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DOE OSTI2020

Efficient DNA sequence compression with neural networks

Abstract Background The increasing production of genomic data has led to an intensified need for models that can cope efficiently with the lossless compression of DNA sequences. Important applications include long-term storage and compression-based data analysis. In the literature, only a few recent articles propose the use of neural networks for DNA sequence compression. However, they fall short when compared with specific DNA compression tools, such as GeCo2. This limitation is due to the absence of models specifically designed for DNA sequences. In this work, we combine the power of neural networks with specific DNA models. For this purpose, we created GeCo3, a new genomic sequence compressor that uses neural networks for mixing multiple context and substitution-tolerant context models. Findings We benchmark GeCo3 as a reference-free DNA compressor in 5 datasets, including a balanced and comprehensive dataset of DNA sequences, the Y-chromosome and human mitogenome, 2 compilations of archaeal and virus genomes, 4 whole genomes, and 2 collections of FASTQ data of a human virome and ancient DNA. GeCo3 achieves a solid improvement in compression over the previous version (GeCo2) of $2.4\%$, $7.1\%$, $6.1\%$, $5.8\%$, and $6.0\%$, respectively. To test its performance as a reference-based DNA compressor, we benchmark GeCo3 in 4 datasets constituted by the pairwise compression of the chromosomes of the genomes of several primates. GeCo3 improves the compression in $12.4\%$, $11.7\%$, $10.8\%$, and $10.1\%$ over the state of the art. The cost of this compression improvement is some additional computational time (1.7–3 times slower than GeCo2). The RAM use is constant, and the tool scales efficiently, independently of the sequence size. Overall, these values outperform the state of the art. Conclusions GeCo3 is a genomic sequence compressor with a neural network mixing approach that provides additional gains over top specific genomic compressors. The proposed mixing method is portable, requiring only the probabilities of the models as inputs, providing easy adaptation to other data compressors or compression-based data analysis tools. GeCo3 is released under GPLv3 and is available for free download at https://github.com/cobilab/geco3.

Silva, Milton↗

NASA NTRS1993

Visual Earth observation performance in the space environment. Human performance measurement 4: Flight experiments

A wide variety of secondary payloads have flown on the Space Transportation System (STS) since its first flight in the 1980's. These experiments have typically addressed specific issues unique to the zero-gravity environment. Additionally, the experiments use the experience and skills of the mission and payload specialist crew members to facilitate data collection and ensure successful completion. This paper presents the results of the Terra Scout experiment, which flew aboard STS-44 in November 1991. This unique Earth Observation experiment specifically required a career imagery analyst to operate the Spaceborne Direct-View Optical System (SpaDVOS), a folded optical path telescope system designed to mount inside the shuttle on the overhead aft flight deck windows. Binoculars and a small telescope were used as backup optics. Using his imagery background, coupled with extensive target and equipment training, the payload specialist was tasked with documenting the following: (1) the utility of the equipment; (2) his ability to acquire and track ground targets; (3) the level of detail he could discern; (4) the atmospheric conditions; and (5) other in-situ elements which contributed to or detracted from his ability to analyze targets. Special emphasis was placed on the utility of a manned platform for research and development of future spaceborne sensors. The results and lessons learned from Terra Scout will be addressed including human performance and equipment design issues.

Huth, John F.↗

NASA NTRS2019

Development of Human-Spacesuit Interaction Models

Today’s astronaut corps represents a wide range of various anthropometric dimensions. Accommodating this wide range of anthropometry and protecting for size variations in future crews, makes spacesuit sizing and fit a challenging and necessary aspect of suit development. Spacesuit fit can play an important role in performance, but a suit fit assessment, especially in dynamic postures, is difficult without extensive human-in-the-loop testing. One approach to address this issue is to model and simulate the human-spacesuit interactions for a target population early in the design process. The Anthropometry and Biomechanics Facility (ABF) at the NASA Johnson Space Center has been working to incorporate parametric human models based on 3D full-body scan data with spacesuit CAD models that can be driven by the user or imported motion capture data. An articulated spacesuit model combined with a poseable high-fidelity human model allows comparisons to be made between spacesuit capabilities and normal human ranges of motion. Furthermore, predictions can be made as to how a specific individual or population may perform in the suit from the perspective of reach and mobility. In this paper, we will present case study examples of reach, mobility, and fit analyses that can be done with these models and the methodology developed thus far. These models have the potential to become powerful tools for evaluating future spacesuit design architectures from the perspective of optimizing fit and performance.

Jarvis, Sarah↗

DOE OSTI2020

Veridical data science

Building and expanding on principles of statistics, machine learning, and scientific inquiry, we propose the predictability, computability, and stability (PCS) framework for veridical data science. Our framework, composed of both a workflow and documentation, aims to provide responsible, reliable, reproducible, and transparent results across the data science life cycle. The PCS workflow uses predictability as a reality check and considers the importance of computation in data collection/storage and algorithm design. It augments predictability and computability with an overarching stability principle. Stability expands on statistical uncertainty considerations to assess how human judgment calls impact data results through data and model/algorithm perturbations. As part of the PCS workflow, we develop PCS inference procedures, namely PCS perturbation intervals and PCS hypothesis testing, to investigate the stability of data results relative to problem formulation, data cleaning, modeling decisions, and interpretations. We illustrate PCS inference through neuroscience and genomics projects of our own and others. Moreover, we demonstrate its favorable performance over existing methods in terms of receiver operating characteristic (ROC) curves in high-dimensional, sparse linear model simulations, including a wide range of misspecified models. Finally, we propose PCS documentation based on R Markdown or Jupyter Notebook, with publicly available, reproducible codes and narratives to back up human choices made throughout an analysis. The PCS workflow and documentation are demonstrated in a genomics case study available on Zenodo.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1997

Analysis of strontium metabolism in humans on the basis of the Techa river data

Age and sex features of strontium metabolism have been analyzed on studies of the population residing on the banks of the Techa river which was contaminated by fission products during the years 1949-1956. Measurements of 90Sr body burden have been performed since 1974 using a whole-body counter, and these have made it possible to estimate age-specific long-term retention and elimination rates for men and women. Regarding the retention that correlated with the respective maturation ages, distinct sex differences have been observed for adolescents, whereas only postmenopausal women showed a sharp increase of their elimination rates. There were no differences concerning the reproductive ages. Our experimental findings have a clear physiological interpretation and can be used to develop metabolic models for bone-seeking radionuclides.

NASA Discipline Radiation Health↗

NASA NTRS2010

Human Perception of Ambiguous Inertial Motion Cues

Human daily activities on Earth involve motions that elicit both tilt and translation components of the head (i.e. gazing and locomotion). With otolith cues alone, tilt and translation can be ambiguous since both motions can potentially displace the otolithic membrane by the same magnitude and direction. Transitions between gravity environments (i.e. Earth, microgravity and lunar) have demonstrated to alter the functions of the vestibular system and exacerbate the ambiguity between tilt and translational motion cues. Symptoms of motion sickness and spatial disorientation can impair human performances during critical mission phases. Specifically, Space Shuttle landing records show that particular cases of tilt-translation illusions have impaired the performance of seasoned commanders. This sensorimotor condition is one of many operational risks that may have dire implications on future human space exploration missions. The neural strategy with which the human central nervous system distinguishes ambiguous inertial motion cues remains the subject of intense research. A prevailing theory in the neuroscience field proposes that the human brain is able to formulate a neural internal model of ambiguous motion cues such that tilt and translation components can be perceptually decomposed in order to elicit the appropriate bodily response. The present work uses this theory, known as the GIF resolution hypothesis, as the framework for experimental hypothesis. Specifically, two novel motion paradigms are employed to validate the neural capacity of ambiguous inertial motion decomposition in ground-based human subjects. The experimental setup involves the Tilt-Translation Sled at Neuroscience Laboratory of NASA JSC. This two degree-of-freedom motion system is able to tilt subjects in the pitch plane and translate the subject along the fore-aft axis. Perception data will be gathered through subject verbal reports. Preliminary analysis of perceptual data does not indicate that the GIF resolution hypothesis is completely valid for non-rotational periodic motions. Additionally, human perception of translation is impaired without visual or spatial reference. The performance of ground-base subjects in estimating tilt after brief training is comparable with that of crewmembers without training.

Zhang, Guan-Lu↗

NASA NTRSDate not supplied

Inflight Medical Conditions Risk – Overview and Strategic Approach

The risk of adverse health outcomes and decrements in performance due to inflight medical conditions is among NASA’s “red” risks for Mars missions, scored at the highest likelihood and consequence on the rating scale. Importantly, this risk encompasses all possible medical conditions that might occur in spaceflight. At thesame time, exploration spaceflight will have significant resource constraints (mass, power, volume, data, etc.) and supplying the full complement of medical capabilities available on Earth will be impossible. Inevitably, medical conditions will develop during a human Mars mission and having inadequate inflight capabilities will have a negative impact on the health and performance of the astronauts, leading to adverse crew and/or mission outcomes.

B D Easter↗

NASA NTRS2019

A Global Climatology of Extratropical Transition Part II: Statistical Performance of the Cyclone Phase Space

This study analyzes the differences between an objective, automated identification of tropical cyclones (TCs) that undergo extratropical transition (ET), and the designation of ET determined subjectively by human forecasters in best-track data in all basins globally. The objective identification of ET is based on the cyclone phase space (CPS), calculated from the Japanese 55-year Reanalysis (JRA-55) or the ECMWF Interim Reanalysis (ERA-Interim). The resulting classification into “ET storms” and “non-ET storms” underlies the global climatology of ET presented in Part I of this study. Here, the authors investigate how well the CPS classifications agree with those in the best-track records calculated from JRA-55 or from ERA-Interim data. According to F1 scores and Matthews correlation coefficients (MCCs), the classification of ET storms in the CPS agrees best with the best-track classification in the Western North Pacific (MCC > 0.7) and the North Atlantic (MCC > 0.5). In other basins, the correlation between the CPS classification and the best-track classification is only slightly higher than that of a random classification. The JRA-55 classification achieves higher performance scores than does the ERA-Interim classification, and the differences are statistically significant in all basins. The lower performance of ERA-Interim is mainly due to a higher false alarm rate, particularly in the Eastern North Pacific. Overall, the results show that while the CPS-based classifications are good enough to be useful for many purposes, there is almost certainly room for improvement – in the representation of the storms in reanalyses, in our objective metrics of ET, and in our scientific understanding of the ET process.

Melanie Bieli↗

NASA NTRS2006

NASA Crew Launch Vehicle Flight Test Process

In response to the Vision for Space Exploration, the National Aeronautics and Space Administration (NASA) has defined a new space exploration architecture to return humans to the Moon and to prepare for human exploration of Mars. One of the first new developments will be the Crew Launch Vehicle (CLV) , which will carry the Crew Exploration Vehicle (CEV) into Low Earth Orbit (LEO) to support International Space Station (ISS) missions and, later, to support lunar missions. As part of the CLV development, NASA will perform a series of CLV flight tests. The tests will provide data that will inform the engineering and design process and verify the flight hardware and software. In addition, the data gained from the flight tests will be used to certify the new CLV/CEV vehicle for human space flight. This paper will provide an overview of the CLV flight test process and details of the individual flight tests

Davis, Stephan R.↗

NASA NTRS2009

Predicting Pilot Performance in Off-Nominal Conditions: A Meta-Analysis and Model Validation

Pilot response to off-nominal (very rare) events represents a critical component to understanding the safety of next generation airspace technology and procedures. We describe a meta-analysis designed to integrate the existing data regarding pilot accuracy of detecting rare, unexpected events such as runway incursions in realistic flight simulations. Thirty-five studies were identified and pilot responses were categorized by expectancy, event location, and whether the pilot was flying with a highway-in-the-sky display. All three dichotomies produced large, significant effects on event miss rate. A model of human attention and noticing, N-SEEV, was then used to predict event noticing performance as a function of event salience and expectancy, and retinal eccentricity. Eccentricity is predicted from steady state scanning by the SEEV model of attention allocation. The model was used to predict miss rates for the expectancy, location and highway-in-the-sky (HITS) effects identified in the meta-analysis. The correlation between model-predicted results and data from the meta-analysis was 0.72.

Wickens, C.D.↗

NASA NTRS2007

POST2 End-To-End Descent and Landing Simulation for the Autonomous Landing and Hazard Avoidance Technology Project

The Program to Optimize Simulated Trajectories II (POST2) is used as a basis for an end-to-end descent and landing trajectory simulation that is essential in determining the design and performance capability of lunar descent and landing system models and lunar environment models for the Autonomous Landing and Hazard Avoidance Technology (ALHAT) project. This POST2-based ALHAT simulation provides descent and landing simulation capability by integrating lunar environment and lander system models (including terrain, sensor, guidance, navigation, and control models), along with the data necessary to design and operate a landing system for robotic, human, and cargo lunar-landing success. This paper presents the current and planned development and model validation of the POST2-based end-to-end trajectory simulation used for the testing, performance and evaluation of ALHAT project system and models.

Fisher, Jody l.↗

NASA NTRSDate not supplied

Computational Investigation of Retropropulsion Operating Environments with a GPU-Enabled Detached Eddy Simulation Approach

Human exploration of the surface of Mars will require an extended powered descent phase of flight, during which aerodynamic-propulsive interference effects can be significant. Characterization of these environments to enable implementation of this technology into a flight vehicle will rely heavily on computational simulation. This work advances the understanding of retropropulsion aerodynamics through application of a massively parallel detached eddy simulation approach on a GPU-accelerated computational framework, yielding data that are largely unachievable with conventional high-performance computing resources. This work includes time-dependent and time-averaged forces and moments on a conceptual, full-scale vehicle in environments and operating conditions relevant to human Mars exploration. Conditions are examined where the engine exhaust flow transitions between over-expanded and under-expanded flow structures, and flight operation will require the ability to maintain control of the vehicle during such a transition. These transitions occur as the vehicle decelerates, and as such, this investigation includes supersonic, transonic, and subsonic flight conditions. Options for vehicle control during powered flight include differential throttling of the engines. This paper provides an overview of the computational campaign, approach, and discussion of results in characterizing the resulting aerodynamics for differential throttling with retropropulsion in atmospheric environments.

EDL↗

DOE OSTI2018

UAVs for Radiological Monitoring: Determining Ideal Operational Parameters From GEANT4 Simulations - 18025

Owing in no small part to the enormous advances in radiation detector technology (size, sensitivity and spectral-resolution), there has been an increased drive and requirement to accurately map both the spatial extent and magnitude of radiological contamination at the greatest possible spatial resolutions. To undertake this, a range of different methods have been devised and include the use of cars and human, but also planes (and more recently) unmanned aerial vehicles (UAVs). However, critical to the remote sensing using such UAVs in contrast to ground-based sensing, is (i) the selection of the ideal operational parameters to attain the best on-ground resolution in addition to, (ii) understanding the correct normalisation procedures and other influences on results that surveys at these reduced altitudes might present. Resulting from earlier works, through employing combined modelling and experimental data, the optimal height for a UAV survey using the more realistic 'area' radioactive source term (opposed to an infinitely-small 'point-source') is determined to be approximately 5 m - suitably maximizing cross detector counts. At greater altitudes than this, the influence of variations in neighboring topology / topography and nearby structures are observed to be negligible. However, at this and further-reduced altitudes (where optimal count-rates exists), small height-related variations are observed to result, and impact considerably on the complexity of the data normalisation. Whilst not occurring as a tool to entirely replace ground-based surveys, UAV systems are able to perform in challenging or dangerous environments, inadvisable or problematic to send humans. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Data-centric framework for crystal structure identification in atomistic simulations using machine learning

Atomic-level modeling performed at large scales enables the investigation of mesoscale materials properties with atom-by-atom resolution. The spatial complexity of such cross-scale simulations renders them unsuitable for simple human visual inspection. Instead, specialized structure characterization techniques are required to aid interpretation. These have historically been challenging to construct, requiring significant intuition and effort. Here we propose an alternative framework for a fundamental structural characterization task: classifying atoms according to the crystal structure to which they belong. Our approach is data-centric and favors the employment of Machine Learning over heuristic rules of classification. A group of data-science tools and simple local descriptors of atomic structure are employed together with an efficient synthetic training set. We also introduce the first standard and publicly available benchmark data set for evaluation of algorithms for crystal-structure classification. Further, it is demonstrated that our data-centric framework outperforms all of the most popular heuristic methods—especially at high temperatures when lattices are the most distorted—while introducing a systematic route for generalization to new crystal structures. Moreover, through the use of outlier detection algorithms our approach is capable of discerning between amorphous atomic motifs (i.e., noncrystalline phases) and unknown crystal structures, making it uniquely suited for exploratory materials synthesis simulations.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Bone-marrow densitometry: Assessment of marrow space of human vertebrae by single energy high resolution-quantitative computed tomography

Purpose: Accurate noninvasive assessment of vertebral bone marrow fat fraction is important for diagnostic assessment of a variety of disorders and therapies known to affect marrow composition. Moreover, it provides a means to correct fat-induced bias of single energy quantitative computed tomography (QCT) based bone mineral density (BMD) measurements. The authors developed new segmentation and calibration methods to obtain quantitative surrogate measures of marrow-fat density in the axial skeleton. Methods: The authors developed and tested two high resolution-QCT (HR-QCT) based methods which permit segmentation of bone voids in between trabeculae hypothesizing that they are representative of bone marrow space. The methods permit calculation of marrow content in units of mineral equivalent marrow density (MeMD). The first method is based on global thresholding and peeling (GTP) to define a volume of interest away from the transition between trabecular bone and marrow. The second method, morphological filtering (MF), uses spherical elements of different radii (0.1–1.2 mm) and automatically places them in between trabeculae to identify regions with large trabecular interspace, the bone-void space. To determine their performance, data were compared ex vivo to high-resolution peripheral CT (HR-pQCT) images as the gold-standard. The performance of the methods was tested on a set of excised human vertebrae with intact bone marrow tissue representative of an elderly population with low BMD. Results: 86% (GTP) and 87% (MF) of the voxels identified as true marrow space on HR-pQCT images were correctly identified on HR-QCT images and thus these volumes of interest can be considered to be representative of true marrow space. Within this volume, MeMD was estimated with residual errors of 4.8 mg/cm{sup 3} corresponding to accuracy errors in fat fraction on the order of 5% both for GTP and MF methods. Conclusions: The GTP and MF methods on HR-QCT images permit noninvasive localization and densitometric assessment of marrow fat with residual accuracy errors sufficient to study disorders and therapies known to affect bone marrow composition. Additionally, the methods can be used to correct BMD for fat induced bias. Application and testing in vivo and in longitudinal studies are warranted to determine the clinical performance and value of these methods.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS2021

Lunar Surface Operations Modeling Using Digital Astronaut Simulation

During Apollo, crew members experienced a number of falls while engaging in extravehicular activity. The Digital Astronaut Simulation (DAS) expanded human biomechanics modeling tools to begin investigating this prospective mission safety and success challenge for the Artemis program. A core capability was developed to detect if a motion is dynamically feasible in a given gravitational environment. Fed by motion capture and mass properties data, this technology enables observation of whether tasks performed in 1G can be performed the same way in lunar gravity or if they require modifications.

Long Duration Health↗

NASA NTRS1992

Metabolic energy requirements for space flight

The international space community, including the USSR, Japan, Germany, the European Space Agency, and the US, is preparing for extended stays in space. Much of the research planned for space will be tended by humans, thus, maintaining adequate nutritional status during long stays in space has lately become an issue of much interest. Historically, it appears that minimum nutritional requirements are being met during stays in space. Thus far, crewmembers have been able to consume food adequate for maintaining nominal performance in microgravity. The physiological data obtained from ground-based and flight research that may enable us to understand the biochemical alterations that effect energy utilization and performance. Focus is on energy utilization during the Apollo lunar missions, Skylab's extended space lab missions, and Space Shuttle flights. Available data includes those recorded during intra- and extravehicular activities as well as during microgravity simulation (bed rest). Data on metabolism during flight and during bed rest are discussed, with a follow-up on human gastrointestinal function.

Lane, Helen W.↗

DOE OSTI2019

Improvement of prostate cancer detection combining a computer-aided diagnostic system with TRUS-MRI targeted biopsy

Purpose: To validate a novel consensus method, called target-in-target, combining human analysis of mpMRI with automated CAD system analysis, with the aim to increasing the prostate cancer detection rate of targeted biopsies. Methods: A cohort of 420 patients was enrolled and 253 patients were rolled out, due to exclusion criteria. 167 patients, underwent diagnostic 3T MpMRI. Two expert radiologists evaluated the exams adopting PI-RADSv2 and CAD system. When a CAD target overlapped with a radiologic one, we performed the biopsy in the overlapping area which we defined as target-in-target. Targeted TRUS-MRI fusion biopsy was performed in 63 patients with a total of 212 targets. The MRI data of all targets were quantitatively analyzed, and diagnostic findings were compared to pathologist’s biopsy reports. Results: CAD system diagnostic performance exhibited sensitivity and specificity scores of 55.2% and 74.1% [AUC = 0.63 (0.54 ÷ 0.71)] , respectively. Human readers achieved an AUC value, in ROC analysis, of 0.71 (0.63 ÷ 0.79). The target-in-target method provided a detection rate per targeted biopsy core of 81.8 % vs. a detection rate per targeted biopsy core of 68.6 % for pure PI-RADS based on target definitions. The higher per-core detection rate of the target-in-target approach was achieved irrespective of the presence of technical flaws and artifacts. Conclusions: A novel consensus method combining human reader evaluation with automated CAD system analysis of mpMRI to define prostate biopsy targets was shown to improve the detection rate per biopsy core of TRUS-MRI fusion biopsies. Results suggest that the combination of CAD system analysis and human reader evaluation is a winning strategy to improve targeted biopsy efficiency.

62 RADIOLOGY AND NUCLEAR MEDICINE↗