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All sources NASA NTRS DOE OSTI

DOE OSTI2018

Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

Antibiotic resistance in pathogens is extensively studied, and yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leveraged genomes from metagenomes to investigate how genes of the premature infant gut resistome correspond to the ability of bacteria to survive under certain environmental and clinical conditions. We found that formula feeding impacts the resistome. Random forest models corroborated by statistical tests revealed that the gut resistome of formula-fed infants is enriched in class D beta-lactamase genes. Interestingly, Clostridium difficile strains harboring this gene are at higher abundance in formula-fed infants than C. difficile strains lacking this gene. Organisms with genes for major facilitator superfamily drug efflux pumps have higher replication rates under all conditions, even in the absence of antibiotic therapy. Using a machine learning approach, we identified genes that are predictive of an organism’s direction of change in relative abundance after administration of vancomycin and cephalosporin antibiotics. The most accurate results were obtained by reducing annotated genomic data to five principal components classified by boosted decision trees. Among the genes involved in predicting whether an organism increased in relative abundance after treatment are those that encode subclass B2 beta-lactamases and transcriptional regulators of vancomycin resistance. This demonstrates that machine learning applied to genome-resolved metagenomics data can identify key genes for survival after antibiotics treatment and predict how organisms in the gut microbiome will respond to antibiotic administration.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1995

Replicator for characterization of cirrus and polar stratospheric cloud particles

A formvar replicator for installation in an aircraft pod has been designed, built, and flight tested on the NASA DC-8. The system incorporates a deicing capability (which can be pressure activated) to enable climb out through icing situations prior to deployment. The system can be operated at preselected speeds such that data can be recorded over a period of one to ten hours on 200 ft of 16mm film. A x2 speed control can be used during flight. Capability exists for detection of chemical constituents by appropriate doping of the formvar solution. An article entitled 'Measurements of ice particles in tropical cirrus anvils: importance in radiation balance' is attached as appendix A.

Hallett, John↗

NASA NTRS1995

Replicator for characterization of cirrus and polar stratospheric cloud particles

A formvar replicator for installation in an aircraft pod has been designed, built, and flight tested on the NASA DC-8. The system incorporates a deicing capability (which can be pressure activated) to enable climb out through icing situations prior to deployment. The system can be operated at preselected speeds such that data can be recorded over a period of 1 to ten hours on 200 ft of 16mm film. A x2 speed control can be used during flight. Capability exists for detection of chemical constituents by appropriate doping of formvar solution.

Hallett, John↗

NASA NTRSDate not supplied

Low-Earth Orbit Flight Test of an Inflatable Decelerator (LOFTID) Aeroshell Performance

On November 10, 2022, NASA launched the Low-earth Orbit Flight Test of an Inflatable Decelerator (LOFTID) reentry vehicle (RV)as a secondary payload mounted inside the launch vehicle (LV) adaptor on an Atlas V 401 out of the Vandenburg Space Force Base (VSFB). The primary payload, Joint Polar Satellite System-2 (JPSS-2), was delivered successfully to a sun-synchronous trajectory shortly after launch, at which point the Centaur upper stage performed a burn to de-orbit the system. Once on the desired trajectory to enter the atmosphere, the top of the payload adaptor was ejected to expose the LOFTID RV. Next, the LOFTID aeroshell, a Hypersonic Inflatable Aerodynamic Decelerator (HIAD), was deployed and inflated without issue. The Centaur pointed the LOFTID RV to the desired attitude to enter the atmosphere, spun the assembly to three rpm, separated the LOFTID RV, and finally performed a divert maneuver to prevent the Centaur from re-contacting the LOFTID RV after atmospheric entry. The LOFTID RV maintained the design attitude and spin rate from separation to atmospheric entry, a duration of roughly 30 minutes, demonstrating the aeroshell did not experience any energy damping from inflatable structure flexibility. The LOFTID RV entered the atmosphere over Alaska at >8km/sec and decelerated as designed, demonstrating aerodynamically stable flight from hypersonic entry through subsonic parachute deployment. On-board visible-spectrum cameras captured the physical response of the heatshield through all phases of flight. Co-located infrared cameras captured the temperature distribution of the aftside of the heat shield anchored to a distribution of thermocouples on the inflatable structure (IS) in the field of view. Thermocouples were also embedded in the forward side of the aeroshell both in the Flexible Thermal Protection System (FTPS) as well as the IS. This paper will document aeroshell’s response to the atmospheric entry. The visible-spectrum cameras captured mechanical response of the deployable aeroshell to the loads encountered in the different phases of entry. Events seen on the visible-spectrum cameras correlate with the measurements of the load cell pins on webbing elements that attach the aeroshell to the centerbody structure. Thermocouple data captured verifies the aerothermal response of the aeroshell was in-kind with pre-flight analysis predictions although somewhat lower in most locations. This data will enable enhancement of HIAD predictive capability. Post-flight inspection of the aeroshell after splashdown and ocean recovery shows that all the aeroshell materials and manufacturing techniques developed over the past two decades of HIAD technology development performed as expected at large scale, a scale which cannot be replicated in ground test facilities. The LOFTID RV remained high in the water after touching down under parachute, and maintained buoyancy and integrity for the hour it took to position the recovery vessel near the vehicle after splashdown. There was no indication the HIAD would have experienced an issue maintaining buoyancy for many more hours after water impact as the component maintained adequate inflation pressure more than 24 hours after water extraction with no additional inflation gas in tanks, as the inflation gas remaining in the tank was purposely vented prior to splashdown.

HIAD↗

NASA NTRS2012

Optical Signature Analysis of Tumbling Rocket Bodies via Laboratory Measurements

The NASA Orbital Debris Program Office has acquired telescopic lightcurve data on massive intact objects, specifically spent rocket bodies, in order to ascertain tumble rates in support of the Active Debris Removal (ADR) task to help remediate the LEO environment. Rotation rates are needed to plan and develop proximity operations for potential future ADR operations. To better characterize and model optical data acquired from ground-based telescopes, the Optical Measurements Center (OMC) at NASA/JSC emulates illumination conditions in space using equipment and techniques that parallel telescopic observations and source-target-sensor orientations. The OMC employs a 75-watt Xenon arc lamp as a solar simulator, an SBIG CCD camera with standard Johnson/Bessel filters, and a robotic arm to simulate an object's position and rotation. The light source is mounted on a rotary arm, allowing access any phase angle between 0 -- 360 degrees. The OMC does not attempt to replicate the rotation rates, but focuses on how an object is rotating as seen from multiple phase angles. The two targets studied are scaled (1:48), SL-8 Cosmos 3M second stages. The first target is painted in the standard government "gray" scheme and the second target is primary white, as used for commercial missions. This paper summarizes results of the two scaled rocket bodies, each rotated about two primary axes: (a) a spin-stabilized rotation and (b) an end-over-end rotation. The two rotation states are being investigated as a basis for possible spin states of rocket bodies, beginning with simple spin states about the two primary axes. The data will be used to create a database of potential spin states for future works to convolve with more complex spin states. The optical signatures will be presented for specific phase angles for each rocket body and shown in conjunction with acquired optical data from multiple telescope sources.

Cowardin, H.↗

DOE OSTI2018

HMGB1 mediates HAdV-7 infection-induced pulmonary inflammation in mice

Highlights: • HMGB1 was associated with HAdV-7-induced lung inflammation and pathology. • HMGB1 promoted HAdV-7 replication and bound to TLR-4, TLR-9, and RAGE receptors. • Receptor engagement by HMGB1 activated NF-κB, inducing inflammatory mediators. • Thus, HMGB1 could serve as a therapeutic target in HAdV-7 infection. Human adenovirus (HAdV) is a common respiratory pathogen in children, with no safe and effective treatment currently available. HAdV type 7 (HAdV-7), in particular, causes severe pediatric pneumonia with a high incidence of sequelae and mortality. Clinical data and animal experiments suggest that HAdV-7-induced pneumonia promotes cell necrosis, releasing a large number of inflammatory mediators. In recent years, the high mobility group box-1 (HMGB1) protein, released by necrotic cells, has been shown to play important roles in several viral infections. Here, we show that HMGB1 levels gradually increased in the media supernatants of HAdV-7 infected A549 cells, starting at 12 h post-infection. In vivo, HMGB1 levels in BALF and mRNA levels in lung tissues significantly increased after 3 days of HAdV-7 infection. Among the HMGB1 receptor genes, TLR-4 and TLR-9 expression increased, and so did the receptor for advanced glycation end-products (RAGE). Interestingly, NF-κB levels also increased concomitantly. Conversely, when HMGB1 was blocked, the pathological scores from lung tissues, inflammatory mediator levels, and viral copy number all were reduced significantly; in addition, HMGB1-related signaling pathway molecules, namely TLR-4, TLR-9, RAGE, and NF-κB were also reduced. We conclude that HMGB1 promotes HAdV-7 replication and signals through TLR-4, TLR-9, and RAGE receptors to activate NF-κB, stimulating the release of inflammatory mediators and contributing to adenoviral pathology. Thus, HMGB1 could be used as a therapeutic target in HAdV-7 infection.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

TRIMe7-CypA, an alternative splicing isoform of TRIMCyp in rhesus macaque, negatively modulates TRIM5α activity

Highlights: • TRIMe7-CypA expresses in rhesus and pig-tailed, but not long-tailed macaques. • TRIMe7-CypA does not show the restriction to a HIV-GFP report virus in vitro. • It acts as a negative modulator to TRIM5α likely by competitive inhibition. - Abstract: The existence of innate, host-specific restriction factors is a major obstacle to the development of nonhuman primate models for AIDS studies, and TRIM5α is one of the most important of these restriction factors. In recent years, a TRIM5 chimeric gene that was retrotransposed by a cyclophilin A (CypA) cDNA was identified in certain macaque species. The TRIM5α-CypA fusion protein, TRIMCyp, which was expressed in these monkeys, had lost its restriction ability toward HIV-1. We previously found that TRIMe7-CypA, an alternative splicing isoform of the TRIMCyp transcripts, was expressed in pig-tailed and rhesus macaques but absent in long-tailed macaques. In this study, the anti-HIV-1 activity of TRIMe7-CypA in the rhesus macaque (RhTRIMe7-CypA) was investigated. The over-expression of RhTRIMe7-CypA in CrFK, HeLa and HEK293T cells did not restrict the infection or replication of an HIV-1-GFP reporter virus in these cells. As a positive control, rhesus (rh)TRIM5α strongly inhibited the reporter virus. Intriguingly, the anti-HIV-1 activity of RhTRIM5α was significantly reduced in a dose-dependent manner by the co-repression of RhTRIMe7-CypA. Our data indicate that although the RhTRIMe7-CypA isoform does not appear to restrict HIV-1, it may act as a negative modulator of TRIM family proteins, presumably by competitive inhibition.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Accurate model annotation of a near-atomic resolution cryo-EM map

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo- EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Remote Sensor Design for Visual Recognition with Convolutional Neural Networks

While deep learning technologies for computer vision have developed rapidly since 2012, modeling of remote sensing systems has remained focused around human vision. In particular, remote sensing systems are usually constructed to optimize sensing cost-quality trade-offs with respect to human image interpretability. While some recent studies have explored remote sensing system design as a function of simple computer vision algorithm performance, there has been little work relating this design to the state-of-the-art in computer vision: deep learning with convolutional neural networks. We develop experimental systems to conduct this analysis, showing results with modern deep learning algorithms and recent overhead image data. Our results are compared to standard image quality measurements based on human visual perception, and we conclude not only that machine and human interpretability differ significantly, but that computer vision performance is largely self-consistent across a range of disparate conditions. This repository contains all the code required to replicate the results of our research paper, and the corresponding docker environment in which that code can be executed. All code is written in Python3 and utilizes the PyTorch library (v1.0) for neural network model training and evaluation. Jupyter notebooks are used to visualize images transformed with our code, in addition to plotting experimental results. We also include the specific parameter files used to execute our experiments, with the intent that these experiments can be replicated.

Zelinski, michaelE.↗

DOE OSTI2020

Soil chemistry data across a catena in the Luquillo Experimental Forest, Puerto Rico

Landscape topography can influence biogeochemical processes across the wet tropical forest soils. This dataset contains soil chemistry data such as pH and dissolved organic carbon (DOC) from April 1, 2017 to May 1, 2018 across a catena in the Luquillo Experimental Forest, Puerto Rico. The attached CSV file contains information on sampling date, location (El Verde field station) in LEF, topographic positions (ridge, slope, and valley, respectively), field replicate number, laboratory replicate number, water extractable pH, CaCl2 extractable pH, and DOC (unit: mg/g). Overall, soil pH values were highest in the valley, followed by slope, and lowest in the ridge topographic positions. However, DOC values followed the opposite trend: ridge>slope>valley. This dataset can facilitate our understanding of the biogeochemical cycling of carbon and nutrient associated with complex topography in wet tropical forest soils.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1990

Advances in atomic oxygen simulation

Atomic oxygen (AO) present in the atmosphere at orbital altitudes of 200 to 700 km has been shown to degrade various exposed materials on Shuttle flights. The relative velocity of the AO with the spacecraft, together with the AO density, combine to yield an environment consisting of a 5 eV beam energy with a flux of 10(exp 14) to 10(exp 15) oxygen atoms/sq cm/s. An AO ion beam apparatus that produces flux levels and energy similar to that encountered by spacecraft in low Earth orbit (LEO) has been in existence since 1987. Test data was obtained from the interaction of the AO ion beam with materials used in space applications (carbon, silver, kapton) and with several special coatings of interest deposited on various surfaces. The ultimate design goal of the AO beam simulation device is to produce neutral AO at sufficient flux levels to replicate on-orbit conditions. A newly acquired mass spectrometer with energy discrimination has allowed 5 eV neutral oxygen atoms to be separated and detected from the background of thermal oxygen atoms of approx 0.2 eV. Neutralization of the AO ion beam at 5 eV was shown at the Martin Marietta AO facility.

Froechtenigt, Joseph F.↗

NASA NTRS2017

Implementation of Real-Time Hardware in the Loop Simulation for WAVE Instrument Avionics

The Regolith and Environment Science and Oxygen and Lunar Volatile Extraction (RESOLVE) payload will lead the Resource Prospector rover to hydrogen-rich locations on the moon supporting NASA's in-situ resource utilization (ISRU) mission. The Water Analysis and Volatile Extraction (WAVE) system will be responsible for heating up regolith samples and analyzing their volatiles in a vaporized state. Given the space environment, testing flight hardware and software using the scientific instruments can be costly and time consuming, which can hold back progress involving the instruments. A hardware-in-the-loop (HITL) simulation will test the Avionics Data Acquisition as well as the Instrument Interface Unit, through simulating sensors and actuators involved in supporting the WAVE instruments. HITL is a platform for testing and developing WAVE's avionics and software, where the simulation plant will imitate the LAVA and OVEN instruments, thus allowing for an accessible, efficient, and replicable testing environment.

Al Qaraghuli, Ali↗

DOE OSTI2025

Conservative projection-based data-driven model order reduction of a fluid-kinetic spectral solver

Kinetic simulations are computationally intensive due to six-dimensional phase space discretization. Many kinetic spectral solvers use the asymmetrically weighted Hermite expansion due to its conservation and fluid-kinetic coupling properties, i.e., the lower-order Hermite moments capture and describe the macroscopic fluid dynamics, and higher-order Hermite moments describe the microscopic kinetic dynamics. We leverage this structure by developing a parametric data-driven reduced-order model based on the proper orthogonal decomposition, which projects the higher-order kinetic moments while retaining the fluid moments intact. We demonstrate analytically and numerically that the method ensures local and global mass, momentum, and energy conservation. The numerical results show that the proposed method effectively replicates the high-dimensional spectral simulations at a fraction of the computational cost and memory, as validated on the weak Landau damping and two-stream instability benchmark problems.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2014

TH-E-18A-01: Developments in Monte Carlo Methods for Medical Imaging

Monte Carlo simulation methods are widely used in medical physics research and are starting to be implemented in clinical applications such as radiation therapy planning systems. Monte Carlo simulations offer the capability to accurately estimate quantities of interest that are challenging to measure experimentally while taking into account the realistic anatomy of an individual patient. Traditionally, practical application of Monte Carlo simulation codes in diagnostic imaging was limited by the need for large computational resources or long execution times. However, recent advancements in high-performance computing hardware, combined with a new generation of Monte Carlo simulation algorithms and novel postprocessing methods, are allowing for the computation of relevant imaging parameters of interest such as patient organ doses and scatter-to-primaryratios in radiographic projections in just a few seconds using affordable computational resources. Programmable Graphics Processing Units (GPUs), for example, provide a convenient, affordable platform for parallelized Monte Carlo executions that yield simulation times on the order of 10{sup 7} xray/ s. Even with GPU acceleration, however, Monte Carlo simulation times can be prohibitive for routine clinical practice. To reduce simulation times further, variance reduction techniques can be used to alter the probabilistic models underlying the x-ray tracking process, resulting in lower variance in the results without biasing the estimates. Other complementary strategies for further reductions in computation time are denoising of the Monte Carlo estimates and estimating (scoring) the quantity of interest at a sparse set of sampling locations (e.g. at a small number of detector pixels in a scatter simulation) followed by interpolation. Beyond reduction of the computational resources required for performing Monte Carlo simulations in medical imaging, the use of accurate representations of patient anatomy is crucial to the virtual generation of medical images and accurate estimation of radiation dose and other imaging parameters. For this, detailed computational phantoms of the patient anatomy must be utilized and implemented within the radiation transport code. Computational phantoms presently come in one of three format types, and in one of four morphometric categories. Format types include stylized (mathematical equation-based), voxel (segmented CT/MR images), and hybrid (NURBS and polygon mesh surfaces). Morphometric categories include reference (small library of phantoms by age at 50th height/weight percentile), patient-dependent (larger library of phantoms at various combinations of height/weight percentiles), patient-sculpted (phantoms altered to match the patient's unique outer body contour), and finally, patient-specific (an exact representation of the patient with respect to both body contour and internal anatomy). The existence and availability of these phantoms represents a very important advance for the simulation of realistic medical imaging applications using Monte Carlo methods. New Monte Carlo simulation codes need to be thoroughly validated before they can be used to perform novel research. Ideally, the validation process would involve comparison of results with those of an experimental measurement, but accurate replication of experimental conditions can be very challenging. It is very common to validate new Monte Carlo simulations by replicating previously published simulation results of similar experiments. This process, however, is commonly problematic due to the lack of sufficient information in the published reports of previous work so as to be able to replicate the simulation in detail. To aid in this process, the AAPM Task Group 195 prepared a report in which six different imaging research experiments commonly performed using Monte Carlo simulations are described and their results provided. The simulation conditions of all six cases are provided in full detail, with all necessary data on material composition, source, geometry, scoring and other parameters provided. The results of these simulations when performed with the four most common publicly available Monte Carlo packages are also provided in tabular form. The Task Group 195 Report will be useful for researchers needing to validate their Monte Carlo work, and for trainees needing to learn Monte Carlo simulation methods. In this symposium we will review the recent advancements in highperformance computing hardware enabling the reduction in computational resources needed for Monte Carlo simulations in medical imaging. We will review variance reduction techniques commonly applied in Monte Carlo simulations of medical imaging systems and present implementation strategies for efficient combination of these techniques with GPU acceleration. Trade-offs involved in Monte Carlo acceleration by means of denoising and “sparse sampling” will be discussed. A method for rapid scatter correction in cone-beam CT (<5 min/scan) will be presented as an illustration of the simulation speeds achievable with optimized Monte Carlo simulations. We will also discuss the development, availability, and capability of the various combinations of computational phantoms for Monte Carlo simulation of medical imaging systems. Finally, we will review some examples of experimental validation of Monte Carlo simulations and will present the AAPM Task Group 195 Report. Learning Objectives: Describe the advances in hardware available for performing Monte Carlo simulations in high performance computing environments. Explain variance reduction, denoising and sparse sampling techniques available for reduction of computational time needed for Monte Carlo simulations of medical imaging. List and compare the computational anthropomorphic phantoms currently available for more accurate assessment of medical imaging parameters in Monte Carlo simulations. Describe experimental methods used for validation of Monte Carlo simulations in medical imaging. Describe the AAPM Task Group 195 Report and its use for validation and teaching of Monte Carlo simulations in medical imaging.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Evidence for Evolved Stellar Binary Mergers in Observed B-type Blue Supergiants

Blue supergiants are the brightest stars in their host galaxies, and yet their evolutionary status has been a long-standing problem in stellar astrophysics. In this pioneering work, we present a large sample of 59 early B-type supergiants in the Large Magellanic Cloud with newly derived stellar parameters and identify the signatures of stars born from binary mergers among them. We simulate novel 1D merger models of binaries consisting of post main-sequence giants with helium-rich cores (primaries) and main-sequence companions (secondaries), and consider the effects of interaction of the secondary with the core of the primary along with the mixing induced by the merger in the envelope. Thereafter, the evolution of the newborn 17–43 M ⊙ stars is followed until core-carbon depletion, close to their final pre-explosion stage. Unlike stars born alone with comparable masses, stars born from mergers of evolved binaries are blue throughout their core helium-burning phase and replicate the surface gravities and Hertzsprung–Russell diagram positions of most of our sample, thus indicating that B-type supergiants structurally resemble stars born from such mergers. Moreover, the large nitrogen-to-carbon and nitrogen-to-oxygen number ratios, coupled with helium enhancements exhibited by at least half our data sample, is uniquely reproduced by our merger models. Collectively, these findings provide compelling evidence toward the important role of binary mergers in producing the currently observed population of blue supergiants in our Universe.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

NGEE Arctic Plant Traits: Plant Aboveground Biomass, NPP and Traits, Kougarok Road Mile Marker 64, Seward Peninsula, Alaska, beginning 2016

Aboveground biomass was determined in twelve plots at the Kougarok hillslope site Kougarok Road, Mile Marker 64 (KG_MM64), Seward Peninsula, Alaska, from samples collected in late July of 2016. The sampled plots were located across six ecotypes present at this site (n=2 replicates per ecotype). Methods employed included destructive harvests to sample understory species (Understory Clip plots) and shrub surveys combined with existing allometric relationships to determine the aboveground biomass of tall shrub species (Shrub Clip Plots). Current year leaves and stems were separated to quantify net primary production of leaves and stems. This data package contains two CSV data files, one pdf and one zip file.The October 2020 update (*.v3) now provides of aboveground biomass and net primary production data (NPP) by plant species and tissue type. The initial release (*.v2) reported just aboveground biomass by plant functional type. Both versions are provided.Foliar specific leaf area, %C, %N, %P, d15N and d13C were measured on an array of vascular plant leaves collected at the Kougarok hillslope site starting in 2016. Leaves were collected during various plant harvests, including understory clip plots, shrub clip plots, nodule biomass plots, N fixation rate measurements and alder point-center-quarter transects. Paired observations from these harvests are also available through the NGEE Arctic data catalogue (see supplemental files).This October 2020 update (*v3) only removed the Ecotype column. No data were changed from initial release (*v2). Both versions are provided.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a 10-year research effort (2012-2022) to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2013

Matrix multiplication operations with data pre-conditioning in a high performance computing architecture

Mechanisms for performing matrix multiplication operations with data pre-conditioning in a high performance computing architecture are provided. A vector load operation is performed to load a first vector operand of the matrix multiplication operation to a first target vector register. A load and splat operation is performed to load an element of a second vector operand and replicating the element to each of a plurality of elements of a second target vector register. A multiply add operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the matrix multiplication operation. The partial product of the matrix multiplication operation is accumulated with other partial products of the matrix multiplication operation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp

Proliferating cell nuclear antigen (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of proteins involved in DNA metabolic processes. PCNA has two structurally similar domains (I and II) linked by a long loop (inter-domain connector loop, IDCL) on the outside of each monomer of the trimeric structure that makes up the DNA clamp. All proteins that bind to PCNA do so via a PCNA-interacting peptide (PIP) motif that binds near the IDCL. A small protein, called TIP, binds to PCNA and inhibits PCNA-dependent activities although it does not contain a canonical PIP motif. The X-ray crystal structure of TIP bound to PCNA reveals that TIP binds to the canonical PIP interaction site, but also extends beyond it through a helix that relocates the IDCL. TIP alters the relationship between domains I and II within the PCNA monomer such that the trimeric ring structure is broken, while the individual domains largely retain their native structure. Small angle X-ray scattering (SAXS) confirms the disruption of the PCNA trimer upon addition of the TIP protein in solution and together with the X-ray crystal data, provides a structural basis for the mechanism of PCNA inhibition by TIP.

59 BASIC BIOLOGICAL SCIENCES↗