlingame, A. L.↗
NASA NTRS1989

Future prospects for space life sciences from a NASA perspective

Plans for future NASA research programs in the life sciences are reviewed. Consideration is given to international cooperation in space life science research, the NASA approach to funding life science research, and research opportunities using the Space Shuttle, the Space Station, and Biological Satellites. Several specific programs are described, including the Centrifuge Project to provide a controlled acceleration environment for microgravity studies, the Rhesus Project to conduct biomedical research using rhesus monkeys, and the LifeSat international biosatellite project. Also, the Space Biology Initiative to design and develop life sciences laboratory facilities for the Space Shuttle and the Space Station and the Extended Duration Crew Operations program to study crew adaptation needs are discussed.

White, Ronald J.↗
DOE OSTI2022

Making Common Fund data more findable: catalyzing a data ecosystem

The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes of Health Common Fund without requiring that data owners move, reformat, or rehost those data. This system is centered on a catalog that integrates detailed descriptions of biomedical datasets from individual Common Fund Programs’ Data Coordination Centers (DCCs) into a uniform metadata model that can then be indexed and searched from a centralized portal. This Crosscut Metadata Model (C2M2) supports the wide variety of data types and metadata terms used by individual DCCs and can readily describe nearly all forms of biomedical research data. We detail its use to ingest and index data from 11 DCCs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
NASA NTRS1975

Foundations of Space Biology and Medicine. Volume 3: Space Medicine and Biotechnology

The results of medical and biological research in space are presented. Specific topics discussed include: methods of providing life support systems for astronauts, characteristics of integrated life support systems, protection against adverse factors of space flight, selection and training of astronauts, and future space biomedical research.

Calvin, M.↗
NASA NTRS1999

Extended Duration Orbiter Medical Project

Biomedical issues have presented a challenge to flight physicians, scientists, and engineers ever since the advent of high-speed, high-altitude airplane flight in the 1940s. In 1958, preparations began for the first manned space flights of Project Mercury. The medical data and flight experience gained through Mercury's six flights and the Gemini, Apollo, and Skylab projects, as well as subsequent space flights, comprised the knowledge base that was used to develop and implement the Extended Duration Orbiter Medical Project (EDOMP). The EDOMP yielded substantial amounts of data in six areas of space biomedical research. In addition, a significant amount of hardware was developed and tested under the EDOMP. This hardware was designed to improve data gathering capabilities and maintain crew physical fitness, while minimizing the overall impact to the microgravity environment. The biomedical findings as well as the hardware development results realized from the EDOMP have been important to the continuing success of extended Space Shuttle flights and have formed the basis for medical studies of crew members living for three to five months aboard the Russian space station, Mir. EDOMP data and hardware are also being used in preparation for the construction and habitation of International Space Station. All data sets were grouped to be non-attributable to individuals, and submitted to NASA s Life Sciences Data Archive.

Sawin, Charles F.↗
DOE OSTI2016

Semantic similarity between ontologies at different scales

In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗
NASA NTRS2011

An Earthling to an Astronaut: Medical Challenges

Humans can travel safely into space in low Earth orbit (LEO) or to near-Earth objects if several medical, physiological, environmental, and human factors issues risks are mitigated. Research must be performed in order to set standards in these four areas, and current NASA standards are contained in the Space Flight Human System Standards volumes 1 and 2, and crew medical certification standards. These three sets of standards drive all of the clinical, biomedical research and environmental technology development for the NASA human space flight program. These standards also drive the identification of specific risks to crew health and safety, and we currently manage 65 human system risks within the human space flight program. Each risk has a specific program of research, technology development, and development of operational procedures to mitigate the risks. Some of the more important risks tat will be discussed in this talk include exposure to radiation, behavioral health due to confinement in a closed cabin, physiological changes such as loss of bone, muscle and exercise capability, reduction in immune system capability, environmental threats of maintaining an adequate atmosphere and water for drinking, avoidance of toxic or infectious material, protection of hearing, and human factors issues of equipment and task design. A nutritious and varied food supply must also be provided. All of these risks will be discussed and current strategies for mitigating these risks for long-duration human space flight. In mitigating these 65 human system risks, novel approaches to problem solving must be employed to find the most appropriate research and technology based applications. Some risk mitigations are developed internally to NASA while others are found through research grants, technology procurements, and more recently open innovation techniques to seek solutions from the global technical community. Examples and results will be presented from all of these approaches including the more recent use of prizes to stimulate innovation.

Davis, Jeffrey R.↗