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At least 973 records · Page 54

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DOE OSTI2019

Structure Based Prediction of Neoantigen Immunogenicity

The development of immunological therapies that incorporate peptide antigens presented to T cells by MHC proteins is a long sought-after goal, particularly for cancer, where mutated neoantigens are being explored as personalized cancer vaccines. Although neoantigens can be identified through sequencing, bioinformatics and mass spectrometry, identifying those which are immunogenic and able to promote tumor rejection remains a significant challenge. Here we examined the potential of high-resolution structural modeling followed by energetic scoring of structural features for predicting neoantigen immunogenicity. After developing a strategy to rapidly and accurately model nonameric peptides bound to the common class I MHC protein HLA-A2, we trained a neural network on structural features that influence T cell receptor (TCR) and peptide binding energies. The resulting structurally-parameterized neural network outperformed methods that do not incorporate explicit structural or energetic properties in predicting CD8 + T cell responses of HLA-A2 presented nonameric peptides, while also providing insight into the underlying structural and biophysical mechanisms governing immunogenicity. Our proof-of-concept study demonstrates the potential for structure-based immunogenicity predictions in the development of personalized peptide-based vaccines.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

SN 2012cg: Evidence for interaction between a normal SN Ia and a non-degenerate binary companion

We report evidence for excess blue light from the Type Ia supernova (Sn Ia) SN 2012cg at 15 and 16 days before maximum B-band brightness. The emission is consistent with predictions for the impact of the supernova on a non-degenerate binary companion. This is the first evidence for emission from a companion to a normal SN Ia. Sixteen days before maximum light, the B−V color of SN 2012cg is 0.2 mag bluer than for other normal SN Ia. At later times, this supernova has a typical SN Ia light curve, with extinction-corrected M{sub B}=−19.62±0.02 mag and Δm{sub 15}(B)=0.86±0.02. Our data set is extensive, with photometry in seven filters from five independent sources. Early spectra also show the effects of blue light, and high-velocity features are observed at early times. Near maximum, the spectra are normal with a silicon velocity v{sub Si} = −10,500 km s{sup −1}. Comparing the early data with models by Kasen favors a main-sequence companion of about six solar masses. It is possible that many other SN Ia have main-sequence companions that have eluded detection because the emission from the impact is fleeting and faint.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1982

On the reality of a boundary in the H-R diagram between late-type stars with and without high temperature outer atmospheres

The Linsky-Haisch hypothesis (1979) that a boundary exists in the H-R diagram separating yellow giants from red giants and supergiants is tested. IUE 1150-2000 A low-resolution spectra of 10 stars chosen to constitute a reverse bias sample are presented and discussed. Despite the bias, weak C IV emission indicative of high-temperature plasma was observed in four of the six stars chosen to be probable red stars, while no C IV emission was detected in the four stars chosen to be yellows. In a second test using the entire sample of 39 stars, nearly all of the yellow giants and supergiants were found to have an emission feature at 1549 A, which is attributed to C IV. The large magnitude dispersion could be attributed to temporal or spatial variability, differing magnetic field strengths and geometries, or age-related effects during post-main-sequence evolution. It is concluded that the Linsky-Haisch transition region boundary is a real phenomenon.

Simon, T.↗

NASA NTRS1989

Optical polarimetry and thermal imaging of the disc around Beta Pictoris

The dust disk around the main-sequence A5 star Beta Pic is characterized on the basis of recently obtained data. Optical polarimetry indicates that the disk has polarization of about 15 percent and polarization vectors normal to the scattering plane, indicating that the features observed are indeed a dust disk made visible by scattering. Thermal images of the central 13-arcsec-diameter region, obtained at 10 and 20 microns by Telesco et al. (1988) using the NASA Marshall 20-pixel bolometer array, suggest that the dust grains in the disk have a mean diameter of 1 micron or smaller. Also discussed are (1) unsuccessful searches for other nearby stars with disks and (2) the potential value of Hubble Space Telescope images for understanding the structure of Beta Pic.

Wolstencroft, R. D.↗

NASA NTRS1992

Characterization and modeling for dilute and dense sprays

The present numerical modeling of dilute and dense spray combustion solves the governing gas-phase equations in Eulerian coordinates by means of a time-marching multiple pressure correction procedure that is based on the operator-splitting technique. A sequence of validating cases involving (1) nonevaporating, (2) evaporating, (3) burning, (4) dilute, and (5) dense spray cases is undertaken; it is found that in the combusting dilute spray case, the present procedure correctly predicts the general features of flows and yields qualitative agreement with experimental data. In the other cases, reasonably good agreement with experimental results is obtained.

Chen, C. P.↗

NASA NTRS1999

Time-Distance Helioseismology with f Modes as a Method for Measurement of Near-Surface Flows

Travel times measured for the f mode have been used to study flows near the solar surface in conjunction with simultaneous measurements of the magnetic field. Previous flow measurements of doppler surface rotation, small magnetic feature rotation, supergranular pattern rotation, and surface meridional circulation have been confirmed. In addition, the flow in supergranules due to Coriolis forces has been measured. The spatial and temporal power spectra for a six-day observing sequence has been measured.

Duvall, Thomas L., Jr.↗

NASA NTRS1990

Shell structure and distribution of Cloudina, a potential index fossil for the terminal Proterozoic

Cloudina-bearing biosparites and biomicrites in the lower part of the Nama Group, Namibia, contain a wide morphological diversity of shell fragments that can all be attributed to the two named species C. hartmannae and C. riemkeae. The curved to sinuous tubular shells of Cloudina were multi-layered. Each shell layer was 8 to 50 micrometers thick and in the form of a slightly flaring tube with one end open and the other closed. Growth appears to have been periodic with successive shell layers forming within older layers. Each added layer was slightly elevated from the previous layer at the proximal end and was asymmetrically placed within the older layer so that only a portion of the new shell layer was fused to the previous layer. This type of growth left a relatively large unminerialized area between the shell layers which was often partially or fully occluded by early marine cements. The thin shell layers exhibit both plastic and brittle deformation and were likely formed of a rigid CaCO3-impregnated organic-rich material. Often the shell layers are preferentially dolomitized suggesting an original mineralogy of high-magnesian calcite. Both species in the Nama Group formed thickets, or perhaps bioherms, and this sedentary and gregarious habit suggests that Cloudina was probably a filter-feeding metazoan of at least a cnidarian grade of organization. The unusual shell structure of Cloudina gives rise to a characteristic suite of taphonomic and diagenetic features that can be used to identify Cloudina-bearing deposits within the Nama Group and in other terminal Proterozoic deposits around the world. Species of Cloudina occur in limestones from Brazil, Spain, China, and Oman in sequences consistent with a latest Proterozoic age assignment. In addition, supposed lower Cambrian, pre-trilobitic, shelly fossils from northwest Mexico and the White-Inyo Mountains in California and Nevada, including Sinotubulites, Nevadatubulus, and Wyattia, are all either closely related to or con-generic with Cloudina. Hence, it is probable that these outcrops are latest Proterozoic in age, and that Cloudina or Cloudina-like organisms were widely distributed at that time. It is possible, moreover, to suggest that metazoan biomineralization occurred on a global scale by the latest Proterozoic, at the same time that evidence for complex multicellularity and locomotion in animals appears in siliciclastic "Ediacaran" rocks in the form of body and trace fossils.

NASA Program Exobiology↗

NASA NTRS2001

Apparatus and process for freeform fabrication of composite reinforcement preforms

A solid freeform fabrication process and apparatus for making a three-dimensional reinforcement shape. The process comprises the steps of (1) operating a multiple-channel material deposition device for dispensing a liquid adhesive composition and selected reinforcement materials at predetermined proportions onto a work surface; (2) during the material deposition process, moving the deposition device and the work surface relative to each other in an X-Y plane defined by first and second directions and in a Z direction orthogonal to the X-Y plane so that the materials are deposited to form a first layer of the shape; (3) repeating these steps to deposit multiple layers for forming a three-dimensional preform shape; and (4) periodically hardening the adhesive to rigidize individual layers of the preform. These steps are preferably executed under the control of a computer system by taking additional steps of (5) creating a geometry of the shape on the computer with the geometry including a plurality of segments defining the preform shape and each segment being preferably coded with a reinforcement composition defining a specific proportion of different reinforcement materials; (6) generating programmed signals corresponding to each of the segments in a predetermined sequence; and (7) moving the deposition device and the work surface relative to each other in response to these programmed signals. Preferably, the system is also operated to generate a support structure for any un-supported feature of the 3-D preform shape.

Yang, Junsheng↗

DOE OSTI2020

Disruption of evolutionarily correlated tRNA elements impairs accurate decoding

Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide sequences. In the tRNA anticodon stem-loop, the anticodon sequence is correlated with a base pair in the anticodon loop (nucleotides 32 and 38) to tune the binding of each tRNA to the decoding center in the ribosome. Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tRNAs. The molecular basis for how these two tRNA features combine to ensure accurate decoding is unclear. In this work, we solved structures of the bacterial ribosome containing either wild-type tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ or tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ containing a reversed 32–38 pair on cognate and near-cognate codons. Structures of wild-type tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ bound to the ribosome reveal 23S ribosomal RNA (rRNA) nucleotide A1913 positional changes that are dependent on whether the codon-anticodon interaction is cognate or near cognate. Further, the 32–38 pair is destabilized in the context of a near-cognate codon-anticodon pair. Reversal of the pairing in tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ ablates A1913 movement regardless of whether the interaction is cognate or near cognate. These results demonstrate that disrupting 32–38 and anticodon sequences alters interactions with the ribosome that directly contribute to misreading.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1980

Structural features of the nonionic surfactants stabilizing long-lived bubble nuclei

A study of the effects of various electrolytes and one organic compound on bubble production in agarose gels is presented. Several preparations of ultrapure agarose were compared for 42 electrolytes and phenol to identify trends in bubble formation. The anion and cation sequences of bubble suppression are similar to processes for salting out of nonionic surfactants. The reduction of bubble number by polyvalent ions and 1% phenol suggests that the polar portions of these nonionic surfactants represent amide groups. The evidence for amide groups is consistent with the relative positions of Mg(2+) in all cation sequences; this result makes it unlikely that either linkages contribute to the hydrophilicity of the nonionic surfactants stabilizing bubble nuclei in the different aqueous gels tested.

Darrigo, J. S.↗

DOE OSTI2019

Using N-Terminal Coordination of Cu(II) and Ni(II) to Isolate the Coordination Environment of Cu(I) and Cu(II) Bound to His13 and His14 in Amyloid-$β$(4–16)

The amyloid-β (Aβ) peptide is a cleavage product of the amyloid precursor protein and has been implicated as a central player in Alzheimer’s disease. The N-terminal end of Aβ is variable, and different proportions of these variable-length A βpeptides are present in healthy individuals and those with the disease. The N-terminally truncated form of Aβstarting at position 4 (Aβ 4–x ) has a His residue as the third amino acid (His6 using the formal Aβ numbering). The N-terminal sequence Xaa-Xaa-His is known as an amino terminal copper and nickel binding motif (ATCUN), which avidly binds Cu(II). This motif is not present in the commonly studied Aβ1–xpeptides. In addition to the ATCUN site, Aβ 4–x contains an additional metal binding site located at the tandem His residues (bis-His at His13 and 14) which is also found in other isoforms of Aβ. Using the ATCUN and bis-His motifs, the Aβ 4–x peptide is capable of binding multiple metal ions simultaneously. We confirm that Cu(II)bound to this particular ATCUN site is redox silent, but the second Cu(II) site is redox active and can be readily reduced with ascorbate. In this work, we have employed surrogate metal ions to block copper coordination at the ATCUN or the tandem His site in order to isolate spectral features of the copper coordination environment for structural characterization using extended X-ray absorption fine structure (EXAFS) spectroscopy. This approach reveals that each copper coordination environment is independent in the Cu 2 Aβ 4–x state. The identification of two functionally different copper binding environments within theAβ 4–x sequence may have important implications for this peptide in vivo.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1993

Toward an Autonomous Feature-based Pointing System for Planetary Missions

Although the analytical groundwork for understanding two-dimensional object images and various aspects of computer vision has been laid, we have not yet applied these concepts to automating the process of obtaining science images during space exploration missions. Our current approach in specifying pointing-command sequences relies heavily on target predicts, based on predicted target and spacecraft ephemerides, that propagate the target position as a function of time during pointing operations.

Computer↗

DOE OSTI2017

Structure of an unconventional SH3 domain from the postsynaptic density protein Shank3 at ultrahigh resolution

The Shank family comprises three large multi-domain proteins playing central roles as protein scaffolds in the neuronal postsynaptic density. The Shank proteins are closely linked to neuropsychiatric diseases, such as autism spectrum disorders. One characteristic domain in the Shank family is the SH3 domain, assumed to play a role in protein-protein interactions; however, no specific ligand binding to any Shank SH3 domain has been described. We solved the crystal structure of the SH3 domain from Shank3 at sub-atomic resolution. While the structure presents the canonical SH3 domain fold, the binding site for proline-rich peptides is not conserved. In line with this, no binding of Pro-rich sequences by the Shank3 SH3 domain was observed. Sequence comparisons indicate that all Shank isoforms have similarly lost the classical Pro-rich peptide binding site from the SH3 domain. Whether the corresponding site in the Shank SH3 domains has evolved to bind a non-poly-Pro target sequence is currently not known. Our work provides an intriguing example of the evolution of a well-characterized protein-protein interaction domain within the context of multi-domain protein scaffolds, allowing the conservation of structural features, but losing canonical functional sites. The data are further discussed in light of known mutations in the SH3 domain or its vicinity in the different Shank isoforms. - Highlights: • The SH3 domain from Shank3 was studied at sub-atomic resolution. • The Shank family has lost the canonical peptide-binding site of the SH3 domain. • The Shank SH3 domain may have lost or altered canonical SH3 domain functions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Deep learning with plasma plume image sequences for anomaly detection and prediction of growth kinetics during pulsed laser deposition

Abstract Materials synthesis platforms that are designed for autonomous experimentation are capable of collecting multimodal diagnostic data that can be utilized for feedback to optimize material properties. Pulsed laser deposition (PLD) is emerging as a viable autonomous synthesis tool, and so the need arises to develop machine learning (ML) techniques that are capable of extracting information from in situ diagnostics. Here, we demonstrate that intensified-CCD image sequences of the plasma plume generated during PLD can be used for anomaly detection and the prediction of thin film growth kinetics. We develop multi-output (2 + 1)D convolutional neural network regression models that extract deep features from plume dynamics that not only correlate with the measured chamber pressure and incident laser energy, but more importantly, predict parameters of an auto-catalytic film growth model derived from in situ laser reflectivity experiments. Our results demonstrate how ML with in situ plume diagnostics data in PLD can be utilized to maintain deposition conditions in an optimal regime. Further, the predictive capabilities of plume dynamics on the kinetics of film growth or other film properties prior to deposition provides a means for rapid pre-screening of growth conditions for the non-expert, which promises to accelerate materials optimization with PLD.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Absence of genome reduction in diverse, facultative endohyphal bacteria

Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Surface Morphology and Structure of Plasma Coatings

Specific features of the structure formation in rapidly quenched high-cobalt alloy coatings formed by plasma sputtering have been investigated. The structural state of the investigated coatings has been identified by the X-ray diffraction technique. The sequence and kinetics of structural transformations occurring in the specified time-temperature heating regimes have been examined using differential thermal analysis. It has been established that heat generation and crystallization temperature depend on the conditions of formation of bulk amorphous coatings.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

NASA NTRS1975

The McIDAS system

The man-computer interactive data access system (McIDAS) hardware and software design is outlined, with emphasis on meteorological applications. The McIDAS system features a flexible digital image enhancement device. Theory of operation, the McIDAS language, the McIDAS executive monitor, image acquisition, image parameters, image display, graphics, image navigation, and image massaging are explained. The WINDCO/CLDHGT system, developed to align time sequences of geosynchronous satellite pictures and to determine the motion and height of selected cloud targets, is also described.

Smith, E. A.↗

NASA NTRS1980

Three-dimensional interactions and vortical flows with emphasis on high speeds

Diverse kinds of three-dimensional regions of separation in laminar and turbulent boundary layers are discussed that exist on lifting aerodynamic configurations immersed in flows from subsonic to hypersonic speeds. In all cases of three dimensional flow separation, the assumption of continuous vector fields of skin-friction lines and external-flow streamlines, coupled with simple topology laws, provides a flow grammar whose elemental constituents are the singular points: nodes, foci, and saddles. Adopting these notions enables one to create sequences of plausible flow structures, to deduce mean flow characteristics, expose flow mechanisms, and to aid theory and experiment where lack of resolution in numerical calculations or wind tunnel observation causes imprecision in diagnosing the three dimensional flow features.

Peake, D. J.↗