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At least 811 records · Page 45

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DOE OSTI2021

Genetic Subtypes and Natural Resistance Mutations in HCV Genotype 4 Infected Saudi Arabian Patients

This study aimed to characterize the HCV genetic subtypes variability and the presence of natural occurring resistance-associated substitutions (RASs) in Saudi Arabia patients. A total of 17 GT patients were analyzed. Sequence analysis of NS3, NS5A, and NS5B regions was performed by direct sequencing, and phylogenetic analyses were used to determine genetic subtypes, RAS, and polymorphisms. Nine patients were infected by GT 4a, two with GT 4o and three with GT 4d. Two patients were infected with apparent recombinant virus (4a/4o/4a in NS3/NS5A/NS5B), and one patient was infected with a previously unknown, unclassifiable, virus of GT 4. Natural RASs were found in six patients (35%), including three infected by GT 4a, two by GT 4a/GT 4o/GT 4a, and one patient infected by an unknown, unclassifiable, virus of GT 4. In particular, NS3-RAS V170I was demonstrated in three patients, while NS5A-RASs (L28M, L30R, L28M + M31L) were detected in the remaining three patients. All patients were treated with sofosbuvir plus daclatasvir; three patients were lost to follow-up, whereas 14 patients completed the treatment. A sustained virological response (SVR) was obtained in all but one patient carrying NS3-RAS V170I who later relapsed. GT 4a is the most common subtype in this small cohort of Saudi Arabia patients infected with hepatitis C infection. Natural RASs were observed in about one-third of patients, but only one of them showed a treatment failure.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research

Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as “prime editing,” has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Oxidation of the Interiors of Carbide Exoplanets

Astrophysical measurements have shown that some stars have sufficiently high carbon-to-oxygen ratios such that the planets they host would be mainly composed of carbides instead of silicates. We studied the behavior of silicon carbide in the presence of water under the high pressure–temperature conditions relevant to planetary interiors in the laser-heated diamond-anvil cell. When reacting with water, silicon carbide converts to silica (stishovite) and diamond at pressures up to 50 GPa and temperatures up to 2500 K: $\mathrm{SiC}+2{{\rm{H}}}_{2}{\rm{O}}\to {\mathrm{SiO}}_{2}+{\rm{C}}+2{{\rm{H}}}_{2}$. Therefore, if water can be incorporated into carbide planets during their formation or through later delivery, they could be oxidized and have mineralogy dominated by silicates and diamond in their interiors. The reaction could produce CH 4 at shallower depths and H 2 at greater depths that could be degassed from the interior, causing the atmospheres of the converted carbon planets to be rich in reducing gases. Excess water after the reaction can be stored in dense silica polymorphs in the interiors of the converted carbon planets. Such conversion of mineralogy to diamond and silicates would decrease the density of carbon-rich planet, making the converted planets distinct from silicate planets in mass–radius relations for the 2–8 Earth mass range.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

HLA Class I Supertype Classification Based on Structural Similarity

HLA class I proteins, a critical component in adaptive immunity, bind and present intracellular Ags to CD8+ T cells. The extreme polymorphism of HLA genes and associated peptide binding specificities leads to challenges in various endeavors, including neoantigen vaccine development, disease association studies, and HLA typing. Supertype classification, defined by clustering functionally similar HLA alleles, has proven helpful in reducing the complexity of distinguishing alleles. However, determining supertypes via experiments is impractical, and current in silico classification methods exhibit limitations in stability and functional relevance. In this study, by incorporating three-dimensional structures we present a method for classifying HLA class I molecules with improved breadth, accuracy, stability, and flexibility. Critical for these advances is our finding that structural similarity highly correlates with peptide binding specificity. The new classification should be broadly useful in peptide-based vaccine development and HLA–disease association studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18

Genome-wide association studies for non-syndromic orofacial clefting (OFC) have identified single nucleotide polymorphisms (SNPs) at loci where the presumed risk-relevant gene is expressed in oral periderm. The functional subsets of such SNPs are difficult to predict because the sequence underpinnings of periderm enhancers are unknown. We applied ATAC-seq to models of human palate periderm, including zebrafish periderm, mouse embryonic palate epithelia, and a human oral epithelium cell line, and to complementary mesenchymal cell types. We identified sets of enhancers specific to the epithelial cells and trained gapped-kmer support-vector-machine classifiers on these sets. We used the classifiers to predict the effects of 14 OFC-associated SNPs at 12q13 near KRT18. All the classifiers picked the same SNP as having the strongest effect, but the significance was highest with the classifier trained on zebrafish periderm. Reporter and deletion analyses support this SNP as lying within a periderm enhancer regulating KRT18/KRT8 expression.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths ( Bradypus variegatus ), the first from a non-human host

Kerstersia gyiorum is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of K. gyiorum is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about K. gyiorum is very limited, especially from non-human hosts. In this work, we sequenced 12 K. gyiorum genomes isolated from healthy free-living brown-throated sloths (Bradypus variegatus) in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these K. gyiorum strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth K. gyiorum diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various K. gyiorum lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific K. gyiorum genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in K. gyiorum (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in K. gyiorum genomes. Gene content variation may be important for the adaptation of K. gyiorum to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of K. gyiorum, by presenting and analyzing the first genomes of non-human isolates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Nonclassical Crystallization Pathway in Biomolecular Self-assembly

Biomolecular self-assembly plays a vital role in synthetic and biological material systems and has therefore attracted tremendous interest due to its great potential for applications in biomedical and tissue engineering, biosensing, materials science, and nanotechnology. Although there have been numerous studies focusing on these systems’ designs, structures, and functions, little attention has been given to the mechanisms by which they nucleate. In this chapter, we review some recent advances in understanding the nucleation pathways of self-assembling biomolecular systems. We will mainly focus on crystallization via nonclassical nucleation mechanisms, which involve the addition of oligomers and more complex species or passage through transient metastable states, including dense liquids, amorphous clusters, and crystalline polymorphs. However, some cases that go through classical pathways are also introduced and discussed.

Chen, Jiajun↗

DOE OSTI2022

ϵ-VOPO 4 cathode for lithium ion batteries

The epsilon polymorph of vanadyl phosphate, ε-VOPO 4 , made from the solvothermally synthesized H 2 VOPO 4 , is a high density cathode material for lithium-ion batteries optimized to reversibly intercalate two Li-ions to reach the full theoretical capacity at least 50 cycles with a coulombic efficiency of 98%. This material adopts a stable 3D tunnel structure and can extract two Li-ions per vanadium ion, giving a theoretical capacity of 305 mAh/g, with an upper charge/discharge plateau at around 4.0 V, and one lower at around 2.5 V.

25 ENERGY STORAGE↗

DOE OSTI2022

Stabilized birnessite cathode for high power and high energy density applications

A battery comprises a housing, an electrolyte disposed in the housing, an anode disposed in the housing, a stabilized cathode disposed in the housing and comprising a cathode material. The cathode material comprises a composition selected from birnessite or layered-polymorph of manganese dioxide (δ-MnO2), the composition being stabilized by bismuth and copper ions, a conductive carbon, and a binder. The anode can be at least 50% (m/m) lithium, magnesium, aluminum, or zinc.

Yadav, Gautam G.↗

DOE OSTI2023

Instability of Rock-Salt Cubic NbN in Density Functional Calculations

All-nitride semiconductor/superconductor heterojunctions utilizing cubic niobium nitride (NbN) are a promising approach to superconducting quantum circuits for next-generation quantum-information systems. However, there are fundamental open questions on the atomic structure of NbN. In calculations with several levels of density functional theory (DFT), we find that the cubic rocksalt structure NbN (Fm-3m, 225) is energetically very unstable against the ground state hexagonal NbN in a tungsten carbide (P-6m2, 187) type lattice. To better understand the appearance of a cubic phase in numerous experiments, we perform a DFT study on possible NbN structures, determining the energy ordering between different polymorphs from databases and structure prediction. We perform supercell calculations of disordered NbN, finding that the rocksalt structure is dynamically unstable and relaxes to a lower energy monoclinic phase (C2/m, 12), which retains an approximate average cubic symmetry. However, the associated energy gain is not substantial enough for a plausible explanation for cubic NbN. We further investigate the role of external factors such as in-plane strain during epitaxial growth as well as the presence of off-stoichiometry and impurity doping on the energy ordering.

CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SU↗

DOE OSTI2022

Formation of high quality alane

Methods for forming alane are described. The method includes addition of toluene at a temperature above the crystallization temperature of alane to a lower temperature solution that includes alane adduct, ether, and toluene. Upon the addition, a crystallization mixture is formed that is at or near the crystallization temperature of alane. The alane of the mixture crystallizes over a period of time to form a high purity alane polymorph.

Zidan, Ragaiy↗

DOE OSTI2023

ϵ-VOPO 4 cathode for lithium ion batteries

25 ENERGY STORAGE↗

DOE OSTI2020

(Oxy)hydroxides Formed on Aluminum Fuel Materials After Irradiation and Long-Term Wet Storage - 20354

The aluminum cladding of research-reactor fuel experiences general corrosion when in contact with water during in-reactor service and post-discharge wet storage, resulting in the formation of adherent aluminum (oxy)hydroxide films. These (oxy)hydroxides contain chemically-bound water that poses challenges for extended dry storage due to the risk of thermal or radiolytic decomposition releasing free water and/or hydrogen and oxygen gases. This study describes characterization of the (oxy)hydroxides present on several aluminum materials used in reactor operation and subsequently stored wet in the L-Basin storage facility at the Savannah River Site (SRS) for an extended period. Characterization data providing insight into the loading, composition, and morphology of (oxy)hydroxides to be expected on service-exposed aluminum cladding provides valuable benchmarks for designing adequate drying and dry-storage approaches. This work is part of a broader investigation to address knowledge gaps and technical data needs for dry storage of aluminum-clad spent nuclear fuel (ASNF), which included in-lab growth of (oxy)hydroxide films on aluminum alloy substrates to investigate formation behavior, investigation of drying methods to remove existing (oxy)hydroxides from ASNF cladding, and measurement of radiolytic yield of hydrogen from (oxy)hydroxide powders and films. In this study, (oxy)hydroxide films were characterized for three aluminum-alloy materials used in reactors and subsequently stored wet for up to approximately 40 years in L-Basin at SRS: one cropping from a Missouri University Research Reactor (MURR) fuel element (Al-6061 alloy), one cropping from a Universal Sleeve Housing (USH) (Al-6063 alloy), and one Mark-16B fuel assembly (either Al-6061 or Al- 6063). The USH and Mark-16B were used in SRS production reactors. Characterization of the as-received (oxy)hydroxides included scanning electron microscopy (SEM) in both plan-view and cross-section to characterize the (oxy)hydroxide layer's morphology, thickness, and structure. X-ray diffraction (XRD) was used to identify the chemical composition and distinguish between the various aluminum (oxy)hydroxides known to form under reactor and storage conditions. XRD analysis revealed both bayerite (Al(OH)3) and boehmite (AlOOH) on the surface of the MURR and USH samples, as well as bayerite, boehmite, and gibbsite (another Al(OH)3 polymorph) on the surface of the Mark-16B sample. The aluminum trihydroxides, bayerite and gibbsite, are typically associated with corrosion in low-temperature (<80 deg. C) water, while boehmite is expected to form at higher water temperature (>80 deg. C). The presence of bayerite on the USH, which is believed to have operated close to 90 deg. C, suggests that boehmite formed during in-reactor exposure was not protective against further hydroxide growth in low-temperature wet storage. Cross-section scanning electron microscopy (SEM) showed total (oxy)hydroxide layer thicknesses of ∼5- 10 μm for the MURR and ∼5-15 μm for the Mark-16B. The thickness of the USH's (oxy)hydroxide layer was indiscernible by the current mounting and imaging method, despite plan-view SEM and XRD confirming the presence of an (oxy)hydroxide layer. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

ε-VOPO 4 cathode for lithium ion batteries

Siu, Carrie↗

DOE OSTI2024

Gyromagnetic nonlinear transmission line for radio frequency signal generation and pulse compression

Disclosed are non-linear transmission lines using ferromagnetic materials to generate ferromagnetic resonance oscillations. In one aspect, a non-linear transmission line apparatus is disclosed. The apparatus includes an outer conductor having a first side and a second internally facing side, and an inner conductor positioned internal to the non-linear transmission line apparatus. The apparatus further includes a ferromagnetic material surrounding the inner conductor, wherein the ferromagnetic material comprises nanoparticles of an ε-polymorph of iron oxide expressed as ε-Fe2O3. The apparatus also includes a first dielectric material positioned between the outer conductor and the inner conductor, the dielectric material in contact with both the ferromagnetic material and with the second internally facing side of the outer conductor, wherein the outer conductor, the inner conductor, the dielectric material and the ferromagnetic material form the nonlinear transmission line.

Schneider, Joseph Devin↗

DOE OSTI2024

Adoption of ROOT RNTuple for the next main event data storage technology in the ATLAS production framework Athena

Since the start of LHC in 2008, the ATLAS experiment has relied on ROOT to provide storage technology for all its processed event data. Internally, ROOT files are organized around TTree structures that are capable of storing complex C++ objects. The capabilities of TTrees developed over the years and are now offering support for advanced concepts like polymorphism, schema evolution and user defined collections and ATLAS makes use of these features to handle its EDM. But some original TTrees concepts, like the POSIX file model and sequential writing, remain unchanged since the beginning and could be an obstacle to achieving the performance required for High Luminosity LHC. With the HL-LHC performance goals in mind, the ROOT project developed a new storage format - the RNTuple. RNTuple, with its accompanying user API, is now in the final development stage and is planned to be production-ready at the end of 2024. Soon after that, the TTree will become a legacy format. ATLAS intends to have its main Event processing framework Athena ready to use RNTuple in the production environment as early as possible. The work on adopting RNTuple as another ROOT storage technology in Athena started already in 2021 and is now nearly complete. Although the initial goal was to focus on derived-AOD products (PHYS and PHYSLITE), with a little added effort all ATLAS data products: RDO, HITS, ESD, AOD and DAOD can be now stored in RNTuple format and transparently read back. In this paper we will describe the current state of RNTuple adoption in the Athena framework and explain the ATLAS EDM requirements that had to be met on the ROOT side to successfully integrate both environments. We will demonstrate the ability to run standard ATLAS production workflows, based on RNTuple as the Event data storage technology, and point out key advantages of the new format.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Remote Instrumentation and Data Acquisition: An Internship Research Report

This report outlines the development and implementation of a remote data acquisition system for waveform analysis using a Rohde & Schwarz oscilloscope. The project involved capturing waveform data, and transferring it to a local machine for visualization and analysis. The core logic was developed in C++ with a focus on object oriented programming and the use of polymorphism so the main application can interact with any instrument without knowing its exact type, simplifying the overall logic and making it easier to add or swap out components without changing the rest of the codebase.. The system issues Standard Commands for Programmable Instruments (SCPI) via a socket connection and parses the oscilloscope’s ASCII waveform data. The C++ application was containerized using Docker for ease of portability, and reproducibility. Emphasis was placed on secure networking practices, error handling, and effective data capture. The report describes the technical steps taken, challenges encountered, and lessons learned, providing insight into the practical integration of hardware interfacing with remote computational environments.

Parikh, Jaymil [Fermilab]↗