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DOE OSTI2016

Integrated sequence and immunology filovirus database at Los Alamos

The Ebola outbreak of 2013–15 infected more than 28,000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. We report that as this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

SU-F-19A-07: Is a Day30 Scan Necessary to Evaluate Activity-Based Regulatory Compliance in Permanent Interstitial Brachytherapy for Prostate Cancer?

Purpose: To evaluate the Medical Event (ME) criteria for I-125 prostate implants based on the assessment of post implant dosimetry on “Day0”/“Day30” imaging. The new ME criteria do not mandate a timeframe for this assessment. The compliance criteria are: more than 80% of the activity from the written directive for treatment site (TS) must be implanted inside TS, and doses to 1cc of either uninvolved rectum (D1-UR) or uninvolved bladder (D1-UB), or 2cc of other non-specified tissue (D2-UT) must be less than 150% of the planned dose. Methods: “Day0”/“Day30” post-implant analyses for 25 patients were evaluated. Treatment plans had a peripheral loading pattern with 2 core needles placed at least 10 mm away from urethra, with several seeds planned outside of the prostate for adequate target coverage. TS were a uniform 5 mm expansion of the prostate, except posteriorly (no expansion). Results: “Day0”/“Day30”analyses found no MEs. The relative changes for D1-UR, D1-UB, and D2-UT were (ranges): [−37.0, 38.2]%, [−96.5, 74.7]%, and [−41.2, 37.7]%. Furthermore, changes did not correlate with prostate volume changes of −18.7% [σ:16.0%, range:−60.5%, +6.4%]. These unfavorable changes did not lead to ME at “Day30” because these values were generally well below 150% at “Day0”. However, D2-UT dose values exceeded those for D1-UR and D1-UB at both “Day0”/“Day30”. Conclusion: The total activity was relatively insensitive to changes in target volume from “Day0” to ”Day30”. The dose metrics of interest, albeit susceptible to large, often unfavorable changes, remained less than the 150% threshold. Data from this study suggest that “Day0” can be used for the regulatory compliance evaluation. However, further evaluation at “Day30” is advisable if D2-UT is 110% or above (based on the largest D2-UT increase of 37.7% observed in this patient population). Future rigorous statistical analysis of a larger cohort will afford a refinement of this recommendation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

An open source knowledge graph ecosystem for the life sciences

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoint resources and abstraction algorithms), and benchmarks (e.g., prebuilt KGs). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 different large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2025

Magnetic structure evolution of LiFe 1- x Co x PO 4 olivines upon delithiation

We present a comprehensive study of the nuclear and magnetic structures of the mixed olivine solid solution series LiFe 1-x Co x PO 4 as well as their delithiated counterparts, for metal concentrations x = 0.2 - 0.6. Through neutron powder diffraction studies, we find that the LiFe 1-x Co x PO 4 series orders in the magnetic space group Pnma', consistent with their Li(Fe/Co)PO 4 parent structures. After chemical delithiation using peracetic acid, however, the removal of over 30% of the lithium from the lattice results in a transition from an A y -type to an A x -type antiferromagnetic structure. The magnetic space group consistent with A x antiferromagnetism was found to be Pn'm'a'. Interestingly, magnetic susceptibility measurements of both series reveal that delithiation increases the magnetic transition temperature, T N , from 50 K to 115 K. We find through analysis of the diffraction data that the unit cell parameters change linearly as a function of x; consequently, the exchange pathways between the Fe/Co magnetic cations are affected by the delithiation. Here, we discuss how exchange pathways, metal oxidation states, and d-orbital occupation all contribute to the observed magnetic symmetries and trends in T N in both series.

Antiferromagnet↗

DOE OSTI2015

Post-Service Examination of PWR Baffle Bolts, Part I. Examination and Test Plan

In support of extended service and current operations of the US nuclear reactor plants, the Oak Ridge National Laboratory (ORNL), through the Department of Energy (DOE), Light Water Reactor Sustainability (LWRS) Program, is coordinating with Ginna Nuclear Power Plant, The Westinghouse Electric Company, LLC, and ATI Consulting, the selective procurement of baffle bolts that were withdrawn from service in 2011 and currently stored on site at Ginna. The goal of this program is to perform detailed microstructural and mechanical property characterization of baffle former bolts following in-service exposures. This report outlines the selection criteria of the bolts and the techniques to be used in this study. The bolts available are the original alloy 347 steel fasteners used in holding the baffle plates to the baffle former structures within the lower portion of the pressurized water reactor vessel. Of the eleven possible bolts made available for this work, none were identified to have specific damage. The bolts, however, did show varying levels of breakaway torque required in their removal. The bolts available for this study varied in peak fluence (highest dose within the head of the bolt) between 9.9 and 27.8x10 21 n/cm 2 (E>1MeV). As no evidence for crack initiation was determined for the available bolts from preliminary visual examination, two bolts with the higher fluence values were selected for further post-irradiation examination. The two bolts showed different breakaway torque levels necessary in their removal. The information from these bolts will be integral to the LWRS program initiatives in evaluating end of life microstructure and properties. Furthermore, valuable data will be obtained that can be incorporated into model predictions of long-term irradiation behavior and compared to results obtained in high flux experimental reactor conditions. The two bolts selected for the ORNL study will be shipped to Westinghouse with bolts of interest to their collaborative efforts with the Electric Power Research Institute. Westinghouse will section the ORNL bolts into samples specified in this report and return them to ORNL. Samples will include bend bars for fracture toughness and crack propagation studies along with thin sections from which specimens for bend testing, subscale tensile and microstructural analysis can be obtained. Additional material from the high stress concentration region at the transition between the bolt head and shank will also be preserved to allow for further investigation of possible crack initiation sites.

42 ENGINEERING↗

DOE OSTI2021

Modeling Within-Host Dynamics of SARS-CoV-2 Infection: A Case Study in Ferrets

The pre-clinical development of antiviral agents involves experimental trials in animals and ferrets as an animal model for the study of SARS-CoV-2. Here, we used mathematical models and experimental data to characterize the within-host infection dynamics of SARS-CoV-2 in ferrets. We also performed a global sensitivity analysis of model parameters impacting the characteristics of the viral infection. We provide estimates of the viral dynamic parameters in ferrets, such as the infection rate, the virus production rate, the infectious virus proportion, the infected cell death rate, the virus clearance rate, as well as other related characteristics, including the basic reproduction number, pre-peak infectious viral growth rate, post-peak infectious viral decay rate, pre-peak infectious viral doubling time, post-peak infectious virus half-life, and the target cell loss in the respiratory tract. These parameters and indices are not significantly different between animals infected with viral strains isolated from the environment and isolated from human hosts, indicating a potential for transmission from fomites. While the infection period in ferrets is relatively short, the similarity observed between our results and previous results in humans supports that ferrets can be an appropriate animal model for SARS-CoV-2 dynamics-related studies, and our estimates provide helpful information for such studies.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1985

Fatigue life analysis of a turboprop reduction gearbox

A fatigue life analysis of the Allison T56/501 turboprop reduction gearbox was developed. The life and reliability of the gearbox was based on the lives and reliabilities of the main power train bearings and gears. The bearing and gear lives were determined using the Lundberg-Palmgren theory and a mission profile. The five planet bearing set had the shortest calculated life among the various gearbox components, which agreed with field experience where the planet bearing had the greatest incidences of failure. The analytical predictions of relative lives among the various bearings were in reasonable agreement with field experience. The predicted gearbox life was in excellent agreement with field data when the material life adjustment factors alone were used. The gearbox had a lower predicted life in comparison with field data when no life adjustment factors were used or when lubrication life adjustment factors were used either alone or in combination with the material factors.

Lewicki, D. G.↗

NASA NTRS1986

Fatigue life analysis of a turboprop reduction gearbox

Lewicki, D. G.↗

NASA NTRS1988

Development of the NASA/FLAGRO computer program

A preliminary version of a new computer program has been developed for calculating crack propagation in cyclically loaded structures. The new program, titled NASA/FLAGRO, has numerous enhanced features over previous programs used for safe life analysis on space systems. The essential features of the new program consist of modular design, promptive input using a cathode ray tube terminal, improved crack growth rate analytical methods, many new crack case solutions, and incorporation of user-defined files for material properties and fatigue spectrums. Also, five options made available in the program are to compute: (1) safe life of a part with a preexisting crack; (2) critical crack size for a specified stress level; (3) stress-intensity factor numerical values for making comparisons or checks of solutions; (4) least-squares fit of growth rate equations to crack growth rate data; and (5) the conversion of a versus N data to Delta K versus da/dN.

Forman, Royce G.↗

NASA NTRS1988

Independent Orbiter Assessment (IOA): CIL issues resolution report, volume 1

The results of the Independent Orbiter Assessment (IOA) of the Failure Modes and Effects Analysis (FMEA) and Critical Items List (CIL) are presented. This report contains IOA assessment worksheets showing resolution of outstanding IOA CIL issues that were summarized in the IOA FMEA/CIL Assessment Interim Report, dated 9 March 1988. Each assessment worksheet has been updated with CIL issue resolution and rationale. The NASA and Prime Contractor post 51-L FMEA/CIL documentation assessed is believed to be technically accurate and complete. No assessment issues remain that has safety implications. Volume 1 contain worksheets for the following sybsystems: Landing and Deceleration Subsystem; Purge, Vent and Drain Subsystem; Active Thermal Control and Life Support Systems; Crew Equipment Subsystem; Instrumentation Subsystem; Data Processing Subsystem; Atmospheric Revitalization Pressure Control Subsystem; Hydraulics and Water Spray Boiler Subsystem; and Mechanical Actuation Subsystem.

Urbanowicz, Kenneth J.↗

NASA NTRS2003

Clarifying Objectives and Results of Equivalent System Mass Analyses for Advanced Life Support

This paper discusses some of the analytical decisions that an investigator must make during the course of a life support system trade study. Equivalent System Mass (ESM) is often applied to evaluate trade study options in the Advanced Life Support (ALS) Program. ESM can be used to identify which of several options that meet all requirements are most likely to have lowest cost. It can also be used to identify which of the many interacting parts of a life support system have the greatest impact and sensitivity to assumptions. This paper summarizes recommendations made in the newly developed ALS ESM Guidelines Document and expands on some of the issues relating to trade studies that involve ESM. In particular, the following three points are expounded: 1) The importance of objectives: Analysis objectives drive the approach to any trade study, including identification of assumptions, selection of characteristics to compare in the analysis, and the most appropriate techniques for reflecting those characteristics. 2) The importance of results inferprefafion: The accuracy desired in the results depends upon the analysis objectives, whereas the realized accuracy is determined by the data quality and degree of detail in analysis methods. 3) The importance of analysis documentation: Documentation of assumptions and data modifications is critical for effective peer evaluation of any trade study. ESM results are analysis-specific and should always be reported in context, rather than as solitary values. For this reason, results reporting should be done with adequate rigor to allow for verification by other researchers.

Levri, Julie A.↗

NASA NTRS2010

Use of Modal Acoustic Emission to Monitor Damage Progression in Carbon Fiber/Epoxy and Implications for Composite Structures

Broad-band modal acoustic emission (AE) data was used to characterize micromechanical damage progression in uniaxial IM7 and T1000 carbon fiber-epoxy tows and an IM7 composite overwrapped pressure vessel (COPV) subjected to an intermittent load hold tensile stress profile known to activate the Felicity ratio (FR). Damage progression was followed by inspecting the Fast Fourier Transforms (FFTs) associated with acoustic emission events. FFT analysis revealed the occurrence of cooperative micromechanical damage events in a frequency range between 100 kHz and 1 MHz. Evidence was found for the existence of a universal damage parameter, referred to here as the critical Felicity ratio, or Felicity ratio at rupture (FR*), which had a value close to 0.96 for the tows and the COPV tested. The implications of using FR* to predict failure in carbon/epoxy composite materials and related composite components such as COPVs are discussed. Trends in the FFT data are also discussed; namely, the difference between the low and high energy events, the difference between early and late-life events, comparison of IM7 and T1000 damage progression, and lastly, the similarity of events occurring at the onset of significant acoustic emission used to calculate the FR.

Waller, J. M.↗

NASA NTRS2012

Technical Evaluation of the NASA Model for Cancer Risk to Astronauts Due to Space Radiation

At the request of NASA, the National Research Council's (NRC's) Committee for Evaluation of Space Radiation Cancer Risk Model1 reviewed a number of changes that NASA proposes to make to its model for estimating the risk of radiation-induced cancer in astronauts. The NASA model in current use was last updated in 2005, and the proposed model would incorporate recent research directed at improving the quantification and understanding of the health risks posed by the space radiation environment. NASA's proposed model is defined by the 2011 NASA report Space Radiation Cancer Risk Projections and Uncertainties--2010 . The committee's evaluation is based primarily on this source, which is referred to hereafter as the 2011 NASA report, with mention of specific sections or tables. The overall process for estimating cancer risks due to low linear energy transfer (LET) radiation exposure has been fully described in reports by a number of organizations. The approaches described in the reports from all of these expert groups are quite similar. NASA's proposed space radiation cancer risk assessment model calculates, as its main output, age- and gender-specific risk of exposure-induced death (REID) for use in the estimation of mission and astronaut-specific cancer risk. The model also calculates the associated uncertainties in REID. The general approach for estimating risk and uncertainty in the proposed model is broadly similar to that used for the current (2005) NASA model and is based on recommendations by the National Council on Radiation Protection and Measurements. However, NASA's proposed model has significant changes with respect to the following: the integration of new findings and methods into its components by taking into account newer epidemiological data and analyses, new radiobiological data indicating that quality factors differ for leukemia and solid cancers, an improved method for specifying quality factors in terms of radiation track structure concepts as opposed to the previous approach based on linear energy transfer, the development of a new solar particle event (SPE) model, and the updates to galactic cosmic ray (GCR) and shielding transport models. The newer epidemiological information includes updates to the cancer incidence rates from the life span study (LSS) of the Japanese atomic bomb survivors, transferred to the U.S. population and converted to cancer mortality rates from U.S. population statistics. In addition, the proposed model provides an alternative analysis applicable to lifetime never-smokers (NSs). Details of the uncertainty analysis in the model have also been updated and revised. NASA's proposed model and associated uncertainties are complex in their formulation and as such require a very clear and precise set of descriptions. The committee found the 2011 NASA report challenging to review largely because of the lack of clarity in the model descriptions and derivation of the various parameters used. The committee requested some clarifications from NASA throughout its review and was able to resolve many, but not all, of the ambiguities in the written description.

Source record↗

NASA NTRS1986

The fossil record of evolution: Analysis of extinction

There is increasing evidence that events in space have had direct effects on Earth history and on the history of life on Earth. Nowhere is this more evident than in mass extinction. The biosphere has undergone repeated devastation caused by relatively short-lived environmental stress, with species kill rates up to 80 and 95%. For five of the mass extinctions, geochemical or other evidence was reported suggesting large body impact as the cause of the environmental stress producing the extinctions. It was argued on statistical ground that the major extinction events are uniformly periodic in geological time. If it is true that large body impact is a principal cause of mass extinctions and if the periodicity is real, than a cosmic driving mechanism is inescapable. Paleontological data sets were developed which detail the ranges in geological time of about 4,000 families and 25,000 genera of fossil marine organisms. Analyses to date have concentrated on the most recent 250 million years. Associated with these studies are analyses of other aspects of Earth history which may have signatures indicative of extraterrestrial effects.

Raup, D. M.↗

DOE OSTI2014

Identification of Leakage Spectra from Neutron Activation in Glass/Cherenkov Detectors - Paper 96

Oak Ridge National Laboratory has developed a new detector system concept that can be deployed in major US cities to identify the leakage spectrum of a nuclear weapon detonation. The detector is based on a small piece of glass that has been doped with an element that has a high activation cross section and creates a radioactive activation product with a reasonable length half-life. The decay of the activation product(s) after exposure creates Cherenkov light which can propagate to a photomultiplier and can be turned into a count-rate signal. The signal from each glass in each detector in a city can be individually analyzed to determine the amount of activation products produced in the initial exposure. Several activation products can be determined in a single glass if the half-lives are not the same. With a known source location and a detailed 3D model of a city, neutron transport simulations can be made by using a library of known sources to predict the activation amounts each source would have made in the glass detectors. A simple comparison of the measured activation amounts and the predicted activation amounts can identify the source spectrum contained in the library that is the best match. Choosing dopants with a large range in the threshold energy for the activation reactions can help to differentiate the spectra in the library. The method of matching the measured activation amounts to the predicted activation amounts to identify the source spectrum is similar to the analysis used for the passive Activation Foil Integrated Detector System (AFIDS), also developed at Oak Ridge National Laboratory. In AFIDS, wires or foils of known mass and isotopic composition are deployed before and then collected after exposure. Counting gammas in a nearby laboratory determines the activation amounts. The glass/Cherenkov system is active - it uses a battery-powered detector to count flashes of Cherenkov light and to communicate its count rates to a remote location for further analysis. Work has been performed in several areas, including glass making, automated detection and communication systems and software tools for analysis of the signal and source spectrum identification. Bell and Boatner have developed phosphate glasses that incorporate elements with high capture cross sections, and Hayward has simulated the response with Geant4 and measured the response with isotopic gamma sources. This paper will focus on the software tools for determining the activation amounts from the Cherenkov count-rate signal and finding the best matching source spectrum. A test problem in an urban environment is used to demonstrate the potential of a spectrum identification system using neutron activation. The analysis methods developed to identify the neutron leakage spectra from Cherenkov light given off by neutron activation in doped glasses work well. The calculation used to unfold the count-rate information into the number of actual activation products uses robust algorithms that can also compute associated uncertainties. These uncertainties and the known uncertainties of the glass tube material compositions are incorporated into the matching analysis to determine which of the source spectra in the library best matches the measured activation data. Any measurement method used to identify a neutron source spectrum relies at some point on a comparison against known sources; no identification method is definitive. Detection systems measure some physical aspect of the source, not its serial number. Many systems measure the physical aspect to determine that the source has some property, and then leave it to experts to determine which potential sources share that property. The analysis system presented here incorporates the comparison into the analysis itself. The statistical tests show which of the known library sources match the measured data the best and whether that match is a good match. If the best match still does not fit the measured data well (a very high χ{sup 2} value), that indicates the true source is not one of the sources in the library. This is still valuable information for decision makers. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2018

Use of computational modeling combined with advanced visualization to develop strategies for the design of crop ideotypes to address food security

Sustainable crop production is a contributing factor to current and future food security. Innovative technologies are needed to design strategies that will achieve higher crop yields on less land and with fewer resources. Computational modeling coupled with advanced scientific visualization enables researchers to explore and interact with complex agriculture, nutrition, and climate data to predict how crops will respond to untested environments. These virtual observations and predictions can direct the development of crop ideotypes designed to meet future yield and nutritional demands. This review surveys modeling strategies for the development of crop ideotypes and scientific visualization technologies that have led to discoveries in “big data” analysis. Combined modeling and visualization approaches have been used to realistically simulate crops and to guide selection that immediately enhances crop quantity and quality under challenging environmental conditions. Lastly, this survey of current and developing technologies indicates that integrative modeling and advanced scientific visualization may help overcome challenges in agriculture and nutrition data as large-scale and multidimensional data become available in these fields.

3D crop modeling↗

DOE OSTI2021

Mapping the Path Forward to Next Generation Algal Technologies: Workshop on Understanding the Rules of Life and Complexity in Algal Systems

Algal technology offers enormous potential as a source of renewable biomass and bioproducts for fuels, biochemicals, nutrients, and numerous other applications. While tremendous opportunities exist, significant challenges are also present in harnessing and utilizing this valuable and potentially sustainable bioproduction platform. Funded by a joint partnership between the Bioenergy Technologies Office (BETO) at the Department of Energy (DOE) and the National Science Foundation (NSF), the recent virtual workshop, "Understanding the Rules of Life: Complexity in Algal Systems Workshop," was organized to bring together thought leaders from academia, national laboratories and other government agencies, and industry to identify key challenges and propose research strategies to overcome these barriers. Two parallel sessions were undertaken: 1) algae strain and toolkit development and 2) algal ecosystem and microbiome dynamics, in order to advance algae engineering and cultivation efforts. In each session, attendees discussed the most pressing challenges from the perspective of model systems and omics analysis. Themes such as genetic engineering toolboxes, translation from the laboratory to outdoor cultivation, functional genomics, metabolomics, algal ecology, consortial design, microbiome dynamics, mathematical models, and data analytics emerged from the discussion. Overall, this workshop has served to elucidate the key hurdles and many opportunities present as we continue to advance algal science and technology from the laboratory and into the commercial realm.

09 BIOMASS FUELS↗

DOE OSTI2016

Arabidopsis mitochondrial protein slow embryo development1 is essential for embryo development

The plant seeds formation are crucial parts in reproductive process in seed plants as well as food source for humans. Proper embryo development ensure viable seed formation. Here, we showed an Arabidopsis T-DNA insertion mutant slow embryo development1 (sed1) which exhibited retarded embryogenesis, led to aborted seeds. Embryo without SED1 developed slower compared to normal one and could be recognized at early globular stage by its white appearance. In later development stage, storage accumulated poorly with less protein and lipid body production. In vitro culture did not rescue albino embryo. SED1 encoded a protein targeted to mitochondria. Transmission electron microscopic analysis revealed that mitochondria developed abnormally, and more strikingly plastid failed to construct grana in time in sed1/sed1 embryo. These data indicated that SED1 is indispensable for embryogenesis in Arabidopsis, and the mitochondria may be involved in the regulation of many aspects of seed development. -- Highlights: •Arabidopsis SED1 is essential for embryo development. •The sed1 embryo accumulates less storage and has abnormal ultrastructure. •SED1 localizes to the mitochondrion.

60 APPLIED LIFE SCIENCES↗