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DOE OSTI2023

Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study

Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2"), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec 57395 were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

A structure-preserving machine learning framework for accurate prediction of structural dynamics for systems with isolated nonlinearities

The nonlinearities present in structural systems are often found in isolated regions within the structure, such as those containing joints or interfaces. However, despite the localized nature of these nonlinearities their presence serves to couple together the modes of the underlying linear system and significantly complicate the development of appropriate reduced-order models; the localized nonlinearities have a global effect on the dynamics of the system. Further, in the presence of evolving structural health the nonlinearities can arise from accumulating damage, with dynamics distinct from those observed in the healthy state. The present work develops a data-driven formulation to identify and include the contributions of the isolated nonlinearities on the dynamics of the underlying linear structure. A novel coordinate separation is developed that decomposes those nonlinearities restricted to the isolated subdomain from the known linear system defined over the entire domain, and the influence of the isolated nonlinearities is reintroduced as an appropriately identified traction at the boundary of the isolated subdomain, referred to as the deviatoric force. In the region exterior to the nonlinear subdomain the response of the ideal linear system recovers that of the original nonlinear system. In this work, the deviatoric force component is predicted using a structure-preserving multilayer perceptron, based only on measured responses at the boundary of the isolated subdomain. Therefore introduction of the perceptron is able to bypass the direct numerical simulation of the nonlinearities within the isolated subdomain. This approach is illustrated through a simple structural system in which an interior region contains cubic nonlinearities and hysteretic damping. Once trained, the machine learning system is able to accurately predict the deviatoric force so that the ideal system recovers the response of the original system in the region outside the isolated nonlinear subdomain. Moreover, the data-driven approach is able to accurately predict the response when the system is subject to differing initial conditions and external excitation without the need for retraining, so that the proposed approach provides a robust description of the structural dynamics of the overall system.

Machine learning↗

DOE OSTI2021

Revisiting the guidelines for ending isolation for COVID-19 patients

Since the start of the COVID-19 pandemic, two mainstream guidelines for defining when to end the isolation of SARS-CoV-2-infected individuals have been in use: the one-size-fits-all approach (i.e. patients are isolated for a fixed number of days) and the personalized approach (i.e. based on repeated testing of isolated patients). We use a mathematical framework to model within-host viral dynamics and test different criteria for ending isolation. By considering a fixed time of 10 days since symptom onset as the criterion for ending isolation, we estimated that the risk of releasing an individual who is still infectious is low (0–6.6%). However, this policy entails lengthy unnecessary isolations (4.8–8.3 days). In contrast, by using a personalized strategy, similar low risks can be reached with shorter prolonged isolations. The obtained findings provide a scientific rationale for policies on ending the isolation of SARS-CoV-2-infected individuals.

Jeong, Yong Dam↗

DOE OSTI2021

Seismic isolation: A pathway to standardized advanced nuclear reactors

Standardizing advanced nuclear reactors is a pathway to substantially reducing their overnight capital cost and achieving parity with other power sources, including renewables and fossil fuels. The seismic load case has thwarted standardization of nuclear power plants because site-specific seismic hazard and local near-surface geology has triggered soil-structure-interaction analysis, design, equipment qualification, regulatory review, and licensing, ensuring that each build is different. To achieve standardized or site-independent certified advanced reactor designs, the impact of the seismic load case on the engineering and construction cost and time must be substantially mitigated. Seismic isolation is a mature technology that has been used for more than 30 years in non-nuclear sectors to substantially reduce earthquake demands in buildings and other infrastructure. In this paper, seismic isolation is used to enable standardization of advanced reactor designs, aimed at the complete re-use of a site-independent, certified design and repeated procurement of safety-class equipment. A pathway to standardized designs using seismic isolation is demonstrated for two fundamentally different advanced reactors: a molten salt reactor and a high temperature gas reactor. Each reactor building is equipped with three specialized pieces of safety-class equipment, namely, a reactor vessel, a steam generator, and a control rod drive mechanism housing that is attached to the reactor head. Analysis is performed per ASCE and ASME standards to design the buildings and the equipment for two base conditions: conventional (fixed base) and base isolated. The impact of the seismic load case is characterized for the reinforced concrete walls in the buildings and for the equipment, measured using vessel wall thickness and horizontal accelerations. Here the analysis results show that the fixed-base buildings, designed for a site of low seismic hazard (peak ground acceleration, PGA = 0.15 g) could be constructed at a site of much greater seismic hazard (PGA = 0.7 g) if seismic base isolation is employed. Importantly, the scope of the site-specific analysis, design, and qualification would be limited to the seismic isolators and the isolated substructure, drastically reducing plant-specific engineering, review, and licensing, and time to construction start. Regulatory challenges and opportunities with standardized reactor designs are identified.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

BONCAT-Live for isolation and cultivation of active environmental bacteria

In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.

Analytical Methods↗

DOE OSTI2023

Dissecting Phenotype from Genotype with Clinical Isolates of SARS-CoV-2 First Wave Variants

The emergence and availability of closely related clinical isolates of SARS-CoV-2 offers a unique opportunity to identify novel nonsynonymous mutations that may impact phenotype. Global sequencing efforts show that SARS-CoV-2 variants have emerged and then been replaced since the beginning of the pandemic, yet we have limited information regarding the breadth of variant-specific host responses. Using primary cell cultures and the K18-hACE2 mouse, we investigated the replication, innate immune response, and pathology of closely related, clinical variants circulating during the first wave of the pandemic. Mathematical modeling of the lung viral replication of four clinical isolates showed a dichotomy between two B.1. isolates with significantly faster and slower infected cell clearance rates, respectively. While isolates induced several common immune host responses to infection, one B.1 isolate was unique in the promotion of eosinophil-associated proteins IL-5 and CCL11. Moreover, its mortality rate was significantly slower. Lung microscopic histopathology suggested further phenotypic divergence among the five isolates showing three distinct sets of phenotypes: (i) consolidation, alveolar hemorrhage, and inflammation, (ii) interstitial inflammation/septal thickening and peribronchiolar/perivascular lymphoid cells, and (iii) consolidation, alveolar involvement, and endothelial hypertrophy/margination. Together these findings show divergence in the phenotypic outcomes of these clinical isolates and reveal the potential importance of nonsynonymous mutations in nsp2 and ORF8.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Coxsackievirus B4 sewage-isolate induces pancreatitis after oral infection of mice

ABSTRACT Numerous serotypes which belong to the genus Enterovirus (EV) show variability in their virulence and clinical manifestations. They are also known to undergo changes caused by mutations and recombination during their circulation in the environment and the population. Various EV serotypes are prevalent in groundwater, wastewater and surface waters. Our previous studies showed that oral infection induces pancreatitis depending on specific conditions, such as gravidity, in an outbred murine model. Our aim in the present study was to further explore the pancreatic histopathology in an outbred mouse model following oral infection with clinical isolates from a patient who had aseptic meningitis and an isolate from a treated-sewage sample recovered from the residential area of the patient. The isolates were identified as coxsackievirus B4 (CVB4) in tissue culture. The CVB4 sewage-isolate induced pancreatitis after oral infection. In contrast, pancreatitis was absent following infection with the clinical isolates. Comparison of polyprotein sequences showed that the treated-sewage strains differed from the patient's isolates by 9 and 11 amino acids. We conclude that the isolates of clinical and environmental origin differed in their pathogenic properties and showed genetic variation.

Benkoova, Brigita↗

DOE OSTI2023

Genomic analysis of 1710 surveillance-based Neisseria gonorrhoeae isolates from the USA in 2019 identifies predominant strain types and chromosomal antimicrobial-resistance determinants

This study characterized high-quality whole-genome sequences of a sentinel, surveillance-based collection of 1710 Neisseria gonorrhoeae (GC) isolates from 2019 collected in the USA as part of the Gonococcal Isolate Surveillance Project (GISP). It aims to provide a detailed report of strain diversity, phylogenetic relationships and resistance determinant profiles associated with reduced susceptibilities to antibiotics of concern. The 1710 isolates represented 164 multilocus sequence types and 21 predominant phylogenetic clades. Common genomic determinants defined most strains’ phenotypic, reduced susceptibility to current and historic antibiotics (e.g. bla TEM plasmid for penicillin, tetM plasmid for tetracycline, gyrA for ciprofloxacin, 23S rRNA and/or mosaic mtr operon for azithromycin, and mosaic penA for cefixime and ceftriaxone). The most predominant phylogenetic clade accounted for 21 % of the isolates, included a majority of the isolates with low-level elevated MICs to azithromycin (2.0 µg ml –1 ), carried a mosaic mtr operon and variants in PorB, and showed expansion with respect to data previously reported from 2018. The second largest clade predominantly carried the GyrA S91F variant, was largely ciprofloxacin resistant (MIC ≥1.0 µg ml –1 ), and showed significant expansion with respect to 2018. Overall, a low proportion of isolates had medium- to high-level elevated MIC to azithromycin ((≥4.0 µg ml –1 ), based on C2611T or A2059G 23S rRNA variants). One isolate carried the penA 60.001 allele resulting in elevated MICs to cefixime and ceftriaxone of 1.0 µg ml –1 . This high-resolution snapshot of genetic profiles of 1710 GC sequences, through a comparison with 2018 data (1479 GC sequences) within the sentinel system, highlights change in proportions and expansion of select GC strains and the associated genetic mechanisms of resistance. The knowledge gained through molecular surveillance may support rapid identification of outbreaks of concern. Continued monitoring may inform public health responses to limit the development and spread of antibiotic-resistant gonorrhoea.

(3-6) antimicrobial resistance↗

DOE OSTI2023

Mid–height seismic isolation of equipment in nuclear power plants

An innovative seismic isolation solution for designers of safety-class equipment in advanced nuclear power plants is introduced. The test specimen was a tall, slender, carbon steel vessel that could represent a reactor vessel, steam generator, or a heat exchanger in a nuclear power plant: 240 inches tall, outer diameter of 60 inches, and wall thickness of 1 inch. The vessel was supported by three radial mounts at its mid-height, near its center of gravity, on a steel frame. The vessel was subjected to three-component ground motions using a 6DOF earthquake simulator. The specimen was filled with water for testing to indirectly account for the fluid and internal equipment present inside a prototype vessel. Three configurations were tested: non-isolated, isolated using single Friction Pendulum (SFP) bearings, and isolated using triple Friction Pendulum (TFP) bearings. The test results demonstrate that mid-height seismic isolation is practical and enables a significant reduction in horizontal spectral accelerations. Furthermore, these outcomes are not specific to the spherical sliding bearings used in the experiments but are broadly applicable to mid-height, seismically isolated equipment.

42 ENGINEERING↗

DOE OSTI2022

Advanced Distributed Wind Turbine Controls Series: Part 2-Wind Energy in Isolated Grids – Microgrids, Infrastructure Resilience, and Advanced Controls Launchpad (MIRACL)

In an isolated grid, wind turbines are typically deployed to provide energy to maximize energy production, reduce diesel-fuel consumption, reduce carbon emissions, and reduce costs for energy and fuel transportation. However, in addition to solely providing energy to the power system, wind turbines contain rotating masses and inverter-based controls that can enable various reliability and resilience services through advance controls. As part of the Microgrids, Infrastructure Resilience, and Advanced Controls Launchpad (MIRACL) this paper demonstrates, through desktop simulations, advanced wind turbine controls that can be employed to support higher contributions of wind in isolated grids, and to demonstrate ways that wind can play a role in supporting stability of an isolated grid. This isolated grid used in these desktop simulations is comprised of a wind turbine (600 kW), solar PV (430 kW), battery energy storage system (1 MW/1MWh), a simulated diesel generator (2 MW) and various types of loads (critical, dynamic). We developed a model of the subsystems in MATLAB/Simulink and validated them with available data from real-world components on NREL's Flatirons Campus. These validated models are then configured for various case studies. We compare the output of the desktop simulation with a baseline case with the diesel generator. Active and reactive power control of the wind turbine can help improve frequency and voltage responses in the isolated grid, respectively. By utilizing a small integrated battery energy storage system in the DC-link of the wind turbine, we also demonstrate that wind turbines can help blackstart a critical load comparable to its rated power and support other renewables (e.g. solar PV) come online and pick up an additional load. This report illustrates some of these reliability and resilience services a wind turbine can provide in an isolated grid.

17 WIND ENERGY↗

DOE OSTI2021

Substrate, temperature, and geographical patterns among nearly 2000 natural yeast isolates

Yeasts have broad importance as industrially and clinically relevant microbes and as powerful models for fundamental research, but we are only beginning to understand the roles yeasts play in natural ecosystems. Yeast ecology is often more difficult to study compared to other, more abundant microbes, but growing collections of natural yeast isolates are beginning to shed light on fundamental ecological questions. In this work, we used environmental sampling and isolation to assemble a dataset of 1962 isolates collected from throughout the contiguous United States of America (USA) and Alaska, which were then used to uncover geographic patterns, along with substrate and temperature associations among yeast taxa. We found some taxa, including the common yeasts Torulaspora delbrueckii and Saccharomyces paradoxus, to be repeatedly isolated from multiple sampled regions of the USA, and we classify these as broadly distributed cosmopolitan yeasts. A number of yeast taxon-substrate associations were identified, some of which were novel and some of which support previously reported associations. Further, we found a strong effect of isolation temperature on the phyla of yeasts recovered, as well as for many species. We speculate that substrate and isolation temperature associations reflect the ecological diversity of and niche partitioning by yeast taxa.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Non-linear Wire Rope Isolator Model to Enhance Transportation Simulation of Fragile Equipment

Abstract Introduction Wire rope isolators are often used as means of vibration isolation for the transportation of fragile machine equipment. When deployed as suspension systems in a transportation scenario, a simple spring–damper model is often used to predict the dynamic loads that act on the structure being transported. However, this simple model has proved to be too simplistic to be used in the development of an accurate numerical model that can predict the vibration levels experienced by the inner components of fragile equipment during its transportation. This paper describes the experimental tests conducted on a wire rope isolator used for the transportation of the prototype SSR1 cryomodule. Materials and methods A hysteretic Bouc–Wen model has been used to analytically describe the force–deformation relationship of the wire rope isolators. The developed model of the isolator has been implemented in a larger model to simulate the actual transportation of the prototype SSR1 cryomodule, a section of the new PIP-II linear accelerator under construction at Fermilab. A series of multibody dynamic simulations with rigid and flexible components was used to numerically determine the acceleration of some critical components. Results and conclusions An actual experimental transportation was simulated using two numerical models: the developed Bouc–Wen model and a conventional spring–damper model. It is shown how the Bouc–Wen formulation of the isolator characteristics drastically improves the correspondence between experimental and simulated results if compared to a spring–damper model, especially in the range of 0–30 Hz which is the most critical for transportation problems.

42 ENGINEERING↗

DOE OSTI2022

Electric-field control of the nucleation and motion of isolated three-fold polar vertices

Recently various topological polar structures have been discovered in oxide thin films. Despite the increasing evidence of their switchability under electrical and/or mechanical fields, the dynamic property of isolated ones, which is usually required for applications such as data storage, is still absent. Here, we show the controlled nucleation and motion of isolated three-fold vertices under an applied electric field. At the PbTiO 3 /SrRuO 3 interface, a two-unit-cell thick SrTiO 3 layer provides electrical boundary conditions for the formation of three-fold vertices. Utilizing the SrTiO 3 layer and in situ electrical testing system, we find that isolated three-fold vertices can move in a controllable and reversible manner with a velocity up to ~629 nm s -1 . Microstructural evolution of the nucleation and propagation of isolated three-fold vertices is further revealed by phase-field simulations. This work demonstrates the ability to electrically manipulate isolated three-fold vertices, shedding light on the dynamic property of isolated topological polar structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Revealing oxidative pentose metabolism in new Pseudomonas putida isolates

Abstract The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well‐characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth‐promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism ( xylDXA ) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism ( araDXA ). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Genomic analysis and identification of a novel superantigen, SargEY, in Staphylococcus argenteus isolated from atopic dermatitis lesions

During surveillance of Staphylococcus aureus in lesions from patients with atopic dermatitis (AD), we isolated Staphylococcus argenteus, a species registered in 2011 as a new member of the genus Staphylococcus and previously considered a lineage of S. aureus. Genome sequence comparisons between S. argenteus isolates and representative S. aureus clinical isolates from various origins revealed that the S. argenteus genome from AD patients closely resembles that of S. aureus causing skin infections. We previously reported that 17%–22% of S. aureus isolated from skin infections produce staphylococcal enterotoxin Y (SEY), which predominantly induces T-cell proliferation via the T-cell receptor (TCR) Vα pathway. Complete genome sequencing of S. argenteus isolates revealed a gene encoding a protein similar to superantigen SEY, designated as SargEY, on its chromosome. Population structure analysis of S. argenteus revealed that these isolates are ST2250 lineage, which was the only lineage positive for the SEY-like gene among S. argenteus. Recombinant SargEY demonstrated immunological cross-reactivity with anti-SEY serum. SargEY could induce proliferation of human CD4 + and CD8 + T cells, as well as production of TNF-α and IFN-γ. SargEY showed emetic activity in a marmoset monkey model. S arg EY and SET (a phylogenetically close but uncharacterized SE) revealed their dependency on TCR Vα in inducing human T-cell proliferation. Additionally, TCR sequencing revealed other previously undescribed Vα repertoires induced by SEH. S arg EY and SEY may play roles in exacerbating the respective toxin-producing strains in AD.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Isolation coupler for a structural assembly and method for attenuating a load

An isolation coupler for coupling a functional element to a support structure includes a first bracket. The first bracket includes a number of first-bracket sides. The number of first-bracket sides forms a closed polygonal shape, in plan view. The isolation coupler further includes a number of isolators coupled to each one of the first-bracket sides. The isolation coupler also includes a second bracket. The second bracket includes a number of second-bracket sides. The second bracket sides are coupled to the isolators. The number of second-bracket sides is equal to the number of first-bracket sides and forms the closed polygonal shape, in plan view. The isolators separate each one of the first-bracket sides from a corresponding one of the second-bracket sides to attenuate a load transferred from the first bracket to the second bracket.

Aston, Richard W.↗

DOE OSTI2023

Isolation coupler for a structural assembly and method for attenuating a load

Aston, Richard W.↗

DOE OSTI2023

Inclusive-photon production and its dependence on photon isolation in $pp$ collisions at $\sqrt{s}$ = 13 TeV using 139 fb -1 of ATLAS data

Measurements of differential cross sections are presented for inclusive isolated-photon production in $pp$ collisions at a centre-of-mass energy of 13 TeV provided by the LHC and using 139 -1 fb of data recorded by the ATLAS experiment. The cross sections are measured as functions of the photon transverse energy in different regions of photon pseudorapidity. The photons are required to be isolated by means of a fixed-cone method with two different cone radii. The dependence of the inclusive-photon production on the photon isolation is investigated by measuring the fiducial cross sections as functions of the isolation-cone radius and the ratios of the differential cross sections with different radii in different regions of photon pseudorapidity. The results presented in this paper constitute an improvement with respect to those published by ATLAS earlier: the measurements are provided for different isolation radii and with a more granular segmentation in photon pseudorapidity that can be exploited in improving the determination of the proton parton distribution functions. These improvements provide a more in-depth test of the theoretical predictions. Next-to-leading-order QCD predictions from JETPHOX and SHERPA and next-to-next-to-leading-order QCD predictions from NNLOJET are compared to the measurements, using several parameterisations of the proton parton distribution functions. The measured cross sections are well described by the fixed-order QCD predictions within the experimental and theoretical uncertainties in most of the investigated phase-space region.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗