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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 1,207 records · Page 67

Thionin-D4E1 chimeric protein protects plants against bacterial infections

The generation of a chimeric protein containing a first domain encoding either a pro-thionon or thionin, a second domain encoding D4E1 or pro-D4E1, and a third domain encoding a peptide linker located between the first domain and second domain is described. Either the first domain or the second domain is located at the amino terminal of the chimeric protein and the other domain (second domain or first domain, respectively) is located at the carboxyl terminal. The chimeric protein has antibacterial activity. Genetically altered plants and their progeny expressing a polynucleotide encoding the chimeric protein resist diseases caused by bacteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

RNA-guided nucleic acid modifying enzymes and methods of use thereof

The present disclosure provides CasY proteins, nucleic acids encoding the CasY proteins, and modified host cells comprising the CasY proteins and/or nucleic acids encoding same. CasY proteins are useful in a variety of applications, which are provided. The present disclosure provides CasY guide RNAs that bind to and provide sequence specificity to the CasY proteins, nucleic acids encoding the CasY guide RNAs, and modified host cells comprising the CasY guide RNAs and/or nucleic acids encoding same. CasY guide RNAs are useful in a variety of applications, which are provided. The present disclosure provides methods of identifying a CRISPR RNA-guided endonuclease.

Doudna, Jennifer A.↗

Method and apparatus for data protection in memory devices

An apparatus and method for efficiently transmitting data are described. A transmitter sends data to a receiver. An encoder of the transmitter divides a received first block of data into multiple sub-blocks. The encoder selects a portion of each sub-block to compare to one another. A portion in a particular sub-block has a same offset and a same size as other portions of other sub-blocks. If the encoder determines the multiple portions match one another, the encoder sends, to the receiver, a second block of data corresponding to the first block of data. The second block of data has a same size as a size of the received first block of data, and the second block of data includes security data from one of multiple error correction schemes. Therefore, the second block of data provides security without increasing an amount of data to transmit.

SeyedzadehDelcheh, SeyedMohammad↗

Translation control tool for plants

The present invention provides for a system comprising (a) first polynucleotide encoding a first promoter operatively linked to an open reading frame (ORF) encoding an endoribonuclease, or an enzymatic active fragment thereof, which cleaves a cognition sequence (cog), and (b) a second polynucleotide encoding a second promoter operatively linked to a nucleotide sequence encoding (i) a cog linked to a coding sequence of interest (COI), (ii) a cog linked to the 3′ end of a first COI and the 5′ end of a second COI, or (iii) a cog locating within a LS (or targeting sequence) linked to a COI.

Liang, Yan↗

Deformable phrase level attention: A flexible approach for improving AI based medical coding

Objective: Improving the AI-driven automated medical encoding of clinical text plays a vital role in gathering information on the occurrence of diseases to improve population-level health. This work presents a novel attention mechanism designed to enhance text classification models and ensure appropriate classification of medical concepts in unstructured electronic health records. Materials and Methods: We developed a deformable, phrase-level attention mechanism to identify important lexical word-level and contextual phrase-level information from clinical text documents. We evaluated conventional and transformer-based deep learning models that we extended with our attention mechanism on the extraction of critical cancer information (e.g., site, subsite, laterality, histology, behavior) from 629,908 electronic pathology reports and on the automated medical encoding of 52,722 hospital discharge summaries. Results: Transformer-based models with the deformable, phrase-level attention mechanism achieved the best performance on the extraction of critical cancer information from pathology reports. Conventional- and transformer-based models show similar or better performance than their baseline counterparts on the automated medical encoding of clinical documents. Discussion: The addition of phrase-level information allowed models extended with our proposed method to outperform standard word-level attention. Our method showed favorable properties for the real-world application in terms of model robustness and phenotyping. These results indicate that our method is promising for automated data harmonization for common data models. Conclusion: This work proposes a novel deformable, phrase-level attention mechanism that enhances text classification models in the extraction of medical concepts from clinical text documents. We demonstrate strong performances on two clinical text datasets and showcase real-world deployability of our method.

Automated medical encoding↗

Power System Event Classification and Localization Using a Convolutional Neural Network

Detection and timely identification of power system disturbances are essential for situation awareness and reliable electricity grid operation. Because records of actual events in the system are limited, ensemble simulation-based events are needed to provide adequate data for building event-detection models through deep learning; e.g., a convolutional neural network (CNN). An ensemble numerical simulation-based training data set have been generated through dynamic simulations performed on the Polish system with various types of faults in different locations. Such data augmentation is proven to be able to provide adequate data for deep learning. The synchronous generators’ frequency signals are used and encoded into images for developing and evaluating CNN models for classification of fault types and locations. With a time-domain stacked image set as the benchmark, two different time-series encoding approaches, i.e., wavelet decomposition-based frequency-domain stacking and polar coordinate system-based Gramian Angular Field (GAF) stacking, are also adopted to evaluate and compare the CNN model performance and applicability. The various encoding approaches are suitable for different fault types and spatial zonation. With optimized settings of the developed CNN models, the classification and localization accuracies can go beyond 84 and 91%, respectively.

24 POWER TRANSMISSION AND DISTRIBUTION↗

(abstract) MCD3 - A Constraint Length 15 Viterbi Decoder

JPL is responsible for many space missions, as part of NASA's continuing unmanned exploration of the solar system. Signals from spacecraft at planetary distances arrive at Earth with poor S/N ratio. To reduce errors, the signals are encoded with an inner code of Viterbi encoding. One of the key parameters of Viterbi encoding is the constraint length. Previous space missions have used a constraint length of 7. Newer missions use 15, to give a considerably improved error correction ability. However, the complexity of the Viterbi decoder is increased so as to be 256 times more complex.

communications↗

Fault Tolerant State Machines

State machines are commonly used to control sequential logic in FPGAs and ASKS. An errant state machine can cause considerable damage to the device it is controlling. For example in space applications, the FPGA might be controlling Pyros, which when fired at the wrong time will cause a mission failure. Even a well designed state machine can be subject to random errors us a result of SEUs from the radiation environment in space. There are various ways to encode the states of a state machine, and the type of encoding makes a large difference in the susceptibility of the state machine to radiation. In this paper we compare 4 methods of state machine encoding and find which method gives the best fault tolerance, as well as determining the resources needed for each method.

encoding↗

Crystal structures of OrfX1, OrfX2 and the OrfX1–OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1

Botulinum neurotoxins (BoNTs) are among the most lethal toxins known to humans, comprising seven established serotypes termed BoNT/A–G encoded in two types of gene clusters (ha and orfX) in BoNT-producing clostridia. The ha cluster encodes four non-toxic neurotoxin-associated proteins (NAPs) that assemble with BoNTs to protect and enhance their oral toxicity. However, the structure and function of the orfX-type NAPs remain largely unknown. Here, we report the crystal structures for OrfX1, OrfX2, and an OrfX1–OrfX3 complex, which are encoded in the orfX cluster of a BoNT/E1-producing Clostridium botulinum strain associated with human foodborne botulism. These structures lay the foundation for future studies on the potential roles of OrfX proteins in oral intoxication and pathogenesis of BoNTs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins

In addition to their membrane-bound chlorophyll a/c light-harvesting antenna, the cryptophyte algae have evolved a unique phycobiliprotein antenna system located in the thylakoid lumen. The basic unit of this antenna consists of two copies of an αβ protomer where the α and β subunits scaffold different combinations of a limited number of linear tetrapyrrole chromophores. While the β subunit is highly conserved, encoded by a single plastid gene, the nuclear-encoded α subunits have evolved diversified multigene families. It is still unclear how this sequence diversity results in the spectral diversity of the mature proteins. By careful examination of three newly determined crystal structures in comparison with three previously obtained, we show how the α subunit amino acid sequences control chromophore conformations and hence spectral properties even when the chromophores are identical. Previously we have shown that α subunits control the quaternary structure of the mature αβ.αβ complex (either open or closed), however, each species appeared to only harbor a single quaternary form. Here we show that species of the Hemiselmis genus contain expressed α subunit genes that encode both distinct quaternary structures. Finally, we have discovered a common single-copy gene (expressed into protein) consisting of tandem copies of a small α subunit that could potentially scaffold pairs of light harvesting units. Together, our results show how the diversity of the multigene α subunit family produces a range of mature cryptophyte antenna proteins with differing spectral properties, and the potential for minor forms that could contribute to acclimation to varying light regimes.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure of the extracellular domain of human myelin protein zero

Charcot-Marie-Tooth disease (CMT), a hereditary motor and sensory neuropathy, is the most common genetic neuropathy with an incidence of 1 in 2600. Several forms of CMT have been identified arising from different genomic abnormalities such as CMT1 including CMT1A, CMT1B, and CMTX. CMT1 with associated peripheral nervous system (PNS) demyelination, the most frequent diagnosis, demonstrates slowed nerve conduction velocities and segmental demyelination upon nerve biopsy. One of its subtypes, CMT1A, presents a 1.5-Mb duplication in the p11-p12 region of the human chromosome 17 which encodes peripheral myelin protein 22 (PMP22). CMT1B, a less common form, arises from the mutations in the myelin protein zero (MPZ) gene on chromosome 1, region q22-q23, which encodes the major structural component of the peripheral myelin. A rare type of CMT1 has been found recently and is caused by point mutations in early growth response gene 2 (EGR2), encoding a zinc finger transcription factor in Schwann cells. In addition, CMTX, an X-linked form of CMT, arises from a mutation in the connexin-32 gene. Myelin protein zero, associated with CMT1B, is a transmembrane protein of 219 amino acid residues. Human MPZ consists of three domains: 125 residues constitute the glycosylated immunoglobulin-like extracellular domain; 27 residues span the membrane; and 67 residues comprise the highly basic intracellular domain. MPZ makes up approximately 50% of the protein content of myelin, and is expressed predominantly in Schwann cells, the myelinating cell of the PNS. Myelin protein zero, a homophilic adhesion molecule, is a member of the immunoglobulin super-family and is essential for normal myelin structure and function. In addition, MPZ knockout mice displayed abnormal myelin that severely affects the myelination pathway, and overexpression of MPZ causes congenital hypomyelination of peripheral nerves. Myelin protein zero mutations account for {approx}5% of patients with CMT. To date, over 125 different mutations in the MPZ gene leading to peripheral neuropathy in patients have been reported worldwide (http://www.molgen. ua.ac.be/CMTMutations). All identified mutations resulting in a change or deletion of amino acid residues in MPZ give rise to neuropathy with the exception of R215L, which instead causes a benign polymorphism. Furthermore, more detailed analysis has classified the MPZ mutations into two major groups. In the first group, the mutations disrupt the intracellular processing of MPZ and are primarily associated with early onset neuropathy. It has been proposed that the mutated MPZ is trapped inside the cell rather than being transported to the plasma membrane. However, other evidence suggests that the mutated MPZ protein is expressed on the plasma membrane, but dominant-negatively disrupts the structure of myelin. In the second group, the MPZ mutations are associated with late onset neuropathy as these mutations cause only mild demyelination. The underlying mechanism is elusive with the hypothesis being that the second group of mutations cause minor abnormalities in the myelin sheath that over time may lead to aberrant Schwann cell-axon interactions and subsequently to axonal degeneration. The crystal structure of the extracellular domain of human MPZ (hP0ex) fused with maltose binding protein (MBP) is reported at 2.1 {angstrom} resolution. While the crystal structure of rat MPZ extracellular domain (rP0ex) is available, the crystal structure of the human counterpart is useful for the analysis of the two homologs as well as a comparison between the two species. The hP0ex molecule reveals subtle structural variations between two homologs allowing comparison of the human myelin protein zero to that of the rat protein. The alignment of these homologs is shown in Figure 1(a).

59 BASIC BIOLOGICAL SCIENCES↗

Predictability of Localized Plasmonic Responses in Nanoparticle Assemblies

Design of nanoscale structures with desired optical properties is a key task for nanophotonics. In this work, the correlative relationship between local nanoparticle geometries and their plasmonic responses is established using encoder-decoder neural networks. In the im2spec network, the relationship between local particle geometries and local spectra is established via encoding the observed geometries to a small number of latent variables and subsequently decoding into plasmonic spectra; in the spec2im network, the relationship is reversed. Surprisingly, these reduced descriptions allow high-veracity predictions of local responses based on geometries for fixed compositions and surface chemical states. Analysis of the latent space distributions and the corresponding decoded and closest (in latent space) encoded images yields insight into the generative mechanisms of plasmonic interactions in the nanoparticle arrays. Ultimately, this approach creates a path toward determining configurations that yield the spectrum closest to the desired one, paving the way for stochastic design of nanoplasmonic structures.

nanoparticle arrays↗

Protein Targeting Across and into Chloroplast Membranes [Chapter 13 in Photosynthesis Research Protocols]

Here, the protein complexes in the thylakoid membrane are composed of subunits derived from both the nuclear and chloroplast genomes. While less is known about the mechanisms of delivery of the plastid-encoded subunits, the targeting mechanisms of the nuclear-encoded subunits have been more experimentally tractable. We have described in this chapter the methods used in our laboratory for investigations of the import of nuclear-encoded proteins across the chloroplast envelope membranes, and for their further delivery into or across the thylakoid membrane by one of the four distinct pathways.

59 BASIC BIOLOGICAL SCIENCES↗

Dirac pairings, one-form symmetries and Seiberg-Witten geometries

The Coulomb phase of a quantum field theory, when present, illuminates the analysis of its line operators and one-form symmetries. For 4d $\mathcal{N}$ = 2 field theories the low energy physics of this phase is encoded in the special Kähler geometry of the moduli space of Coulomb vacua. We clarify how the information on the allowed line operator charges and one-form symmetries is encoded in the special Kähler structure. We point out the important difference between the lattice of charged states and the homology lattice of the abelian variety fibered over the moduli space, which, when principally polarized, is naturally identified with a choice of the lattice of mutually local line operators. This observation illuminates how the distinct S-duality orbits of global forms of $\mathcal{N}$ = 4 theories are encoded geometrically.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Islands in cosmology

A quantum extremal island suggests that a region of spacetime is encoded in the quantum state of another system, like the encoding of the black hole interior in Hawking radiation. We study conditions for islands to appear in general spacetimes, with or without black holes. They must violate Bekenstein’s area bound in a precise sense, and the boundary of an island must satisfy several other information-theoretic inequalities. These conditions combine to impose very strong restrictions, which we apply to cosmological models. We find several examples of islands in crunching universes. In particular, in the four-dimensional FRW cosmology with radiation and a negative cosmological constant, there is an island near the turning point when the geometry begins to recollapse. In a two-dimensional model of JT gravity in de Sitter spacetime, there are islands inside crunches that are encoded at future infinity or inside bubbles of Minkowski spacetime. Finally, we discuss simple tensor network toy models for islands in cosmology and black holes.

79 ASTRONOMY AND ASTROPHYSICS↗

Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus

The human gut microbiota, which underpins nutrition and systemic health, is compositionally sensitive to the availability of complex carbohydrates in the diet. The Bacteroidetes comprise a dominant phylum in the human gut microbiota whose members thrive on dietary and endogenous glycans by employing a diversity of highly specific, multi-gene polysaccharide utilization loci (PUL), which encode a variety of carbohydrases, transporters, and sensor/regulators. PULs invariably also encode surface glycan-binding proteins (SGBPs) that play a central role in saccharide capture at the outer membrane. Here, we present combined biophysical, structural, and in vivo characterization of the two SGBPs encoded by the Bacteroides ovatus mixed-linkage β-glucan utilization locus (MLGUL), thereby elucidating their key roles in the metabolism of this ubiquitous dietary cereal polysaccharide. In particular, molecular insight gained through several crystallographic complexes of SGBP-A and SGBP-B with oligosaccharides reveals that unique shape complementarity of binding platforms underpins specificity for the kinked MLG backbone vis-à-vis linear β-glucans. Reverse-genetic analysis revealed that both the presence and binding ability of the SusD homolog BoSGBP MLG -A are essential for growth on MLG, whereas the divergent, multi-domain BoSGBP MLG -B is dispensable but may assist in oligosaccharide scavenging from the environment. Overall, the synthesis of these data illuminates the critical role SGBPs play in concert with other MLGUL components, reveals new structure–function relationships among SGBPs, and provides fundamental knowledge to inform future (meta)genomic, biochemical, and microbiological analyses of the human gut microbiota.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization and modification of enzymes in the 2-ketoisovalerate biosynthesis pathway of Ralstonia eutropha H16

2-Ketoisovalerate is an important cellular intermediate for the synthesis of branched-chain amino acids as well as other important molecules, such as pantothenate, coenzyme A, and glucosinolate. This ketoacid can also serve as a precursor molecule for the production of biofuels, pharmaceutical agents, and flavor agents in engineered organisms, such as the betaproteobacterium Ralstonia eutropha. The biosynthesis of 2-ketoisovalerate from pyruvate is carried out by three enzymes: acetohydroxyacid synthase (AHAS, encoded by ilvBH), acetohydroxyacid isomeroreductase (AHAIR, encoded by ilvC), and dihydroxyacid dehydratase (DHAD, encoded by ilvD). In this study, enzymatic activities and kinetic parameters were determined for each of the three R. eutropha enzymes as heterologously purified proteins. AHAS, which serves as a gatekeeper for the biosynthesis of all three branched-chain amino acids, demonstrated the tightest regulation through feedback inhibition by l-valine (IC50 = 1.2 mM), l-isoleucine (IC50 = 2.3 mM), and l-leucine (IC50 = 5.4 mM). Intermediates in the valine biosynthesis pathway also exhibit feedback inhibitory control of the AHAS enzyme. In addition, AHAS has a very weak affinity for pyruvate (K-M = 10.5 mu M) and is highly selective towards 2-ketobutyrate (R = 140) as a second substrate. AHAIR and DHAD are also inhibited by the branched-chain amino acids, although to a lesser extent when compared to AHAS. Experimental evolution and rational site-directed mutagenesis revealed mutants of the regulatory subunit of AHAS (IlvH) (N11S, T34I, A36V, T104S, N11F, G14E, and N29H), which, when reconstituted with wild-type IlvB, lead to AHAS having reduced valine, leucine, and isoleucine sensitivity. The study of the kinetics and inhibition mechanisms of R. eutropha AHAS, AHAIR, and DHAD has shed light on interactions between these enzymes and the products they produce; it, therefore, can be used to engineer R. eutropha strains with optimal production of 2-ketoisovalerate for value-added materials.

Lu, JN↗