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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Psilocybin: crystal structure solutions enable phase analysis of prior art and recently patented examples

Psilocybin {systematic name: 3-[2-(dimethylamino)ethyl]-1 H -indol-4-yl dihydrogen phosphate} is a zwitterionic tryptamine natural product found in numerous species of fungi known for their psychoactive properties. Following its structural elucidation and chemical synthesis in 1959, purified synthetic psilocybin has been evaluated in clinical trials and has shown promise in the treatment of various mental health disorders. In a recent process-scale crystallization investigation, three crystalline forms of psilocybin were repeatedly observed: Hydrate A, Polymorph A, and Polymorph B. The crystal structure for Hydrate A was solved previously by single-crystal X-ray diffraction. This article presents new crystal structure solutions for the two anhydrates, Polymorphs A and B, based on Rietveld refinement using laboratory and synchrotron X-ray diffraction data, and density functional theory (DFT) calculations. Utilizing the three solved structures, an investigation was conducted via Rietveld method (RM) based quantitative phase analysis (QPA) to estimate the contribution of the three different forms in powder X-ray diffraction (PXRD) patterns provided by different sources of bulk psilocybin produced between 1963 and 2021. Over the last 57 years, each of these samples quantitatively reflect one or more of the hydrate and anhydrate polymorphs. In addition to quantitatively evaluating the composition of each sample, this article evaluates correlations between the crystal forms present, corresponding process methods, sample age, and storage conditions. Furthermore, revision is recommended on characterizations in recently granted patents that include descriptions of crystalline psilocybin inappropriately reported as a single-phase `isostructural variant.' Rietveld refinement demonstrated that the claimed material was composed of approximately 81% Polymorph A and 19% Polymorph B, both of which have been identified in historical samples. In this article, we show conclusively that all published data can be explained in terms of three well-defined forms of psilocybin and that no additional forms are needed to explain the diffraction patterns.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Accelerating Random Forest Classification on GPU and FPGA

Random Forests (RFs) are a commonly used machine learning method for classification and regression tasks spanning a variety of application domains, including bioinformatics, business analytics, and software optimization. While prior work has focused primarily on improving performance of the training of RFs, many applications, such as malware identification, cancer prediction, and banking fraud detection, require fast RF classification. In this work, we accelerate RF classification on GPU and FPGA. In order to provide efficient support for large datasets, we propose a hierarchical memory layout suitable to the GPU/FPGA memory hierarchy. We design three RF classification code variants based on that layout, and we investigate GPU- and FPGA-specific considerations for these kernels. Our experimental evaluation, performed on an Nvidia Xp GPU and on a Xilinx Alveo U250 FPGA accelerator card using publicly available datasets on the scale of millions of samples and tens of features, covers various aspects. First, we evaluate the performance benefits of our hierarchical data structure over the standard compressed sparse row (CSR) format. Second, we compare our GPU implementation with cuML, a machine learning library targeting Nvidia GPUs. Third, we explore the performance/accuracy tradeoff resulting from the use of different tree depths in the RF. Finally, we perform a comparative performance analysis of our GPU and FPGA implementations. Our evaluation shows that for high accuracy targets, our GPU implementation yields 5-9x speedup over CSR, and up to a 2x speedup over cuML.

FPGA, Xilinx FPGA, GPU, Random Forest classificati↗
DOE OSTI2020

Laser metal deposition of refractory high-entropy alloys for high-throughput synthesis and structure-property characterization

Progress in materials development is often paced by the time required to produce and evaluate a large number of alloys with different chemical compositions. This applies especially to refractory high-entropy alloys (RHEAs), which are difficult to synthesize and process by conventional methods. To evaluate a possible way to accelerate the process, high-throughput laser metal deposition was used in this work to prepare a quinary RHEA, TiZrNbHfTa, as well as its quaternary and ternary subsystems by in-situ alloying of elemental powders. Compositionally graded variants of the quinary RHEA were also analyzed. Our results show that the influence of various parameters such as powder shape and purity, alloy composition, and especially the solidification range, on the processability, microstructure, porosity, and mechanical properties can be investigated rapidly. The strength of these alloys was mainly affected by the oxygen and nitrogen contents of the starting powders, while substitutional solid solution strengthening played a minor role.

additive manufacturing↗
DOE OSTI2023

Broad SARS-CoV-2 neutralization by monoclonal and bispecific antibodies derived from a Gamma-infected individual

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has remained a medical threat due to the evolution of multiple variants that acquire resistance to vaccines and prior infection. Therefore, it is imperative to discover monoclonal antibodies (mAbs) that neutralize a broad range of SARS-CoV-2 variants. A stabilized spike glycoprotein was used to enrich antigen-specific B cells from an individual with a primary Gamma variant infection. Five mAbs selected from those B cells showed considerable neutralizing potency against multiple variants, with COVA309-35 being the most potent against the autologous virus, as well as Omicron BA.1 and BA.2, and COVA309-22 having binding and neutralization activity against Omicron BA.4/5, BQ.1.1, and XBB.1. When combining the COVA309 mAbs as cocktails or bispecific antibodies, the breadth and potency were improved. In addition, the mechanism of cross-neutralization of the COVA309 mAbs was elucidated by structural analysis. Altogether these data indicate that a Gamma-infected individual can develop broadly neutralizing antibodies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Mimicking Extradiol Dioxygenase Reactivity on Iridium

Extradiol dioxygenases catalyze the cleavage of benzenediol (catechol) or vicinal aminophenols via oxygen atom insertion into the 2,3- C–C bond. These reactions are most often proposed to proceed through the migratory rearrangement of a d6 alkylperoxide, generating the corresponding d 6 ring expanded product. However, regiospecific insertion remains a rare outcome among synthetic model complexes. Here, a dioxygenated Ir complex (2) converts to (a) the paramagnetic metallatrioxolane (3) and (b) oxygen atom inserted products (4) and (5); all three complexes are third-row metal analogues of enzymatic intermediates. The conversion of 2 to 3 was triggered by an H• abstraction, generating a third-row metallatrioxolane that is one electron reduced from the canonical d 6 alkylperoxide. Alternatively, photolysis of 2 (467 nm) results in ring-expanded product 4, from which an H• can be abstracted to generate 5. This latter complex is also one electron reduced relative to the canonical ring expansion product. Because extradiol mechanisms were largely defined using Fe(II) metallocofactors, 3 and 5 may be especially relevant to the known Co(II) accepting variants. We propose these states became synthetically accessible via the incorporation of a catechol-like substrate into the larger, multidentate ligand L1. This perturbation enhances the affinity of L1 (and related intermediates) to the metal. The same perturbation may have also been key in characterizing the first κ 2 -bound, dianionic ortho ester ligand – the observed binding mode in the x-ray structure of 5. Broadly, we propose through this case study that connecting abiological dioxygen complexes to non-heme oxygenase-like intermediates might be a “roadmap” towards regiospecific aerobic oxygenations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Prefusion-stabilized SARS-CoV-2 S2-only antigen provides protection against SARS-CoV-2 challenge

Ever-evolving SARS-CoV-2 variants of concern (VOCs) have diminished the effectiveness of therapeutic antibodies and vaccines. Developing a coronavirus vaccine that offers a greater breadth of protection against current and future VOCs would eliminate the need to reformulate COVID-19 vaccines. Here, we rationally engineer the sequence-conserved S2 subunit of the SARS-CoV-2 spike protein and characterize the resulting S2-only antigens. Structural studies demonstrate that the introduction of interprotomer disulfide bonds can lock S2 in prefusion trimers, although the apex samples a continuum of conformations between open and closed states. Immunization with prefusion-stabilized S2 constructs elicits broadly neutralizing responses against several sarbecoviruses and protects female BALB/c mice from mouse-adapted SARS-CoV-2 lethal challenge and partially protects female BALB/c mice from mouse-adapted SARS-CoV lethal challenge. These engineering and immunogenicity results should inform the development of next-generation pan-coronavirus therapeutics and vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Evolving dual-trait EPSP synthase variants using a synthetic yeast selection system

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) functions in the shikimate pathway which is responsible for the production of aromatic amino acids and precursors of other essential secondary metabolites in all plant species. EPSPS is also the molecular target of the herbicide glyphosate. While some plant EPSPS variants have been characterized with reduced glyphosate sensitivity and have been used in biotechnology, the glyphosate insensitivity typically comes with a cost to catalytic efficiency. Thus, there exists a need to generate additional EPSPS variants that maintain both high catalytic efficiency and high glyphosate tolerance. Here, we create a synthetic yeast system to rapidly study and evolve heterologous EPSP synthases for these dual traits. Using known EPSPS variants, we first validate that our synthetic yeast system is capable of recapitulating growth characteristics observed in plants grown in varying levels of glyphosate. Next, we demonstrate that variants from mutagenesis libraries with distinct phenotypic traits can be isolated depending on the selection criteria applied. By applying strong dual-trait selection pressure, we identify a notable EPSPS mutant after just a single round of evolution that displays robust glyphosate tolerance (K i of nearly 1 mM) and improved enzymatic efficiency over the starting point (~2.5 fold). Finally, we show the crystal structure of corn EPSPS and the top resulting mutants and demonstrate that certain mutants have the potential to outperform previously reported glyphosate-resistant EPSPS mutants, such as T102I and P106S (denoted as TIPS), in whole-plant testing. Altogether, this platform helps explore the trade-off between glyphosate resistance and enzymatic efficiency.

Science & Technology - Other Topics↗
DOE OSTI2023

Site specific N- and O-glycosylation mapping of the spike proteins of SARS-CoV-2 variants of concern

Abstract The glycosylation on the spike (S) protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, modulates the viral infection by altering conformational dynamics, receptor interaction and host immune responses. Several variants of concern (VOCs) of SARS-CoV-2 have evolved during the pandemic, and crucial mutations on the S protein of the virus have led to increased transmissibility and immune escape. In this study, we compare the site-specific glycosylation and overall glycomic profiles of the wild type Wuhan-Hu-1 strain (WT) S protein and five VOCs of SARS-CoV-2: Alpha, Beta, Gamma, Delta and Omicron. Interestingly, both N- and O-glycosylation sites on the S protein are highly conserved among the spike mutant variants, particularly at the sites on the receptor-binding domain (RBD). The conservation of glycosylation sites is noteworthy, as over 2 million SARS-CoV-2 S protein sequences have been reported with various amino acid mutations. Our detailed profiling of the glycosylation at each of the individual sites of the S protein across the variants revealed intriguing possible association of glycosylation pattern on the variants and their previously reported infectivity. While the sites are conserved, we observed changes in the N- and O-glycosylation profile across the variants. The newly emerged variants, which showed higher resistance to neutralizing antibodies and vaccines, displayed a decrease in the overall abundance of complex-type glycans with both fucosylation and sialylation and an increase in the oligomannose-type glycans across the sites. Among the variants, the glycosylation sites with significant changes in glycan profile were observed at both the N -terminal domain and RBD of S protein, with Omicron showing the highest deviation. The increase in oligomannose-type happens sequentially from Alpha through Delta. Interestingly, Omicron does not contain more oligomannose-type glycans compared to Delta but does contain more compared to the WT and other VOCs. O-glycosylation at the RBD showed lower occupancy in the VOCs in comparison to the WT. Our study on the sites and pattern of glycosylation on the SARS-CoV-2 S proteins across the VOCs may help to understand how the virus evolved to trick the host immune system. Our study also highlights how the SARS-CoV-2 virus has conserved both N - and O - glycosylation sites on the S protein of the most successful variants even after undergoing extensive mutations, suggesting a correlation between infectivity/ transmissibility and glycosylation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease

Pan-betacoronavirus neutralizing antibodies may hold the key to developing broadly protective vaccines against novel pandemic coronaviruses and to more effectively respond to SARS-CoV-2 variants. The emergence of Omicron and subvariants of SARS-CoV-2 illustrates the limitations of solely targeting the receptor-binding domain (RBD) of the spike (S) protein. Here, we isolated a large panel of broadly neutralizing antibodies (bnAbs) from SARS-CoV-2 recovered-vaccinated donors, which targets a conserved S2 region in the betacoronavirus spike fusion machinery. Select bnAbs showed broad in vivo protection against all three deadly betacoronaviruses, SARS-CoV-1, SARS-CoV-2, and MERS-CoV, which have spilled over into humans in the past two decades. Structural studies of these bnAbs delineated the molecular basis for their broad reactivity and revealed common antibody features targetable by broad vaccination strategies. These bnAbs provide new insights and opportunities for antibody-based interventions and for developing pan-betacoronavirus vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

A small-angle neutron scattering study of the physical mechanism that drives the action of a viral fusion peptide

Viruses have evolved a variety of ways for delivering their genetic cargo to a target cell. One mechanism relies on a short sequence from a protein of the virus that is referred to as a fusion peptide. In some cases, the isolated fusion peptide is also capable of causing membranes to fuse. Infection by HIV-1 involves the 23 amino acid N-terminal sequence of its gp41 envelope protein, which is capable of causing membranes to fuse by itself, but the mechanism by which it does so is not fully understood. In this study, a variant of the gp41 fusion peptide that does not strongly promote fusion was studied in the presence of vesicles composed of a mixture of unsaturated lipids and cholesterol by small-angle neutron scattering and circular dichroism spectroscopy to improve the understanding of the mechanism that drives vesicle fusion. The peptide concentration and cholesterol content govern both the peptide conformation and its impact on the bilayer structure. The results indicate that the mechanism that drives vesicle fusion by the peptide is a strong distortion of the bilayer structure by the peptide when it adopts the β-sheet conformation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Disturbance–diversity relationships of microbial communities change based on growth substrate

Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances and how those responses can vary is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that the community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticcacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticcacaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (1.95–7.33 Hill 1 diversity) that peaks at the intermediate disturbance frequency treatment or one disturbance every 3 days. Communities grown on glucose, however, ranged from 1.63 to 5.19 Hill 1 diversity with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency and may potentially explain the variety of diversity–disturbance relationships observed in microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Two-Color IRMPD Applied to Conformationally Complex Ions: Probing Cold Ion Structure and Hot Ion Unfolding

Two-color infrared multiphoton dissociation (2C-IRMPD) spectroscopy is a technique that mitigates spectral distortions due to nonlinear absorption that is inherent to one-color IRMPD. We use a 2C-IRMPD scheme that incorporates two independently tunable IR sources, providing considerable control over the internal energy content and type of spectrum obtained by varying the trap temperature, the time delays and fluences of the two infrared lasers, and whether the first or second laser wavelength is scanned. In this work, we describe the application of this variant of 2C-IRMPD to conformationally complex peptide ions. The 2C-IRMPD technique is used to record near-linear action spectra of both cations and anions with temperatures ranging from 10 to 300 K. In this work, we also determine the conditions under which it is possible to record IR spectra of single conformers in a conformational mixture. Furthermore, we demonstrate the capability of the technique to explore conformational unfolding by recording IR spectra with widely varying internal energy in the ion. The protonated peptide ions YGGFL (NH 3 + -Tyr-Gly-Gly-Phe-Leu, Leu-enkephalin) and YGPAA (NH 3 + -Tyr-Gly-Pro-Ala-Ala) are used as model systems for exploring the advantages and disadvantages of the method when applied to conformationally complex ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Vanadium-enhanced Na 2 FePO 4 F cathodes for high-performance sodium-ion batteries

Sodium fluorophosphate Na 2 FePO 4 F holds great potential for sodium-ion batteries due to its high theoretical capacity, excellent structural stability, abundant resources, and affordability. However, its poor electronic and ionic conductivities limit its practical applications. Therefore, ion doping and carbon coating have been employed as synergistic strategies in this study to overcome these limitations. A one-step, energy-efficient solid-state method using sucrose as a carbon coating source was used to synthesize Na 2 FePO 4 F/C (NFPF/C) and its doped variant, Na 2 Fe 0.85 V 0.1 PO 4 F/C (NFVPF/C). 23 Na-MAS-NMR spectra confirm the existence of two distinct sites for sodium (Na1/Na2). The ex-situ 23 Na-MAS-NMR performed at different states-of-charge reveals the activity of only one sodium. The scanning electron microscopy findings reveal a reduction in the particle size with V-introduction, enhancing the energetic performances. NFVPF/C delivers higher specific capacity of 122 mAh g −1 compared to 116 mAh g −1 for NFPF/C at 0.1C. It also demonstrates improved cycling stability, retaining 81 % of its initial capacity after 120 cycles, in contrast to 46 % for the pristine material. The doped phase outperforms the pristine at higher current rates, delivering specific capacities of 81 and 55 mAh g −1 at 2C and 3C, respectively, compared to 35 and 17 mAh g −1 for NFPF/C.

25 ENERGY STORAGE↗
DOE OSTI2024

In-situ and ex-situ characterization of irradiated AM materials

This study investigates the irradiation performance of laser powder bed fusion (LPBF) 316L and 316H stainless steels (SS), and their wrought counterparts. While LPBF 316L has been more studied, LPBF 316H is relatively new, with little prior data on its irradiation behavior. The research involved fabricating, preparing, irradiating, and characterizing six materials: LPBF 316L (two variants), LPBF 316H (two variants), and wrought 316L and 316H. LPBF materials were subjected to various heat treatments, including solution annealing and stress relief, and were irradiated using in-situ and ex-situ ion techniques at temperatures of 300°C and 600°C, with doses ranging from 0.2 dpa to 25 dpa. Under ex-situ irradiation with 4 MeV Ni 2+ ions at 600°C, the dislocation cell structures in LPBF316L-1 and LPBF316H-1 gradually evolved into a uniform dislocation network. At a low irradiation dose (0.2 dpa), the cell structures were still partially visible. At 2 dpa, a uniform dislocation network formed, though remnants of the original cell structure were still discernible as contrast domains. At 5 dpa and 10 dpa, even the contrast domains vanished. For irradiation at 300°C, the cell structure was still clearly visible at 0.2 dpa for LPBF316L-1. For LPBF316H-1, the dislocation cell structure was less apparent at the same dose but was still recognizable. With further increase in dose at 300°C, the dislocation cell walls were completely replaced by irradiation-induced defects and no longer visible. Void formation was observed for irradiation at 600°C. At 2 dpa, no evident voids were observed in either LPBF316L-1 or LPBF316H-1.

36 MATERIALS SCIENCE↗
NASA NTRS1989

Local intensity adaptive image coding

The objective of preprocessing for machine vision is to extract intrinsic target properties. The most important properties ordinarily are structure and reflectance. Illumination in space, however, is a significant problem as the extreme range of light intensity, stretching from deep shadow to highly reflective surfaces in direct sunlight, impairs the effectiveness of standard approaches to machine vision. To overcome this critical constraint, an image coding scheme is being investigated which combines local intensity adaptivity, image enhancement, and data compression. It is very effective under the highly variant illumination that can exist within a single frame or field of view, and it is very robust to noise at low illuminations. Some of the theory and salient features of the coding scheme are reviewed. Its performance is characterized in a simulated space application, the research and development activities are described.

Huck, Friedrich O.↗
NASA NTRS1993

Design of a recumbent seating system

Future space shuttle missions presented by NASA might require the shuttle to rendezvous with the Russian space station Mir for the purpose of transporting astronauts back to earth. Due to the atrophied state of these astronauts, a special seating system must be designed for their transportation. The main functions of this seating system are to support and restrain the astronauts during normal reentry flight and to dampen some of the loading that might occur in a crash situation. Through research, the design team developed many concept variants for these functional requirements. By evaluating each variant, the concepts were eliminated until the four most attractive designs remained. The team used a decision matrix to determine the best concept to carry through embodiment. This concept involved using struts for support during reentry flight and a spring damper/shock absorber system to dampen crash landing loads. The embodiment design process consisted of defining the layout of each of the main functional components, specifically, the seat structure and the strut structure. Through the use of MCS/pal two, the design was refined until it could handle all required loads and dampen to the forces specified. The auxiliary function carriers were then considered. Following the design of these components, the complete final layout could be determined. It is concluded that the final design meets all specifications outlined in the conceptual design. The main advantages of this design are its low weight, simplicity, and large amount of function sharing between different components. The disassembly of this design could potentially present a problem because of time and size constraints involved. Overall, this design meets or exceeds all functional requirements.

Croyle, Scott↗
NASA NTRS1997

An Inlet Distortion Assessment During Aircraft Departures at High Angle of Attack for an F/A-18A Aircraft

The F404-GE-400-powered F/A-18A High Alpha Research Vehicle (HARV) was used to examine the quality of inlet airflow during departed flight maneuvers, that is, during flight outside the normal maneuvering envelope where control surfaces have little or no effectiveness. Six nose-left and six nose-right departures were initiated at Mach numbers between 0.3 and 0.4 at an altitude of 35 kft. The entry yaw rates were approximately 40 to 90 deg/sec. Engine surges were encountered during three of the nose-left and one of the nose-right departures. Time-variant inlet-total-pressure distortion levels at the engine face did not significantly exceed those at maximum angle-of-attack and sideslip maneuvers during controlled flight. Surges caused by inlet distortion levels resulted from a combination of high levels of inlet distortion and rapid changes in aircraft position. These rapid changes indicate a combination of engine support and gyroscopic loads being applied to the engine structure that impact the aerodynamic stability of the compressor through changes in the rotor-to-case clearances. This document presents the slides from an oral presentation.

Steenken, William G.↗
DOE OSTI2023

Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants

HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem, and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug-resistant HIV-1 intasomes bound to DTG or 4d, with better than 3-Å resolution. These structures, complemented with free energy simulations, virology, and enzymology, explain the mechanisms of DTG resistance involving E138K + G140A/S + Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.

59 BASIC BIOLOGICAL SCIENCES↗