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DOE OSTI2017

NERSC & JGI Seek Elusive Proteins for Gene Editing

A video just released by the Supercomputing 2017 (SC17) conference shows how biologists at UC Berkeley and the Joint Genome Institute (JGI) – a Department of Energy Office of Science User Facility – are using NERSC, the Office of Science’s primary supercomputing center, to identify a class of enzymes capable of editing out genes responsible for disease. This revolutionary work requires petaflops of computing power to sift through billions of DNA sequences in the JGI data portals to identify proteins like Cas9 that, combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), can “edit” a genome. First discovered by researchers at UC Berkeley, the CRISPR-Cas9 system has the power to permanently correct disease-causing mutations in cells, animal models, and eventually human patients to cure certain types of cancer, cardiovascular disease, sickle cell disease, and retinal degeneration. Since the CRISPR system was first identified in the early 2000s, it has become the most promising technology for treating genetic disease in humans and enabling plants to survive stress caused by pests and the environment. The annual SC17 conference will take place November 12-17 in Denver, Colorado. The over 12,000 attendees from academia, government and industry are leaders in researching and delivering high performance computing, networking, data storage and analysis in support of scientific discovery. http://sc17.supercomputing.org

Berkeley Lab, LBNL↗

DOE OSTI2017

NERSC & JGI Seek Elusive Proteins for Gene Editing

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2007

Integrating Human Factors into Crew Exploration Vehicle Design

With NASA's new Vision for Exploration to send humans beyond Earth orbit, it is critical to consider the human as a system that demands early and continuous user involvement, and an iterative prototype/test/redesign process. Addressing human-system interface issues early on can be very cost effective even cost reducing when performed early in the design and development cycle. To achieve this goal within Crew Exploration Vehicle (CEV) Project Office, human engineering (HE) team is formed. Key tasks are to apply HE requirements and guidelines to hardware/software, and provide HE design, analysis and evaluation of crew interfaces. Initial activities included many practice-orientated evaluations using low-fidelity CEV mock-ups. What follows is a description of such evaluations that focused on a HE requirement regarding Net Habitable Volume (NHV). NHV is defined as the total remaining pressurized volume available to on-orbit crew after accounting for the loss of volume due to deployed hardware and structural inefficiencies which decrease functional volume. The goal of the NHV evaluations was to develop requirements providing sufficient CEV NHV for crewmembers to live and perform tasks in support of mission goals. Efforts included development of a standard NHV calculation method using computer models and physical mockups, and crew/ stakeholder evaluations. Nine stakeholders and ten crewmembers participated in the unsuited evaluations. Six crewmembers also participated in a suited evaluation. The mock-up was outfitted with volumetric representation of sub-systems such as seats, and stowage bags. Thirteen scenarios were developed to represent mission/crew tasks and considered to be primary volume drivers (e.g., suit donning) for the CEV. Unsuited evaluations included a structured walkthrough of these tasks. Suited evaluations included timed donning of the existing launch and entry suit to simulate a contingency scenario followed by doffing/ stowing of the suits. All mockup evaluations were videotaped. Structured questionnaires were used to document user interface issues and volume impacts of layout configuration. Computer model and physical measures of the NHV agreed within 1 percent. This included measurement of the gross habitable volume, subtraction of intrusive volumes, and other non-habitable spaces. Calculation method developed was validated as a standard means of measuring NHV, and was recommended as a verification method for the NHV requirements. Evaluations confirmed that there was adequate volume for unsuited scenarios and suit donning/ doffing activity. Seats, suit design stowage and waste hygiene system noted to be critical volume drivers. The low-fidelity mock-up evaluations along with human modeling analysis generated discussions that will lead to high-level systems requirements and human-centered design decisions. This approach allowed HE requirements and operational concepts to evolve in parallel with engineering system concepts and design requirements. As the CEV design matures, these evaluations will continue and help with design decisions, and assessment, verification and validation of HE requirements.

Whitmore, Mihriban↗

NASA NTRS2015

Physics-Based Modeling of Meteor Entry and Breakup

A new research effort at NASA Ames Research Center has been initiated in Planetary Defense, which integrates the disciplines of planetary science, atmospheric entry physics, and physics-based risk assessment. This paper describes work within the new program and is focused on meteor entry and breakup. Over the last six decades significant effort was expended in the US and in Europe to understand meteor entry including ablation, fragmentation and airburst (if any) for various types of meteors ranging from stony to iron spectral types. These efforts have produced primarily empirical mathematical models based on observations. Weaknesses of these models, apart from their empiricism, are reliance on idealized shapes (spheres, cylinders, etc.) and simplified models for thermal response of meteoritic materials to aerodynamic and radiative heating. Furthermore, the fragmentation and energy release of meteors (airburst) is poorly understood. On the other hand, flight of human-made atmospheric entry capsules is well understood. The capsules and their requisite heatshields are designed and margined to survive entry. However, the highest speed Earth entry for capsules is less than 13 km/s (Stardust). Furthermore, Earth entry capsules have never exceeded diameters of 5 m, nor have their peak aerothermal environments exceeded 0.3 atm and 1 kW/cm2. The aims of the current work are: (i) to define the aerothermal environments for objects with entry velocities from 13 to greater than 20 km/s; (ii) to explore various hypotheses of fragmentation and airburst of stony meteors in the near term; (iii) to explore the possibility of performing relevant ground-based tests to verify candidate hypotheses; and (iv) to quantify the energy released in airbursts. The results of the new simulations will be used to anchor said risk assessment analyses. With these aims in mind, state-of-the-art entry capsule design tools are being extended for meteor entries. We describe: (i) applications of current simulation tools to spherical geometries of diameters ranging from 1 to 100 m for an entry velocity of 20 km/s and stagnation pressures ranging from 1 to 100 atm; (ii) the influence of shape and departure of heating environment predictions from those for a simple spherical geometry; (iii) assessment of thermal response models for silica subject to intense radiation; and (iv) results for porosity-driven gross fragmentation of meteors, idealized as a collection of smaller objects. Lessons learned from these simulations will be used to help understand the Chelyabinsk meteor entry up to its first point of fragmentation.

Aerothermodynamics↗

NASA NTRS2014

Use of DES Modeling for Determining Launch Availability for SLS

(1) NASA is developing a new heavy lift launch system for human and scientific exploration beyond Earth orbit comprising of the Space Launch System (SLS), Orion Multi-Purpose Crew Vehicle (MPCV), and Ground Systems Development and Operations (GSDO); (2) The desire of the system is to ensure a high confidence of successfully launching the exploration missions, especially those that require multiple launches, have a narrow Earth departure window, and high investment costs; and (3) This presentation discusses the process used by a Cross-Program team to develop the Exploration Systems Development (ESD) Launch Availability (LA) Technical Performance Measure (TPM) and allocate it to each of the Programs through the use of Discrete Event Simulations (DES).

Watson, Michael↗

NASA NTRS1992

Human performance in the modern cockpit

This panel was organized by the Aerospace Human Factors Committee to illustrate behavioral research on the perceptual, cognitive, and group processes that determine crew effectiveness in modern cockpits. Crew reactions to the introduction of highly automated systems in the cockpit will be reported on. Automation can improve operational capabilities and efficiency and can reduce some types of human error, but may also introduce entirely new opportunities for error. The problem solving and decision making strategies used by crews led by captains with various personality profiles will be discussed. Also presented will be computational approaches to modeling the cognitive demands of cockpit operations and the cognitive capabilities and limitations of crew members. Factors contributing to aircrew deviations from standard operating procedures and misuse of checklist, often leading to violations, incidents, or accidents will be examined. The mechanisms of visual perception pilots use in aircraft control and the implications of these mechanisms for effective design of visual displays will be discussed.

Dismukes, R. K.↗

DOE OSTI2023

Low-temperature oxidation pathways are critical to thermal incineration of PFAS-laden materials

With growing desire to destroy per- and poly-fluoroalkyl substances (PFAS) now known to be detrimental to human health, a sound understanding of fluorocarbon combustion chemistry is important to efficient thermal destruction within incinerators. While most fluorocarbon combustion models and the sets of reactions contained within them were originally developed for the high temperatures encountered in flame suppression applications, they have often been used to assess PFAS destruction in incinerators, which emphasize a lower range of temperatures. We present results that demonstrate that low-temperature fluorocarbon oxidation pathways—not yet known to play a role in fluorocarbon combustion—impact key incinerator performance metrics, including: PFAS surrogate mole fractions, products of incomplete destruction, and waste destruction efficiencies. The results further point to the utility of NO as a potential additive. The present results show the influence of these pathways for CF 3 O 2 , for which some data are available, but analogous pathways would also occur for other fluoroalkylperoxy radicals, for which little is known. Furthermore, the results demonstrate the need for future work to identify and characterize low-temperature pathways more generally, consider such pathways in kinetic model development, and experimentally probe intermediate temperature conditions to better understand, design, and control thermal destruction technologies for improved PFAS management.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Effects of the distribution and evolution of the coefficient of friction along a fault on the assessment of the seismic activity associated with a hypothetical industrial-scale geologic CO 2 sequestration operation

Carbon capture and storage (CCS) in geological formations is considered as a promising option that could limit CO 2 emissions from human activities into the atmosphere. However, there is a risk that pressure buildup inside the storage formation can induce slip along preexisting faults and create seismic event felt by the population. To prevent this to happen a geomechanical fault stability analysis should be performed, considering uncertainties of input parameters. In this paper, we investigate how the distribution of the coefficient of friction and the applied frictional law could influence the assessment of fault stability and the characteristics of potential injection-induced seismic events. Our modelling study is based on a hypothetical industrial-scale carbon sequestration project located in the Southern San Joaquin Basin in California, USA, where the stability on a major (25 km long) fault that bounds the sequestration site is assessed during 50 years of CO 2 injection. We conduct nine simulations in which the distributions of the coefficients of static and dynamic friction are changed to simulate a hardening and softening phase before and during rupture. Here, our main findings are: (i) variations in friction along the fault have an important effect on the predicted seismic activity, with maximum magnitude ranging from 1.88 to 5.88 and number of seismic events ranging from 338 to 3272; (ii) the extreme values of the coefficient of friction (lowest and highest) present along the rupture area control how much stress is accumulated before rupture; and (iii) an argillaceous caprock can prevent the development of large magnitude seismic events but favor the occurrence of a large number of smaller events.

58 GEOSCIENCES↗

DOE OSTI2017

Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A

S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzyme turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Sneezing and asymptomatic virus transmission

The novel coronavirus disease (COVID-19) spread pattern continues to show that geographical barriers alone cannot contain a virus. Asymptomatic carriers play a critical role in the nature of this virus quickly escalating into a global pandemic. Asymptomatic carriers may transmit the virus unintentionally through sporadic sneezing. A novel Computational Fluid Dynamics (CFD) approach has been proposed with a realistic modeling of a human sneeze achieved by the combination of state-of-the-art experimental and numerical methods. This modeling approach may be suitable for future engineering analyses aimed at reshaping public spaces and common areas, with the main objective to accurately predict the spread of aerosol and droplets that may contain pathogens. This study shows that the biomechanics of a human sneeze, including complex muscle contractions and relaxations, can be accurately modeled by the angular head motion and the dynamic pressure response during sneezing. These have been considered as the human factors and were implemented in the CFD simulation by imposing a momentum source term to the coupled Eulerian–Lagrangian momentum equations. The momentum source was modeled by the measured dynamic pressure response in conjunction with the angular head motion. This approach eliminated the need to create an ad hoc set of inlet boundary conditions. With this proposed technique, it is easier to add multiple fixed and/or moving sources of sneezes in complex computational domains. Additionally, extensive sensitivity analyses based on different environmental conditions were performed, and their impact was described in terms of potential virus spread.

42 ENGINEERING↗

DOE OSTI2018

Imaging in Diagnostic Nuclear Medicine

Single-photon emission computed tomography (SPECT) and positron emission tomography (PET) are modern methods for visualization in diagnostic nuclear medicine. SPECT is known as a workhorse in cardiology, and PET is the gold standard in oncology. The development of nuclear medicine is provided by cooperation of physicists, mathematicians, biologists, medical doctors, and radio-chemists. In spite of extensive clinical applications, several problems may lead to false diagnoses. In particular, the correction of attenuation of gamma radiation in human organs must be taken into account. For interpretation and evaluation of such an effect on the clinical results, we perform physico-mathematical simulation of the SPECT diagnostics in cardiology in the absence and presence of the correction of attenuation. A brief review of the state-of-the art is presented. The simulation employs the first Russian anthropomorphic mathematical phantom that describes the distribution of radio-pharmacological agent ({sup 99m }Tc-methoxyisobutylisonitrile) in chest organs of a typical male patient. A model for calculation of raw images is developed with allowance for attenuation of radiation in biological tissues and the effect of collimator and detector. The results of the proposed models and calculated images are compared with clinical images obtained at the Meshalkin Institute of Circulation Pathology (Novosibirsk) and Myasnikov Institute of Clinical Cardiology (Moscow). Statistical algorithms are developed for the solution of the inverse problem of image reconstruction based on the entropy principle. The clinical and physico-mathematical approaches are compared in the evaluation of the effect of correction on the quality of reconstructed images of the left ventricle of myocardium.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2023

Few-shot leaf segmentation

In this work, we use few-shot learning to segment the body and vein architecture of Populus trichocarpa leaves from high-resolution scans obtained in the UC Davis common garden. Leaf and vein segmentation are formulated as separate tasks, in which convolutional neural networks (CNNs) are used to iteratively expand partial segmentations until reaching stopping criteria. Our leaf and vein segmentation approaches use just 50 and 8 manually traced images for training, respectively, and are applied to a set of 2,634 top and bottom leaf scans. We show that both methods achieve high segmentation accuracy, in some cases exceeding even human-level segmentation. The leaf and vein segmentations are subsequently used to extract 68 morphological traits using traditional open-source image processing tools, which are validated using real-world physical measurements. For a biological perspective, we perform a genome-wide association study using the "vein density" trait to discover novel genetic architectures associated with multiple physiological processes relating to leaf development and function. In addition to sharing all of the few-shot learning code, we are releasing all images, manual segmentations, model predictions, 68 extracted leaf phenotypes, and a new set of SNPs called against the v4 P. trichocarpa genome for 1,419 genotypes.

Lagergren, John [Oak Ridge National Lab. (ORNL), O↗

DOE OSTI2026

Satellite Embedding-Based Population Imputation for Areas with Missing Building Footprint Data: A Computer Vision-Based Approach

High-resolution population modeling is important for supporting effective decision-making across diverse sectors. LandScan Mosaic generates population estimates at the level of individual buildings and aggregates them to 3 arc-second grids, and this approach performs well in regions where building footprint data are comprehensive and reliable. However, large portions of the globe still suffer from incomplete, sparse, or entirely missing building stock datasets, creating a structural limitation for strictly building-based population models. To address this research gap, this study proposes a computer vision-based framework that employs Google Earth Engine satellite embeddings and UNet, which allows us to directly impute grid-level population estimates in building-data-deficient areas. Applied to Taiwan as a case study, the framework achieved strong predictive performance with R$^{2}$ of 0.89, RMSE of 18.70, and MAE of 8.41, outperforming traditional machine learning approaches. Notably, the proposed framework effectively addressed building false-positive errors inherent in Global Human Settlement Layer (GHSL) data, correctly identifying uninhabited areas that were erroneously classified as populated. The framework also offers significant advantages for global population mapping, particularly in terms of scalability and temporal consistency, thereby extending the coverage and accuracy of high-resolution population products in data-scarce regions worldwide. Urban planners, decision makers, and related stakeholders can obtain granular population distributions to support more accurate and targeted infrastructure investment, service delivery, resource allocation, and risk assessment decisions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Deep Gaze Velocity Analysis During Mammographic Reading for Biometric Identification of Radiologists

Several studies have confirmed that the gaze velocity of the human eye can be utilized as a behavioral biometric or personalized biomarker. In this study, we leverage the local feature representation capacity of convolutional neural networks (CNNs) for eye gaze velocity analysis as the basis for biometric identification of radiologists performing breast cancer screening. Using gaze data collected from 10 radiologists reading 100 mammograms of various diagnoses, we compared the performance of a CNN-based classification algorithm with two deep learning classifiers, deep neural network and deep belief network, and a previously presented hidden Markov model classifier. The study showed that the CNN classifier is superior compared to alternative classification methods based on macro F1-scores derived from 10-fold cross-validation experiments. Our results further support the efficacy of eye gaze velocity as a biometric identifier of medical imaging experts.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2014

IAA Space Exploration Conference

The NASA Human Health and Performance Center (NHHPC) was established in October 2010 to facilitate development of partnerships and collaborative projects in human health and performance with a focus on Earthspace benefits. The membership, which now stands at over 135 members from around the world, was developed to span the government, academic, industry and non-profit sectors, making the NHHPC a global convener in human health and performance. International members include organizations from Germany, the United Kingdom, Spain, Japan, South Africa, and India. The virtual center facilitates sharing of best practices and development of collaborative opportunities through a variety of vehicles, including annual in-person workshops, Innovation Lecture Series and Member to Member Connect webcasts, quarterly electronic newsletters, web postings, and electronic member announcements. The NHHPC has conducted four workshops leading to several collaborative projects between members, with the most recent workshop held focusing on new organizational business models for accelerating innovation. This short paper will discuss how the NHHPC facilitates partnerships and the collaborative research and technology developments projects with applications to both the NASA mission and life on Earth.

Davis, Jeffrey R.↗

NASA NTRS2021

The Current State and Future of the Former Central Nervous System Risk Managed by Space Radiation Element Part of NASA’s Human Research Program

Historically, the Space Radiation Element, as part of the NASA Human Research Program, was responsible for the scientific strategy and funding of research focused on characterizing and mitigating the effects of space radiation exposure on the central nervous system (CNS). During the past few of years, there have been two major changes that have affected the management of the science associated with the CNS risk. The first major change was the integration of several related risks: CNS (C), Behavioral medicine (B), and sensorimotor (S) to be managed as an integrated effort called CBS. CBS was formed to accelerate research on combined spaceflight stressors, specifically space radiation, microgravity, isolation, and confinement. CBS was managed by Human Factors and Behavioral Performance (HFBP) with support and inputs from Space Radiation as well as Human Health Countermeasures. Secondly, and more recently, the CNS risk was absorbed by the behavioral medicine risk currently also held by HFPB. As a result, the gaps associated with CNS were removed and aspects of them are represented in the BMED gaps (link). However, due to recent changes in element leadership, budget, and timeline, extensive restructuring of CBS is in progress. In addition, in an effort to harmonize datasets to be used in modelling efforts, an Animal Standardization TIM was held in June 2021 to standardize the type of behavioral and cognitive tasks as well as experimental set-ups. This presentation is an effort to communicate with the radiation research community concerning the strategy, management, and future of the former central nervous system risk and the role of the Space Radiation Element.

central nervous system↗

NASA NTRSDate not supplied

The Current State and Future of the Former Central Nervous System Risk Managed by Space Radiation Element Part of NASA’s Human Research Program

Historically, the Space Radiation Element, as part of the NASA Human Research Program, was responsible for the scientific strategy and funding of research focused on characterizing and mitigating the effects of space radiation exposure on the central nervous system (CNS). During the past few years, there have been two major changes that have affected the management of the science associated with the CNS risk. The first major change was the integration of several related risks: CNS (C), behavioral medicine (B), and sensorimotor (S) to be managed as an integrated effort called CBS. CBS was formed to accelerate research on combined spaceflight stressors, specifically space radiation, microgravity, isolation, and confinement. CBS was managed by Human Factors and Behavioral Performance (HFBP) with support and inputs from Space Radiation as well as Human Health Countermeasures. Secondly, and more recently, the CNS risk was absorbed by the behavioral medicine risk currently also held by HFPB. As a result, the gaps associated with CNS were removed and aspects of them are represented in the BMED gaps (link). However, due to recent changes in element leadership, budget, and timeline, extensive restructuring of CBS is in progress. In addition, in an effort to harmonize datasets to be used in modeling efforts, an Animal Standardization TIM was held in June 2021 to standardize the type of behavioral and cognitive tasks as well as experimental set-ups used in animal models of future funded research. This presentation is an effort to communicate with the radiation research community concerning the strategy, management, and future of the former central nervous system risk and the role of the Space Radiation Element.

Janice A Zawaski↗

NASA NTRSDate not supplied

Development of the Artemis Distributed Simulation FOMs

The National Aeronautics and Space Administration (NASA) is formulating and developing the Artemis Program, a collaboration with domestic commercial and international partners that will establish a long term human presence on the Moon and extend human exploration beyond the Earth-Moon system ahead of exploring Mars. These Artemis partners are developing a portfolio of space and surface systems to support human missions to the lunar surface and beyond. The Artemis systems will provide the mobility, habitation, and logistics infrastructure that will support human exploration and foster robust scientific investigations. Each partner will contribute one or more elements to the Artemis Program with NASA having the overarching responsibility for defining the Artemis architecture and guiding the integration of this complex system of space systems. To successfully accomplish this audacious task, NASA will rely on the development and execution of many complex models and simulations. Many of these simulations will be provided by the Artemis partners. While each of these simulations will provide important insight into the characteristics and performance of an associated system, individually they will not provide insight into the integrated performance of the architecture and the system of systems working in concert to execute a given Artemis mission. To address this need, NASA is developing a distributed simulation capability called the Artemis Distributed Simulation (ADS). ADS’s distributed nature supports the complex aggregation of constituent Artemis element simulations. Artemis partner simulations will be able to join into an ADS-based distributed simulation and interact with other Artemis element simulations while limiting the exposure of proprietary designs and data. ADS is defining a distributed simulation capability built on international simulation interoperability standards, specifically the High Level Architecture (HLA) and the Space Reference Federation Object Model (SpaceFOM). While HLA and SpaceFOM provide the substantive necessary technology basis for ADS, additional common datatypes, message definitions, and execution protocols are required. These extensions constitute the ADS Federation Object Model (FOM). This paper describes the fundamental architectural elements of ADS and the FOM extensions needed to support the complex nature of the Artemis Program. This includes the examination of the ADS FOM modules, ADS base datatypes, ADS SpaceFOM Object Class extensions, new ADS Object Classes, and new ADS Interaction Classes.

HLA↗