SEARCH · Search NASA

Results for “encoding”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 379 records · Page 21

All sources NASA NTRS DOE OSTI

DOE OSTI2015

NMR diffusion-encoding with axial symmetry and variable anisotropy: Distinguishing between prolate and oblate microscopic diffusion tensors with unknown orientation distribution

We introduce a nuclear magnetic resonance method for quantifying the shape of axially symmetric microscopic diffusion tensors in terms of a new diffusion anisotropy metric, D{sub Δ}, which has unique values for oblate, spherical, and prolate tensor shapes. The pulse sequence includes a series of equal-amplitude magnetic field gradient pulse pairs, the directions of which are tailored to give an axially symmetric diffusion-encoding tensor b with variable anisotropy b{sub Δ}. Averaging of data acquired for a range of orientations of the symmetry axis of the tensor b renders the method insensitive to the orientation distribution function of the microscopic diffusion tensors. Proof-of-principle experiments are performed on water in polydomain lyotropic liquid crystals with geometries that give rise to microscopic diffusion tensors with oblate, spherical, and prolate shapes. The method could be useful for characterizing the geometry of fluid-filled compartments in porous solids, soft matter, and biological tissues.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Genetically encoded sensors of protein hydrodynamics and molecular proximity

Significance The lumazine binding protein (LUMP) emits a cyan-colored fluorescence and has the longest average fluorescence lifetime of any genetically encoded fluorescent protein complex. Coupled with a small mass of 20 kDa, LUMP and its fusion with capture sequences are exploited as unique sensors of protein hydrodynamics and are shown to enable quantitative fluorescence anisotropy imaging of specific target proteins in vitro and in vivo. Moreover, the surface location of the lumazine probe is shown to improve the efficiency of Förster resonance energy transfer (FRET) with the Venus acceptor protein compared with CFP, which is used in the development of a new class of FRET-based sensor.

Hoepker, Alexander C.↗

DOE OSTI2016

Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding

Rewarding experiences are often well remembered, and such memory formation is known to be dependent on dopamine modulation of the neural substrates engaged in learning and memory; however, it is unknown how and where in the brain dopamine signals bias episodic memory toward preceding rather than subsequent events. Here we found that photostimulation of channelrhodopsin-2–expressing dopaminergic fibers in the dentate gyrus induced a long-term depression of cortical inputs, diminished theta oscillations, and impaired subsequent contextual learning. Computational modeling based on this dopamine modulation indicated an asymmetric association of events occurring before and after reward in memory tasks. In subsequent behavioral experiments, preexposure to a natural reward suppressed hippocampus-dependent memory formation, with an effective time window consistent with the duration of dopamine-induced changes of dentate activity. Altogether, our results suggest a mechanism by which dopamine enables the hippocampus to encode memory with reduced interference from subsequent experience.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Crystal structure of a guanine nucleotide exchange factor encoded by the scrub typhus pathogen Orientia tsutsugamushi

Rho family GTPases regulate an array of cellular processes and are often modulated by pathogens to promote infection. In this work, we identify a cryptic guanine nucleotide exchange factor (GEF) domain in the OtDUB protein encoded by the pathogenic bacterium Orientia tsutsugamushi. A proteomics-based OtDUB interaction screen identified numerous potential host interactors, including the Rho GTPases Rac1 and Cdc42. We discovered a domain in OtDUB with Rac1/Cdc42 GEF activity (OtDUB GEF ), with higher activity toward Rac1 in vitro. While this GEF bears no obvious sequence similarity to known GEFs, crystal structures of OtDUB GEF alone (3.0 Å) and complexed with Rac1 (1.7 Å) reveal striking convergent evolution, with a unique topology, on a V-shaped bacterial GEF fold shared with other bacterial GEF domains. Structure-guided mutational analyses identified residues critical for activity and a mechanism for nucleotide displacement. Ectopic expression of OtDUB activates Rac1 preferentially in cells, and expression of the OtDUBGEF alone alters cell morphology. Cumulatively, this work reveals a bacterial GEF within the multifunctional OtDUB that co-opts host Rac1 signaling to induce changes in cytoskeletal structure.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Dual-rail encoding with superconducting cavities

The design of quantum hardware that reduces and mitigates errors is essential for practical quantum error correction (QEC) and useful quantum computation. To this end, we introduce the circuit-Quantum Electrodynamics (QED) dual-rail qubit in which our physical qubit is encoded in the single-photon subspace, { | 01 〉 , | 10 〉 } , of two superconducting microwave cavities. The dominant photon loss errors can be detected and converted into erasure errors, which are in general much easier to correct. In contrast to linear optics, a circuit-QED implementation of the dual-rail code offers unique capabilities. Using just one additional transmon ancilla per dual-rail qubit, we describe how to perform a gate-based set of universal operations that includes state preparation, logical readout, and parametrizable single and two-qubit gates. Moreover, first-order hardware errors in the cavities and the transmon can be detected and converted to erasure errors in all operations, leaving background Pauli errors that are orders of magnitude smaller. Hence, the dual-rail cavity qubit exhibits a favorable hierarchy of error rates and is expected to perform well below the relevant QEC thresholds with today’s coherence times.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Cyanobacteria from marine oxygen-deficient zones encode both form I and form II Rubiscos

Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon into biomass. To date, all studied cyanobacterial lineages encode carbon fixation machinery relying upon form I Rubiscos within a CO 2 -concentrating carboxysome. Here, we report that the uncultivated anoxic marine zone (AMZ) IB lineage ofProchlorococcusfrom pelagic oxygen-deficient zones (ODZs) harbors both form I and form II Rubiscos, the latter of which are typically noncarboxysomal and possess biochemical properties tuned toward low-oxygen environments. We demonstrate that these cyanobacterial form II enzymes are functional in vitro and were likely acquired from proteobacteria. Metagenomic analysis reveals that AMZ IB are essentially restricted to ODZs in the Eastern Pacific, suggesting that form II acquisition may confer an advantage under low-O 2 conditions. AMZ IB populations express both forms of Rubisco in situ, with the highest form II expression at depths where oxygen and light are low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for carbon sequestration in natural and engineered systems.

Science & Technology - Other Topics↗

DOE OSTI2025

State-dependent motion of a genetically encoded fluorescent biosensor

Genetically encoded biosensors can measure biochemical properties such as small-molecule concentrations with single-cell resolution, even in vivo. Despite their utility, these sensors are “black boxes”: Very little is known about the structures of their low- and high-fluorescence states or what features are required to transition between them. We used LiLac, a lactate biosensor with a quantitative fluorescence-lifetime readout, as a model system to address these questions. X-ray crystal structures and engineered high-affinity metal bridges demonstrate that LiLac exhibits a large interdomain twist motion that pulls the fluorescent protein away from a “sealed,” high-lifetime state in the absence of lactate to a “cracked,” low-lifetime state in its presence. Understanding the structures and dynamics of LiLac will help to think about and engineer other fluorescent biosensors.

Rosen, Paul C. (ORCID:000000017414454X)↗

DOE OSTI2019

Activity and structure of Pseudomonas putida MPE, a manganese-dependent single-strand DNA endonuclease encoded in a nucleic acid repair gene cluster

A recently identified and widely prevalent prokaryal gene cluster encodes a suite of enzymes with imputed roles in nucleic acid repair. The enzymes are as follows: MPE, a DNA endonuclease; Lhr-Core, a 3'–5' DNA helicase; LIG, an ATP-dependent DNA ligase; and Exo, a metallo-β-lactamase-family nuclease. Bacterial and archaeal MPE proteins belong to the binuclear metallophosphoesterase superfamily that includes the well-studied DNA repair nucleases Mre11 and SbcD. Here, in this paper, we report that the Pseudomonas putida MPE protein is a manganese-dependent DNA endonuclease that incises either linear single strands or the single-strand loops of stem-loop DNA structures. MPE has feeble activity on duplex DNA. A crystal structure of MPE at 2.2 Å resolution revealed that the active site includes two octahedrally coordinated manganese ions. Seven signature amino acids of the binuclear metallophosphoesterase superfamily serve as the enzymic metal ligands in MPE: Asp 33 , His 35 , Asp 78 , Asn 112 , His 124 , His 146 , and His 158 . A swath of positive surface potential on either side of the active site pocket suggests a binding site for the single-strand DNA substrate. The structure of MPE differs from Mre11 and SbcD in several key respects: (i) MPE is a monomer, whereas Mre11 and SbcD are homodimers; (ii) MPE lacks the capping domain present in Mre11 and SbcD; and (iii) the topology of the β sandwich that comprises the core of the metallophosphoesterase fold differs in MPE vis-à-vis Mre11 and SbcD. We surmise that MPE exemplifies a novel clade of DNA endonuclease within the binuclear metallophosphoesterase superfamily.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Insights into the transcriptional regulation of poorly characterized alcohol acetyltransferase-encoding genes (HgAATs) shed light into the production of acetate esters in the wine yeast Hanseniaspora guilliermondii

Abstract Hanseniaspora guilliermondii is a well-recognized producer of acetate esters associated with fruity and floral aromas. The molecular mechanisms underneath this production or the environmental factors modulating it remain unknown. Herein, we found that, unlike Saccharomyces cerevisiae, H. guilliermondii over-produces acetate esters and higher alcohols at low carbon-to-assimilable nitrogen (C:N) ratios, with the highest titers being obtained in the amino acid-enriched medium YPD. The evidences gathered support a model in which the strict preference of H. guilliermondii for amino acids as nitrogen sources results in a channeling of keto-acids obtained after transamination to higher alcohols and acetate esters. This higher production was accompanied by higher expression of the four HgAATs, genes, recently proposed to encode alcohol acetyl transferases. In silico analyses of these HgAat’s reveal that they harbor conserved AATs motifs, albeit radical substitutions were identified that might result in different kinetic properties. Close homologues of HgAat2, HgAat3, and HgAat4 were only found in members of Hanseniaspora genus and phylogenetic reconstruction shows that these constitute a distinct family of Aat’s. These results advance the exploration of H. guilliermondii as a bio-flavoring agent providing important insights to guide future strategies for strain engineering and media manipulation that can enhance production of aromatic volatiles.

Seixas, Isabel↗

DOE OSTI2020

Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)–based ranking for concept normalization

Concept normalization, the task of linking phrases in text to concepts in an ontology, is useful for many downstream tasks including relation extraction, information retrieval, etc. We present a generate-and-rank concept normalization system based on our participation in the 2019 National NLP Clinical Challenges Shared Task Track 3 Concept Normalization. The shared task provided 13 609 concept mentions drawn from 100 discharge summaries. We first design a sieve-based system that uses Lucene indices over the training data, Unified Medical Language System (UMLS) preferred terms, and UMLS synonyms to generate a list of possible concepts for each mention. We then design a listwise classifier based on the BERT (Bidirectional Encoder Representations from Transformers) neural network to rank the candidate concepts, integrating UMLS semantic types through a regularizer. Our generate-and-rank system was third of 33 in the competition, outperforming the candidate generator alone (81.66% vs 79.44%) and the previous state of the art (76.35%). During postevaluation, the model’s accuracy was increased to 83.56% via improvements to how training data are generated from UMLS and incorporation of our UMLS semantic type regularizer. Analysis of the model shows that prioritizing UMLS preferred terms yields better performance, that the UMLS semantic type regularizer results in qualitatively better concept predictions, and that the model performs well even on concepts not seen during training. Our generate-and-rank framework for UMLS concept normalization integrates key UMLS features like preferred terms and semantic types with a neural network–based ranking model to accurately link phrases in text to UMLS concepts.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2023

A variational encoder–decoder approach to precise spectroscopic age estimation for large Galactic surveys

Constraints on the formation and evolution of the Milky Way Galaxy require multidimensional measurements of kinematics, abundances, and ages for a large population of stars. Ages for luminous giants, which can be seen to large distances, are an essential component of studies of the Milky Way, but they are traditionally very difficult to estimate precisely for a large data set and often require careful analysis on a star-by-star basis in asteroseismology. Because spectra are easier to obtain for large samples, being able to determine precise ages from spectra allows for large age samples to be constructed, but spectroscopic ages are often imprecise and contaminated by abundance correlations. Here we present an application of a variational encoder–decoder on cross-domain astronomical data to solve these issues. The model is trained on pairs of observations from APOGEE and Kepler of the same star in order to reduce the dimensionality of the APOGEE spectra in a latent space while removing abundance information. The low dimensional latent representation of these spectra can then be trained to predict age with just ∼1000 precise seismic ages. We demonstrate that this model produces more precise spectroscopic ages (∼ 22 per cent overall, ∼ 11 per cent for red-clump stars) than previous data-driven spectroscopic ages while being less contaminated by abundance information (in particular, our ages do not depend on [α/M]). We create a public age catalogue for the APOGEE DR17 data set and use it to map the age distribution and the age-[Fe/H]-[α/M] distribution across the radial range of the Galactic disc.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Analysis of superfast encoding performance for electronic structure simulations

In our recent work, we examined various fermion-to-qubit mappings in the context of quantum simulation including the original Bravyi-Kitaev superfast encoding (OSE) as well as a generalized version (GSE). We return to OSE and compare it against the Jordan-Wigner (JW) transform for quantum chemistry considering the number of qubits required, the Pauli weight of terms in the transformed Hamiltonians, and the L 1 norm of the Hamiltonian. We considered a test set of molecular systems known as the Atomization Energy 6 (AE6) as well as hydrogen lattices. Our results showed that the resource efficiency of OSE is strongly affected by the spatial locality of the underlying single-particle basis. We find that OSE is outperformed by JW when the orbitals in the underlying single-particle basis are highly overlapping, which limits its applicability to near-term quantum chemistry simulations utilizing standard basis sets. In contrast, when orbitals are overlapping with only few others, as is the case of hydrogen lattices with very tight orbitals, OSE fares comparatively better. Furthermore, our results illustrate the importance of choosing the right combination of basis sets and fermion-to-qubit mapping to get the most out of a quantum device when simulating physical systems.