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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

The E2 Domains of APP and APLP1 Share a Conserved Mode of Dimerization

Amyloid precursor protein (APP) is genetically linked to Alzheimer's disease. APP is a type I membrane protein, and its oligomeric structure is potentially important because this property may play a role in its function or affect the processing of the precursor by the secretases to generate amyloid {beta}-peptide. Several independent studies have shown that APP can form dimers in the cell, but how it dimerizes remains controversial. At least three regions of the precursor, including a centrally located and conserved domain called E2, have been proposed to contribute to dimerization. Here we report two new crystal structures of E2, one from APP and the other from APLP1, a mammalian APP homologue. Comparison with an earlier APP structure, which was determined in a different space group, shows that the E2 domains share a conserved and antiparallel mode of dimerization. Biophysical measurements in solution show that heparin binding induces E2 dimerization. The 2.1 {angstrom} resolution electron density map also reveals phosphate ions that are bound to the protein surface. Mutational analysis shows that protein residues interacting with the phosphate ions are also involved in heparin binding. The locations of two of these residues, Arg-369 and His-433, at the dimeric interface suggest a mechanism for heparin-induced protein dimerization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Antiferromagnetic Spin Correlations Between Corner-Shared [FeO 5 ] 7- and [FeO 6 ] 9- Units, in the Novel Iron-Based Compound: BaYFeO 4

A novel quaternary compound in the Ba–Y–Fe-O phase diagram was synthesized by solid-state reaction and its crystal structure was characterized using powder X-ray diffraction. The crystal structure of BaYFeO 4 consists of a unique arrangement of Fe 3+ magnetic ions, which is based on alternate corner-shared units of [FeO 5 ] 7– square pyramids and [FeO 6 ] 9– octahedra. This results in the formation of stairwise channels of FeO polyhedra along the b crystallographic axis. The structure is described in an orthorhombic crystal system in the space group Pnma with lattice parameters a = 13.14455(1) Å, b = 5.694960(5) Å, and c = 10.247630(9) Å. The temperature-dependent magnetic susceptibility data reveal two antiferromagnetic (AFM) transitions at 33 and 48 K. An upturn in the magnetic susceptibility data above these transitions is observed, which does not reach its maximum even at 390 K. The field-dependent magnetization data at both 2 and 300 K show a nearly linear dependence and do not exhibit significant hysteresis. Heat capacity measurements between 2 and 200 K reveal only a broad anomaly without any indication of long-range ordering. The latter data set is not in good agreement with the magnetic susceptibility data, which makes it difficult to exactly determine the magnetic ground state of BaYFeO 4 . Accordingly, a temperature-dependent neutron diffraction study is in order, which will enable resolving this issue. The theoretical study of the relative strengths of magnetic exchange interactions along various possible pathways, using extended Hückel spin dimer analysis, shows that only interactions between square pyramidal and octahedral centers are significant, and among them, the intrachannel correlations are stronger than interchannel interactions. This is the first physical property study in such a magnetic ion substructure.

Wrobel, Friederike↗
DOE OSTI2019

An MPER antibody neutralizes HIV-1 using germline features shared among donors

The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC 50 ). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Quantitative principles of microbial metabolism shared across scales

Metabolism is the complex network of chemical reactions occurring within every cell and organism, maintaining life, mediating ecosystem processes and affecting Earth’s climate. Experiments and models of microbial metabolism often focus on one specific scale, overlooking the connectivity between molecules, cells and ecosystems. Here we highlight quantitative metabolic principles that exhibit commonalities across scales, which we argue could help to achieve an integrated perspective on microbial life. Mass, electron and energy balance provide quantitative constraints on their flow within metabolic networks, organisms and ecosystems, shaping how each responds to its environment. The mechanisms underlying these flows, such as enzyme–substrate interactions, often involve encounter and handling stages that are represented by equations similar to those for cells and resources, or predators and prey. Here we propose that these formal similarities reflect shared principles and discuss how their investigation through experiments and models may contribute to a common language for studying microbial metabolism across scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Finally, our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

AmeriFlux BASE data pipeline to support network growth and data sharing

Abstract AmeriFlux is a network of research sites that measure carbon, water, and energy fluxes between ecosystems and the atmosphere using the eddy covariance technique to study a variety of Earth science questions. AmeriFlux’s diversity of ecosystems, instruments, and data-processing routines create challenges for data standardization, quality assurance, and sharing across the network. To address these challenges, the AmeriFlux Management Project (AMP) designed and implemented the BASE data-processing pipeline. The pipeline begins with data uploaded by the site teams, followed by the AMP team’s quality assurance and quality control (QA/QC), ingestion of site metadata, and publication of the BASE data product. The semi-automated pipeline enables us to keep pace with the rapid growth of the network. As of 2022, the AmeriFlux BASE data product contains 3,130 site years of data from 444 sites, with standardized units and variable names of more than 60 common variables, representing the largest long-term data repository for flux-met data in the world. The standardized, quality-ensured data product facilitates multisite comparisons, model evaluations, and data syntheses.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2017

Transcriptome analysis of Brachypodium during fungal pathogen infection reveals both shared and distinct defense responses with wheat

Fusarium crown rot (FCR) of wheat and barley, predominantly caused by the fungal pathogen Fusarium pseudograminearum, is a disease of economic significance. The quantitative nature of FCR resistance within cultivated wheat germplasm has significantly limited breeding efforts to enhanced FCR resistance in wheat. In this study, we characterized the molecular responses of Brachypodium distachyon (Brachypodium hereafter) to F. pseudograminearum infection using RNA-seq to determine whether Brachypodium can be exploited as a model system towards better understanding of F. pseudograminearum-wheat interaction. The transcriptional response to infection in Brachypodium was strikingly similar to that previously reported in wheat, both in shared expression patterns of wheat homologs of Brachypodium genes and functional overlap revealed through comparative gene ontology analysis in both species. Metabolites produced by various biosynthetic pathways induced in both wheat and Brachypodium were quantified, revealing a high degree of overlap between these two species in metabolic response to infection but also showed Brachypodium does not produce certain defence-related metabolites found in wheat. Functional analyses of candidate genes identified in this study will improve our understanding of resistance mechanisms and may lead to the development of new strategies to protect cereal crops from pathogen infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii

Different intensities of high temperatures affect the growth of photosynthetic cells in nature. To elucidate the underlying mechanisms, we cultivated the unicellular green alga Chlamydomonas reinhardtii under highly controlled photobioreactor conditions and revealed systems-wide shared and unique responses to 24-hour moderate (35°C) and acute (40°C) high temperatures and subsequent recovery at 25°C. We identified previously overlooked unique elements in response to moderate high temperature. Heat at 35°C transiently arrested the cell cycle followed by partial synchronization, up-regulated transcripts/proteins involved in gluconeogenesis/glyoxylate-cycle for carbon uptake and promoted growth. But 40°C disrupted cell division and growth. Both high temperatures induced photoprotection, while 40°C distorted thylakoid/pyrenoid ultrastructure, affected the carbon concentrating mechanism, and decreased photosynthetic efficiency. We demonstrated increased transcript/protein correlation during both heat treatments and hypothesize reduced post-transcriptional regulation during heat may help efficiently coordinate thermotolerance mechanisms. During recovery after both heat treatments, especially 40°C, transcripts/proteins related to DNA synthesis increased while those involved in photosynthetic light reactions decreased. We propose down-regulating photosynthetic light reactions during DNA replication benefits cell cycle resumption by reducing ROS production. Our results provide potential targets to increase thermotolerance in algae and crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Particle-hole asymmetry in the dynamical spin and charge responses of corner-shared 1D cuprates

Although many experiments imply that oxygen orbitals play an essential role in the high-temperature superconducting cuprates, their precise role in collective spin and charge excitations and superconductivity is not yet fully understood. Here, we study the doping-dependent dynamical spin and charge structure factors of single and multi-orbital (pd) models for doped one-dimensional corner-shared spin-chain cuprates using several numerically exact methods. In doing so, we determine the orbital composition of the collective spin and charge excitations of cuprates, with important implications for our understanding of these materials. For example, we observe a particle-hole asymmetry in the orbital-resolved charge excitations, which is directly relevant to resonant inelastic x-ray scattering experiments and not captured by the single-band Hubbard model. Our results imply that one must explicitly include the oxygen degrees of freedom in order to fully understand some experimental observations on cuprate materials.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2014

Infrared detection of (H 2 O) 20 isomers of exceptional stability: A drop-like and a face-sharing pentagonal prism cluster

Water clusters containing fully coordinated water molecules are model systems that mimic the local environment of the condensed phase. Present knowledge about the water cluster size regime in which the transition from the allsurface to the fully solvated water molecules occurs is mainly based on theoretical predictions in lieu of the absence of precisely size resolved experimental measurements. Here, we report size and isomer selective infrared (IR) spectra of (H 2 O) 20 clusters tagged with a sodium atom by employing IR excitation modulated photoionization spectroscopy. The observed absorption patterns in the OH stretching ”fingerprint” region are consistent with the theoretically predicted spectra of two structurally distinct isomers: A drop-like cluster with a fully coordinated (interior) water and an edge-sharing pentagonal prism cluster in which all atoms are on the surface. The observed isomers show exceptional stability and are predicted to be nearly isoenergetic.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Interoperability study of fast wireless charging and normal wireless charging of electric vehicles with a shared receiver

Fast charging of electric vehicles (EVs) has been the trend recently. For conductive charging, normal charging can be realised by an on‐board charger, while fast charging can be realised by a DC charger which is usually off‐board the vehicle. However, for wireless charging, there is a need of a transmitter on the ground and a receiver on the EV side. Therefore, there will be a high‐power receiver and a low‐power receiver in one EV to achieve dual charging capabilities. To reduce the EV‐side cost, weight, and volume, this paper proposes a wireless charging system with a shared receiver compatible of fast wireless charging (FWC) at a small air gap and normal wireless charging (NWC) at a large air gap. The relationship between the coil size and the power level is investigated and a suitable receiver coil size is selected for FWC. The LCC‐LCC topology is selected due to its characteristic of output power proportional to the coupling coefficient. Design procedures of the receiver and transmitters are investigated. The simulations and the experimental results obtained from the downscaled prototype verified the effectiveness of the compatibility design.

Zhang, Yiming↗
DOE OSTI2011

tRNA[superscript His] guanylyltransferase (THG1), a unique 3;#8242;-5;#8242; nucleotidyl transferase, shares unexpected structural homology with canonical 5;#8242;-3;#8242; DNA polymerases

All known DNA and RNA polymerases catalyze the formation of phosphodiester bonds in a 5' to 3' direction, suggesting this property is a fundamental feature of maintaining and dispersing genetic information. The tRNA{sup His} guanylyltransferase (Thg1) is a member of a unique enzyme family whose members catalyze an unprecedented reaction in biology: 3'-5' addition of nucleotides to nucleic acid substrates. The 2.3-{angstrom} crystal structure of human THG1 (hTHG1) reported here shows that, despite the lack of sequence similarity, hTHG1 shares unexpected structural homology with canonical 5'-3' DNA polymerases and adenylyl/guanylyl cyclases, two enzyme families known to use a two-metal-ion mechanism for catalysis. The ability of the same structural architecture to catalyze both 5'-3' and 3'-5' reactions raises important questions concerning selection of the 5'-3' mechanism during the evolution of nucleotide polymerases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Marine algae and land plants share conserved phytochrome signaling systems

Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla , a widely distributed marine picoprasinophyte (<2 µm cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas . The expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Oxidative stress is a shared characteristic of ME/CFS and Long COVID

Over 65 million individuals worldwide are estimated to have Long COVID (LC), a complex multisystemic condition marked by fatigue, post-exertional malaise, and other symptoms resembling myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). With no clinically approved treatments or reliable diagnostic markers, there is an urgent need to define the molecular underpinnings of these conditions. By studying bioenergetic characteristics of peripheral blood lymphocytes in 25 healthy controls, 27 ME/CFS, and 20 LC donors, we find both ME/CFS and LC donors exhibit signs of elevated oxidative stress, especially in the memory subset. Using a combination of flow cytometry, RNA-seq, mass spectrometry, and systems chemistry analysis, we observed aberrations in reactive oxygen species (ROS) clearance pathways including elevated glutathione levels, decreases in mitochondrial superoxide dismutase protein levels, and glutathione peroxidase 4–mediated lipid oxidative damage. Strikingly, these redox pathways changes show sex-specific trends. While ME/CFS females exhibit higher total ROS and mitochondrial calcium levels, males have normal ROS levels, with pronounced mitochondrial lipid oxidative damage. In females, these higher ROS levels correlate with T cell hyperproliferation, consistent with the known role of elevated ROS in initiating proliferation. This hyperproliferation can be attenuated by metformin, suggesting this Food and Drug Administration (FDA)-approved drug as a possible treatment, as also suggested by a recent clinical study of LC patients. Moreover, these results suggest a shared mechanistic basis for the systemic phenotypes of ME/CFS and LC, which can be detected by quantitative blood cell measurements, and that effective, patient-tailored drugs might be discovered using standard lymphocyte stimulation assays.

ME/CFS↗
DOE OSTI2016

Sharing but not caring: dark matter and the baryon asymmetry of the universe

We consider scenarios where Dark Matter (DM) particles carry baryon and/or lepton numbers, which can be defined if there exist operators connecting the dark to the visible sector. As a result, the DM fields become intimately linked to the Standard Model (SM) ones and can be maximally asymmetric just like the ordinary matter. In particular, we discuss minimal scenarios where the DM is a complex scalar or a Dirac fermion coupled to operators with nonzero baryon and/or lepton numbers, and that consist of only SM fields. We consider an initial asymmetry stored in either the SM or the DM sector; the main role of these operators is to properly share the asymmetry between the two sectors, in accordance with observations. After the chemical decoupling, the DM and SM sectors do not care about each other as there is only an ineffective communication between them. Once the DM mass is specified, the Wilson coefficients of these operators are fixed by the requirement of the correct transfer of the asymmetry. We study the phenomenology of this framework at colliders, direct detection and indirect detection experiments. In particular, the LHC phenomenology is very rich and can be tested in different channels such as the two same-sign leptons with two jets, monojet and monojet with a monolepton.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Virtualization of the ATLAS software environment on a shared HPC system

The shared HPC cluster NEMO at the University of Freiburg has been made available to local ATLAS users through the provisioning of virtual machines incorporating the ATLAS software environment analogously to a WLCG center. This concept allows to run both data analysis and production on the HPC host system which is connected to the existing Tier2/Tier3 infrastructure. Schedulers of the two clusters were integrated in a dynamic, on-demand way. An automatically generated, fully functional virtual machine image provides access to the local user environment. The performance in the virtualized environment is evaluated for typical High-Energy Physics applications.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2012

Supporting shared resource usage for a diverse user community: The OSG experience and lessons learned

The Open Science Grid (OSG) supports a diverse community of new and existing users in adopting and making effective use of the Distributed High Throughput Computing (DHTC) model. The LHC user community has deep local support within the experiments. For other smaller communities and individual users the OSG provides consulting and technical services through the User Support area. We describe these sometimes successful and sometimes not so successful experiences and analyze lessons learned that are helping us improve our services. The services offered include forums to enable shared learning and mutual support, tutorials and documentation for new technology, and troubleshooting of problematic or systemic failure modes. For new communities and users, we bootstrap their use of the distributed high throughput computing technologies and resources available on the OSG by following a phased approach. We first adapt the application and run a small production campaign on a subset of friendly sites. Only then do we move the user to run full production campaigns across the many remote sites on the OSG, adding to the community resources up to hundreds of thousands of CPU hours per day. This scaling up generates new challenges - like no determinism in the time to job completion, and diverse errors due to the heterogeneity of the configurations and environments - so some attention is needed to get good results. We cover recent experiences with image simulation for the Large Synoptic Survey Telescope (LSST), small-file large volume data movement for the Dark Energy Survey (DES), civil engineering simulation with the Network for Earthquake Engineering Simulation (NEES), and accelerator modeling with the Electron Ion Collider group at BNL. We will categorize and analyze the use cases and describe how our processes are evolving based on lessons learned.

Garzoglio, Gabriele↗
DOE OSTI2015

The OSG open facility: A sharing ecosystem

The Open Science Grid (OSG) ties together individual experiments’ computing power, connecting their resources to create a large, robust computing grid, this computing infrastructure started primarily as a collection of sites associated with large HEP experiments such as ATLAS, CDF, CMS, and DZero. In the years since, the OSG has broadened its focus to also address the needs of other US researchers and increased delivery of Distributed High Through-put Computing (DHTC) to users from a wide variety of disciplines via the OSG Open Facility. Presently, the Open Facility delivers about 100 million computing wall hours per year to researchers who are not already associated with the owners of the computing sites, this is primarily accomplished by harvesting and organizing the temporarily unused capacity (i.e. opportunistic cycles) from the sites in the OSG. Using these methods, OSG resource providers and scientists share computing hours with researchers in many other fields to enable their science, striving to make sure that these computing power used with maximal efficiency. Furthermore, we believe that expanded access to DHTC is an essential tool for scientific innovation and work continues in expanding this service.

97 MATHEMATICS AND COMPUTING↗