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DOE OSTI2025

Ca X ML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of Ca X ML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2004

Microgravity Materials Research and Code U ISRU

The NASA microgravity research program, simply put, has the goal of doing science (which is essentially finding out something previously unknown about nature) utilizing the unique long-term microgravity environment in Earth orbit. Since 1997 Code U has in addition funded scientific basic research that enables safe and economical capabilities to enable humans to live, work and do science beyond Earth orbit. This research has been integrated with the larger NASA missions (Code M and S). These new exploration research focus areas include Radiation Shielding Materials, Macromolecular Research on Bone and Muscle Loss, In Space Fabrication and Repair, and Low Gravity ISRU. The latter two focus on enabling materials processing in space for use in space. The goal of this program is to provide scientific and technical research resulting in proof-of-concept experiments feeding into the larger NASA program to provide humans in space with an energy rich, resource rich, self sustaining infrastructure at the earliest possible time and with minimum risk, launch mass and program cost. President Bush's Exploration Vision (1/14/04) gives a new urgency for the development of ISRU concepts into the exploration architecture. This will require an accelerated One NASA approach utilizing NASA's partners in academia, and industry.

Curreri, Peter A.↗

NASA NTRS2009

Humanlike Robots - The Upcoming Revolution in Robotics

Humans have always sought to imitate the human appearance, functions and intelligence. Human-like robots, which for many years have been a science fiction, are increasingly becoming an engineering reality resulting from the many advances in biologically inspired technologies. These biomimetic technologies include artificial intelligence, artificial vision and hearing as well as artificial muscles, also known as electroactive polymers (EAP). Robots, such as the vacuum cleaner Rumba and the robotic lawnmower, that don't have human shape, are already finding growing use in homes worldwide. As opposed to other human-made machines and devices, this technology raises also various questions and concerns and they need to be addressed as the technology advances. These include the need to prevent accidents, deliberate harm, or their use in crime. In this paper the state-of-the-art of the ultimate goal of biomimetics, the development of humanlike robots, the potentials and the challenges are reviewed.

EAP↗

NASA NTRS2000

Systematic Sensitivity Analysis of Metabolic Controllers During Reductions in Skeletal Muscle Blood Flow

An acute reduction in oxygen delivery to skeletal muscle is generally associated with profound derangements in substrate metabolism. Given the complexity of the human bioenergetic system and its components, it is difficult to quantify the interaction of cellular metabolic processes to maintain ATP homeostasis during stress (e.g., hypoxia, ischemia, and exercise). Of special interest is the determination of mechanisms relating tissue oxygenation to observed metabolic responses at the tissue, organ, and whole body levels and the quantification of how changes in oxygen availability affect the pathways of ATP synthesis and their regulation. In this study, we apply a previously developed mathematical model of human bioenergetics to study effects of ischemia during periods of increased ATP turnover (e.g., exercise). By using systematic sensitivity analysis the oxidative phosphorylation rate was found to be the most important rate parameter affecting lactate production during ischemia under resting conditions. Here we examine whether mild exercise under ischemic conditions alters the relative importance of pathways and parameters previously obtained.

Radhakrishnan, Krishnan↗

NASA NTRS2006

Space Life Sciences at NASA: Spaceflight Health Policy and Standards

In January 2005, the President proposed a new initiative, the Vision for Space Exploration. To accomplish the goals within the vision for space exploration, physicians and researchers at Johnson Space Center are establishing spaceflight health standards. These standards include fitness for duty criteria (FFD), permissible exposure limits (PELs), and permissible outcome limits (POLs). POLs delineate an acceptable maximum decrement or change in a physiological or behavioral parameter, as the result of exposure to the space environment. For example cardiovascular fitness for duty standards might be a measurable clinical parameter minimum that allows successful performance of all required duties. An example of a permissible exposure limit for radiation might be the quantifiable limit of exposure over a given length of time (e.g. life time radiation exposure). An example of a permissible outcome limit might be the length of microgravity exposure that would minimize bone loss. The purpose of spaceflight health standards is to promote operational and vehicle design requirements, aid in medical decision making during space missions, and guide the development of countermeasures. Standards will be based on scientific and clinical evidence including research findings, lessons learned from previous space missions, studies conducted in space analog environments, current standards of medical practices, risk management data, and expert recommendations. To focus the research community on the needs for exploration missions, NASA has developed the Bioastronautics Roadmap. The Bioastronautics Roadmap, NASA's approach to identification of risks to human space flight, revised baseline was released in February 2005. This document was reviewed by the Institute of Medicine in November 2004 and the final report was received in October 2005. The roadmap defines the most important research and operational needs that will be used to set policy, standards (define acceptable risk), and implement an overall Risk Management and Analysis process. Currently NASA is drafting spaceflight health standards for neurosensory alterations, space radiation exposure, behavioral health, muscle atrophy, cardiovascular fitness, immunological compromise, bone demineralization, and nutrition.

Davis, Jeffrey R.↗

NASA NTRS2016

Novel Musculoskeletal Loading System for Small Exercise Devices

Long duration spaceflight places astronauts at increased risk for muscle strain and bone fracture upon return to a 1-g or partial gravity environment. Functionally limiting decrements in musculoskeletal health are likely during Mars proving-ground and Earth-independent missions given extended transit times and the vehicle limitations for exercise devices (low-mass, small volume, little to no power). This is particularly alarming for exploration missions because astronauts will be required to perform novel and physically demanding tasks (i.e. vehicle egress, exploration, and habitat building activities) on unfamiliar terrain. Accordingly, NASA's exploration roadmap identifies the need for development of small exercise equipment that can prevent musculoskeletal atrophy and has the ability to assess musculoskeletal health at multiple time points during long-duration missions.

Downs, Meghan↗

NASA NTRS2017

Systemic Microgravity Response: Utilizing GeneLab to Develop Hypotheses for Spaceflight Risks

Biological risks associated with microgravity are a major concern for long-term space travel. Although determination of risk has been a focus for NASA research, data examining systemic (i.e., multi- or pan-tissue) responses to space flight are sparse. To perform our analysis, we utilized the NASA GeneLab database which is a publicly available repository containing a wide array of omics results from experiments conducted with: i) with different flight conditions (space shuttle (STS) missions vs. International Space Station (ISS); ii) a variety of tissues; and 3) assays that measure epigenetic, transcriptional, and protein expression changes. Meta-analysis of the transcriptomic data from 7 different murine and rat data sets, examining tissues such as liver, kidney, adrenal gland, thymus, mammary gland, skin, and skeletal muscle (soleus, extensor digitorum longus, tibialis anterior, quadriceps, and gastrocnemius) revealed for the first time, the existence of potential master regulators coordinating systemic responses to microgravity in rodents. We identified p53, TGF1 and immune related pathways as the highly prevalent pan-tissue signaling pathways that are affected by microgravity. Some variability in the degree of change in their expression across species, strain and time of flight was also observed. Interestingly, while certain skeletal muscle (gastrocnemius and soleus) exhibited an overall down-regulation of these genes, some other muscle types such as the extensor digitorum longus, tibialis anterior and quadriceps, showed an up-regulated expression, indicative of potential compensatory mechanisms to prevent microgravity-induced atrophy. Key genes isolated by unbiased systems analyses displayed a major overlap between tissue types and flight conditions and established TGF1 to be the most connected gene across all data sets. Finally, a set of microgravity responsive miRNA signature was identified and based on their predicted functional state and subsequent impact on health, a theoretical health risk score was calculated. The genes and miRNAs identified from our analyses can be targeted for future research involving efficient countermeasure design. Our study thus exemplifies the utility of GeneLab data repository to aid in the process of performing novel hypothesis based spaceflight research aimed at elucidating the global impact of environmental stressors at multiple biological scales.

GeneLab↗

NASA NTRS2000

Ultrasonic Motors (USM) - an emerging actuation technology for planetary applications

A hybrid model that addressed a complete ultrasonic motor as a system was developed. The model allows using powerful commercial FE package to express dynamic characteristics of the stator and the rotor in engineering practice. An analog model couples the finite element models for the stator and rotor for the stator-interface layer-rotor syste. The model provides reasonably accurate results for CAD.

electroactive polymers actuators EAP materials art↗

NASA NTRS1999

Effects of spaceflight conditions on fertilization and embryogenesis in the sea urchin Lytechinus pictus

Calcium loss and muscle atrophy are two of the main metabolic changes experienced by astronauts and crew members during exposure to microgravity in space. Calcium and cytoskeletal events were investigated within sea urchin embryos which were cultured in space under both microgravity and 1 g conditions. Embryos were fixed at time-points ranging from 3 h to 8 days after fertilization. Investigative emphasis was placed upon: (1) sperm-induced calcium-dependent exocytosis and cortical granule secretion, (2) membrane fusion of cortical granule and plasma membranes; (3) microfilament polymerization and microvilli elongation; and (5) embryonic development into morula, blastula, gastrula, and pluteus stages. For embryos cultured under microgravity conditions, the processes of cortical granule discharge, fusion of cortical granule membranes with the plasma membrane, elongation of microvilli and elevation of the fertilization coat were reduced in comparison with embryos cultured at 1 g in space and under normal conditions on Earth. Also, 4% of all cells undergoing division in microgravity showed abnormalities in the centrosome-centriole complex. These abnormalities were not observed within the 1 g flight and ground control specimens, indicating that significant alterations in sea urchin development processes occur under microgravity conditions. Copyright 1999 Academic Press.

STS-77 Shuttle Project↗

NASA NTRS1997

An overview of the issues: physiological effects of bed rest and restricted physical activity

Reduction of exercise capacity with confinement to bed rest is well recognized. Underlying physiological mechanisms include dramatic reductions in maximal stroke volume, cardiac output, and oxygen uptake. However, bed rest by itself does not appear to contribute to cardiac dysfunction. Increased muscle fatigue is associated with reduced muscle blood flow, red cell volume, capillarization and oxidative enzymes. Loss of muscle mass and bone density may be reflected by reduced muscle strength and higher risk for injury to bones and joints. The resultant deconditioning caused by bed rest can be independent of the primary disease and physically debilitating in patients who attempt to reambulate to normal active living and working. A challenge to clinicians and health care specialists has been the identification of appropriate and effective methods to restore physical capacity of patients during or after restricted physical activity associated with prolonged bed rest. The examination of physiological responses to bed rest deconditioning and exercise training in healthy subjects has provided significant information to develop effective rehabilitation treatments. The successful application of acute exercise to enhance orthostatic stability, daily endurance exercise to maintain aerobic capacity, or specific resistance exercises to maintain musculoskeletal integrity rather than the use of surgical, pharmacological, and other medical treatments for clinical conditions has been enhanced by investigation and understanding of underlying mechanisms that distinguish physical deconditioning from the disease. This symposium presents an overview of cardiovascular and musculoskeletal deconditioning associated with reduced physical work capacity following prolonged bed rest and exercise training regimens that have proven successful in ameliorating or reversing these adverse effects.

NASA Program Space Physiology and Countermeasures↗

NASA NTRS2002

Insertional Mutagenesis for Genes involved in Otic/Vestibular Development and Function in Xenopus Tropicalis

Sensitivity to gravity is essential for spatial orientation. Consequently, the gravity receptor system is one of the phylogenetically oldest sensory systems, and the special adaptations that enhance sensitivity to gravity are highly conserved. The main goal of this project is to use Xenopus (frog) to identify genes expressed during vestibular and auditory development. These studies will lead a better understanding of the molecular mechanisms involved in vestibular and auditory development and function. We are using a gene-trap approach in Xenopus tropicalis with the green fluorescent protein (GFP) gene as the transgene reporter. GFP expression occurs only when the GFP gene is correctly integrated in actively transcribed genes. Using the GFP as a tag we can easily identify and clone the mutated gene. In addition, we can study the function of the mutated gene by analyzing the defects generated by insertion of the GFP transgene. To date we have tissue specific GFP expression in X. tropicalis including expression in ear, neural tube, kidney, muscle, eyes and nose. Our transgenic animals will soon reach maturity so that we can outcross them and analyze their progeny. Our next goal is to isolate RNA from our transgenics and clone the tagged genes using RACE-PCR. Currently we are optimizing the RACE-PCR method using transgenics with crystallin GFP expression.

Torrejon, Marcela↗

NASA NTRS2001

Effect of Under-Resolved Grids on High Order Methods

There has been much discussion on verification and validation processes for establishing the credibility of CFD simulations. Since the early 1990s, many of the aeronautical and mechanical engineering related reference journals mandated that any accepted articles in numerical simulations (without known solutions to compared with) need to perform a minimum of one level of grid refinement and time step reduction. Due to the difficulty in analysis, the effect of under-resolved grids and the nonlinear behavior of available spatial discretizations, are scarcely discussed in the literature. Here, an under-resolved numerical simulation is one where the grid spacing being used is too coarse to resolve the smallest physically relevant scales of the chosen continuum governing equations that are of interest to the numerical modeler. With the advent of new developments in fourth-order or higher spatial schemes, it has become common to regard high order schemes as more accurate, reliable and require less grid points. The danger comes when one tries to perform computations with the coarsest grid possible while still hoping to maintain numerical results sufficiently accurate for complex flows, and especially, data-limited problems. On one hand, high order methods when applies to highly coupled multidimensional complex nonlinear problems might have different stability, convergence and reliability behavior than their well studied low order counterparts, especially for nonlinear schemes such as TVD, MUSCL with limiters, ENO, WENO and discrete Galerkin. On the other hand, high order methods involve more operation counts and systematic grid convergence study can be time consuming and prohibitively expansive. At the same time it is difficult to fully understand or categorize the different nonlinear behavior of finite discretizations, especially at the limits of under-resolution when different types of bifurcation phenomena might occur, depending on the combination of grid spacings, time steps, initial conditions and numerical treatments of boundary conditions.

Yee, H. C.↗

NASA NTRS1995

Adaptation to Space: An Introduction

The cardiovascular and musculoskeletal systems are normally exposed to gradients of blood pressure and weight on Earth. These gradients increase blood pressure and tissue weight in dependent tissues of the body. Exposure to actual and simulated microgravity causes blood and tissue fluid to shift from the legs to the head. Studies of humans in space have documented facial edema, space motion sickness, decreased plasma volume, muscle atrophy, and loss of bone strength. Return of astronauts to Earth is accompanied by orthostatic intolerance, decreased neuromuscular coordination, and reduced exercise capacity. These factors decrease performance during descent from orbit and increase risk during emergency egress from the spacecraft. Models of simulated microgravity include 6 deg head-down tilt, immersion, and prolonged horizontal bedrest. Head-down tilt is the most accepted model and studies using this model of up to one year have been performed in Russia. Animal models which offer clear insights into the role of gravity on vertebrates include the developing giraffe and snakes from various habitats. Finally, possible countermeasures to speed readaptation of astronauts to gravity after prolonged space flight will be discussed.

Hargens, Alan R.↗

NASA NTRS1997

Targeted gene expression without a tissue-specific promoter: creating mosaic embryos using laser-induced single-cell heat shock

We have developed a method to target gene expression in the Drosophila embryo to a specific cell without having a promoter that directs expression in that particular cell. Using a digitally enhanced imaging system to identify single cells within the living embryo, we apply a heat shock to each cell individually by using a laser microbeam. A 1- to 2-min laser treatment is sufficient to induce a heat-shock response but is not lethal to the heat-shocked cells. Induction of heat shock was measured in a variety of cell types, including neurons and somatic muscles, by the expression of beta-galactosidase from an hsp26-lacZ reporter construct or by expression of a UAS target gene after induction of hsGAL4. We discuss the applicability of this technique to ectopic gene expression studies, lineage tracing, gene inactivation studies, and studies of cells in vitro. Laser heat shock is a versatile technique that can be adapted for use in a variety of research organisms and is useful for any studies in which it is desirable to express a given gene in only a distinct cell or clone of cells, either transiently or constitutively, at a time point of choice.

Non-NASA Center↗

NASA NTRS1996

Ergonomic Evaluations of Microgravity Workstations

Various gloveboxes (GBXs) have been used aboard the Shuttle and ISS. Though the overall technical specifications are similar, each GBX's crew interface is unique. JSC conducted a series of ergonomic evaluations of the various glovebox designs to identify human factors requirements for new designs to provide operator commonality across different designs. We conducted 2 0g evaluations aboard the Shuttle to evaluate the material sciences GBX and the General Purpose Workstation (GPWS), and a KC-135 evaluation to compare combinations of arm hole interfaces and foot restraints (flexible arm holes were better than rigid ports for repetitive fine manipulation tasks). Posture analysis revealed that the smallest and tallest subjects assumed similar postures at all four configurations, suggesting that problematic postures are not necessarily a function of the operator s height but a function of the task characteristics. There was concern that the subjects were using the restrictive nature of the GBX s cuffs as an upper-body restraint to achieve such high forces, which might lead to neck/shoulder discomfort. EMG data revealed more consistent muscle performance at the GBX; the variability in the EMG profiles observed at the GPWS was attributed to the subjects attempts to provide more stabilization for themselves in the loose, flexible gauntlets. Tests revealed that the GBX should be designed for a 95 percentile American male to accommodate a neutral working posture. In addition, the foot restraint with knee support appeared beneficial for GBX operations. Crew comments were to provide 2 foot restraint mechanical modes, loose and lock-down, to accommodate a wide range of tasks without egressing the restraint system. Thus far, we have developed preliminary design guidelines for GBXs and foot.

Whitmore, Mihriban↗

NASA NTRS2024

3D Scanning System to Assess Gravity-Dependent Body Shape Changes

The human body shows unique physiological and morphological changes when exposed to different gravity conditions, including muscle atrophy, fluid shift, spinal elongation, and body posture adjustments. Such changes need to be incorporated for human-system integration in the vehicle habitat, garment, and spacesuit designs, as inaccurate body measurements can result in suboptimal crew protection that can potentially decrease injury tolerance. However, the traditional linear measurements, such as stature, segment lengths or circumferences measured using a caliper or tape measure, often show limited consistency and are unable to capture the nonlinear characteristics of the human body. While 3D body scanning can provide significant advantages over linear measurements, the technologies have not been fully developed or customized for in-flight scanning. For ground laboratory use, several different scanner types are commercially available. However, in-flight scanning requires additional technical considerations, such as minimal scan time, simplified calibration, and sufficient capture volume. This work aims to develop a prototype 3-D body scanning system that is customized for in-flight use to scan crewmembers, with the configuration and performance optimized for detecting known gravity-dependent body shape and posture changes. A hardware system will be custom built using a network of commercial off-the-shelf 3D sensors. The sensor parameters and settings will be optimized to detect the targeted body shape changes, specifically using body manikins of which the shape and size are iteratively permuted to simulate the known changes by fluid shift and spinal elongation. The capture volume will be also matched for a range of body sizes from a 1st percentile female to 99th percentile male. Unintentional body motions or floating in microgravity will be also simulated and incorporated. A data acquisition software will be developed for efficient in-flight operations with minimal overhead and easy-to-use user interface. A simplified calibration procedure will be designed for robust scanning against frequent vibration or unexpected sensor position shifts. The system will be tested in the ground laboratory for accuracy and reliability against a reference scanning system. New anthropometry measurements will be also identified to sensitively capture the gravity dependent body shape changes, in addition to the traditional anthropometry measurements. A novel landmark-based technique will be tested for consistent anthropometry measurements across posture variations. If successfully developed and deployed, the new system is expected to provide previously unavailable body shape and size data from different gravitational environments, including 0-g, 1/6-g, and 1-g. Such data can improve suit fit, habitat design, exercise efficacy quantification and sizing of orthostatic intolerance garments.

K H Kim↗

NASA NTRS2024

3D Scanning System to Assess Gravity-Dependent Body Shape Changes

K H Kim↗

NASA NTRS1993

The Design of Mechanically Compatible Fasteners for Human Mandible Reconstruction

Mechanically compatible fasteners for use with thin or weakened bone sections in the human mandible are being developed to help reduce large strain discontinuities across the bone/implant interface. Materials being considered for these fasteners are a polyetherertherketone (PEEK) resin with continuous quartz or carbon fiber for the screw. The screws were designed to have a shear strength equivalent to that of compact/trabecular bone and to be used with a conventional nut, nut plate, or an expandable shank/blind nut made of a ceramic filled polymer. Physical and finite element models of the mandible were developed in order to help select the best material fastener design. The models replicate the softer inner core of trabecular bone and the hard outer shell of compact bone. The inner core of the physical model consisted of an expanding foam and the hard outer shell consisted of ceramic particles in an epoxy matrix. This model has some of the cutting and drilling attributes of bone and may be appropriate as an educational tool for surgeons and medical students. The finite element model was exercised to establish boundary conditions consistent with the stress profiles associated with mandible bite forces and muscle loads. Work is continuing to compare stress/strain profiles of a reconstructed mandible with the results from the finite element model. When optimized, these design and fastening techniques may be applicable, not only to other skeletal structures, but to any composite structure.

Roberts, Jack C.↗