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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Distribution and Transfer of Plasmid Replicon Families among Multidrug-Resistant Enterococcus faecalis and Enterococcus faecium from Poultry

The presence and transfer of plasmids from commensal bacteria to more pathogenic bacteria may contribute to the dissemination of antimicrobial resistance. However, the prevalence of plasmids from commensal bacteria, such as the enterococci, in food animals remains largely unknown. In this study, the diversity and prevalence of plasmid families from multidrug-resistant (MDR; resistance to three or more antimicrobials) enterococci from poultry carcasses were determined. Plasmid-positive MDR enterococci were also tested for the ability to transfer plasmids to other enterococci using conjugation. MDR Enterococcus faecalis (n = 98) and Enterococcus faecium (n = 696) that were isolated from poultry carcass rinsates between 2004 and 2011 were tested for the presence of 21 plasmid replicon (rep) families using multiplex PCR. Approximately 48% of E. faecalis (47/98) and 16% of E. faecium (110/696) were positive for at least one rep-family. Fourteen rep-families were detected overall, and ten rep-families were shared between E. faecalis and E. faecium. The rep7 and rep17 families were unique to E. faecalis, while the rep5 and rep8 families were unique to E. faecium. The rep9 family was predominant in both E. faecalis and E. faecium for all the years tested. The greatest number of rep-families detected was in 2005 (n = 10), and the least was in 2009 (n = 1). Eight rep-families were transferred from E. faecalis donors to the E. faecalis JH2-2 recipient using conjugation. Results from this study showed that E. faecalis and E. faecium from poultry carcasses contain numerous and diverse rep-families that are capable of conjugal transfer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Methods of making organic compounds by metathesis

Described are methods of making organic compounds by metathesis chemistry. The methods of the invention are particularly useful for making industrially-important organic compounds beginning with starting compositions derived from renewable feedstocks, such as natural oils. The methods make use of a cross-metathesis step with an olefin compound to produce functionalized alkene intermediates having a pre-determined double bond position. Once isolated, the functionalized alkene intermediate can be self-metathesized or cross-metathesized (e.g., with a second functionalized alkene) to produce the desired organic compound or a precursor thereto. The method may be used to make bifunctional organic compounds, such as diacids, diesters, dicarboxylate salts, acid/esters, acid/amines, acid/alcohols, acid/aldehydes, acid/ketones, acid/halides, acid/nitriles, ester/amines, ester/alcohols, ester/aldehydes, ester/ketones, ester/halides, ester/nitriles, and the like.

Abraham, Timothy W.↗
DOE OSTI2022

Beam-steering system based on a MEMS-actuated vertical-coupler array

An integrated-optics MEMS-actuated beam-steering system is disclosed, wherein the beam-steering system includes a lens and a programmable vertical coupler array having a switching network and an array of vertical couplers, where the switching network can energize of the vertical couplers such that it efficiently emits the light into free-space. The lens collimates the light received from the energized vertical coupler and directs the output beam along a propagation direction determined by the position of the energized vertical coupler within the vertical-coupler array. In some embodiments, the vertical coupler is configured to correct an aberration of the lens. In some embodiments, more than one vertical coupler can be energized to enable steering of multiple output beams. In some embodiments, the switching network is non-blocking.

42 ENGINEERING↗
DOE OSTI2023

Beam-steering system based on a MEMS-actuated vertical-coupler array

An integrated-optics MEMS-actuated beam-steering system is disclosed, wherein the beam-steering system includes a lens and a programmable vertical coupler array having a switching network and an array of vertical couplers, where the switching network can energize of the vertical couplers such that it efficiently emits the light into free-space. The lens collimates the light received from the energized vertical coupler and directs the output beam along a propagation direction determined by the position of the energized vertical coupler within the vertical-coupler array. In some embodiments, the vertical coupler is configured to correct an aberration of the lens. In some embodiments, more than one vertical coupler can be energized to enable steering of multiple output beams. In some embodiments, the switching network is non-blocking.

Zhang, Xiaosheng↗
DOE OSTI2024

Measurement of the muon spin precession frequency using the straw tracking detectors at the Fermilab Muon g-2 experiment

The measurement of the anomalous magnetic dipole moment of the muon ($a_{\mu}$) has long stood as an excellent precision test of the Standard Model (SM). The Fermilab Muon g-2 experiment has recently finished data-taking and in July 2023 published its latest determination of $a_\mu$ with a world-leading precision of 0.2\,ppm. In this publication, it surpassed the systematic uncertainty goal defined in the TDR. The analyses of a dataset approximately four times larger than this recent publication is now underway. The principle measurement of the Muon g-2 experiment measures $a_{\mu}$ by taking the ratio of two frequencies; the anomalous precession frequency ($\omega_a$) and the muon-weighted magnetic field of the experiment's storage ring measured from the precession frequency of protons in water using nuclear magnetic resonance (NMR) probes. In all publications to date, $\omega_a$ has been determined using energy deposits in the 24 calorimeters. However, the Fermilab experiment has t wo straw tracker detectors measuring the time and momentum of charged particles which can in principle also be used to to measure $\omega_a$ and such a measurement can provide an invaluable cross-check of the calorimeter result with different, and reduced, systematic uncertainties. This thesis presents the first (blinded) determination of $\omega_a$ using just charged tracks from the straw tracking detectors as opposed to calorimeter energy deposits. This analysis was undertaken using the Run-2/3 dataset which represents approximately 25\% of the final dataset. A total uncertainty of 2.19\,ppm on $\omega_a$ was obtained which is dominated by the statistical uncertainty of 2.16\,ppm. Additionally two new methodologies important to the analysis of the straw tracking data have been developed: one to better determine the track arrival time ($t_0$) and one to determine the level of pileup in the tracking detectors. The new $t_0$ algorithm which incorporates angular information improves t he resolution on the determination of the $t_0$ by a factor of two and results in 19\% more tracks being successfully reconstructed. The data from the trackers is also used to determine the beam profile that weights the magnetic field in the determination of $a_\mu$ and in determining several of the systematic uncertainties in the calorimeter-based $\omega_a$ analysis. A detailed study of the impact of the internal alignment of the tracker, the $t_0$ and pileup on the determination of the beam position was undertaken and propagated through to an uncertainty in the $\omega_a$ determination. These uncertainties were used in the Fermilab Muon g-2 experiment's recent publication in Phys. Rev. Lett.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

Mutation of active site glutamate in serine hydroxymethyltransferase allows trapping a reactive intermediate: a combined neutron and X-ray crystallography study

Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5′-phosphate (PLP) dependent enzyme that catalyzes a chemical transformation essential for the one-carbon (1C) metabolism. SHMT reversibly converts L-Ser into Gly and transfers a 1C unit to tetrahydrofolate (THF) to give 5,10-methylene-THF (5,10-MTHF). 5,10-MTHF, a 1C-unit donor, plays a crucial role in the downstream biomolecular syntheses required for the cell homeostasis and proliferation. SHMT is a prominent target for the drug discovery to battle bacterial and parasitic infections, and to treat various types of cancer. SHMT-catalyzed chemistry is governed by the general acid-base catalysis. Knowledge of the catalytic mechanism can aid drug design but can only be achieved when the atomic details of each reaction step are mapped, including accurate determination of hydrogen atom positions. Here we utilized the inactive E53Q mutant of Thermus thermophilus ( Tth ) SHMT to directly determine protonation states with room-temperature neutron crystallography and to capture a reactive intermediate containing the PLP-L-Ser external aldimine and THF in the enzyme active site. We observed protonation of the Schiff base nitrogen (N SB ) in the PLP internal aldimine but no change in the protonation states of other ionizable PLP groups and active site residues compared to wild-type Tth SHMT. X-ray structural analysis of the ternary intermediate complex E53Q-Ser-THF that eluded previous structural characterization shows the strategic positioning of the E53Q side chain in close proximity to the external aldimine and THF and reinforces the proposed role for E53 as the driver of proton transfer events along the reaction pathway.

Drago, Victoria N. [Oak Ridge National Laboratory ↗
DOE OSTI2022

Direct Visualization of Magnetic Correlations in Frustrated Spinel ZnFe 2 O 4

Magnetic materials with the spinel structure (A 2+ B 3+ 2 O 4 ) form the core of numerous magnetic devices, and ZnFe 2 O 4 constitutes a peculiar example where the nature of the magnetism is still unresolved. Susceptibility measurements revealed a cusp around T c = 13 K resembling an antiferromagnetic transition, despite the positive Curie–Weiss temperature determined to be Θ CW = 102.8(1) K. Bifurcation of field-cooled and zero-field-cooled data below T c in conjunction with a frequency dependence of the peak position and a non-zero imaginary component below T c shows it is in fact associated with a spin-glass transition. Highly structured magnetic diffuse neutron scattering from single crystals develops between 50 K and 25 K revealing the presence of magnetic disorder which is correlated in nature. Here, the 3D-mΔPDF method is used to visualize the local magnetic ordering preferences, and ferromagnetic nearest-neighbor and antiferromagnetic third nearest-neighbor correlations are shown to be dominant. Their temperature dependence is extraordinary with some flipping in sign and a strongly varying correlation length. The correlations can be explained by orbital interaction mechanisms for the magnetic pathways and a preferred spin cluster. This study demonstrates the power of the 3D-mΔPDF method in visualizing complex quantum phenomena thereby providing a way to obtain an atomic-scale understanding of magnetic frustration.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Line confusion in spectroscopic surveys and its possible effects: shifts in Baryon Acoustic Oscillations position

ABSTRACT Roman Space Telescope will survey about 17 million emission-line galaxies over a range of redshifts. Its main targets are Hα emission-line galaxies at low redshifts (z < 2) and [O iii] emission-line galaxies at high redshifts (z > 2). The Roman Space Telescope will estimate the redshift of these galaxies with single-line identification. This suggests that other emission-line galaxies may be misidentified as the main targets. In particular, it is hard to distinguish between the H β and [O iii] lines as the two lines are close in wavelength and hence the photometric information may not be sufficient to separate them reliably. Misidentifying H β emitter as [O iii] emitter will cause a shift in the inferred radial position of the galaxy by approximately 90 Mpc h−1. This length-scale is similar to the Baryon Acoustic Oscillation (BAO) scale and could shift and broaden the BAO peak, possibly introduce errors in determining the BAO peak position. We qualitatively describe the effect of this new systematic and further quantify it with a light-cone simulation with emission-line galaxies. Our results show a systematic shift in the recovered isotropic BAO positions that depends on the percentage of interlopers (percentage of ${\rm H}\,\beta$) in the sample. The systematic shift can be as large as $0.1{-}0.3\,\mathrm{ per}\,\mathrm{ cent} \, {\rm x}\, {{\%}}{\rm H}\,\beta$ for analysis performed at redshifts z = 1.3−1.9.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A weak subducting slab at intermediate depths below northeast Japan

Knowledge of the state of stress in subducting slabs is essential for understanding their mechanical behavior and the physical processes that generate earthquakes. Here, we develop a framework which uses a high-resolution focal mechanism catalog to determine the change in the position of the neutral plane before and after the M9 Tohoku-oki earthquake to determine that the deviatoric stress within the slab at intermediate depths must be very low (~1 MPa). We show that by combining the static stress calculated from coseismic slip distributions with the stress orientations before and after the mainshock, we can determine the full deviatoric stress tensor within the subducting slab at intermediate depths. These results preclude earthquake source mechanisms that require large background driving stresses, favoring a mechanically weak subducting slab, thus providing quantitative constraints on the physical processes that generate intermediate-depth earthquakes.

58 GEOSCIENCES↗
DOE OSTI2023

Method of transient control for robust enrichment operation in low temperature combustion engine

A method of transient control for enrichment operation in a low-temperature combustion engine. The method includes determining if a current mode of the low-temperature combustion (LTC) engine is a positive valve overlap (PVO) mode. Determining if a previous mode of the LTC engine was also the PVO mode when the current mode is the PVO mode, wherein the previous mode is immediately prior to the current mode. Determining if the previous mode of the LTC engine was a negative valve overlap (NVO) mode when the previous mode was not the PVO mode. Initiating a predetermined enrichment PVO mode for the LTC engine based on the previous mode of the LTC engine. The predetermined enrichment PVO mode includes initiating a deep enrichment PVO mode, when the previous mode of the LTC engine was the NVO mode, and initiating a shallow enrichment PVO mode, when the previous mode of the LTC engine was not the NVO mode.

Yun, Hanho↗
DOE OSTI2026

Mass Spectrometric Determination of Site-Specific O -Acetylation in Rhamnogalacturonan I Oligomers

O-acetylation, a common modification in rhamnogalacturonan I (RG-I), is critical for various biological processes, including plant growth, stress responses, and pathogen defense. Precise determination of the degree and specific positions of acetylation is therefore essential. To date, nuclear magnetic resonance (NMR) and tandem mass spectrometry have been employed to identify O-acetyl positions in pectin oligosaccharides. Although NMR is effective, it requires pure, high-concentration samples. Tandem mass spectrometry (MS), which uses smaller sample amounts, faces challenges due to O-acetyl migration between monosaccharide positions. The multiple steps in pectin sample analysis can further promote O-acetyl migration, especially near free hydroxyl groups. Moreover, during tandem MS, O-acetyl groups may detach, complicating the accurate tracking. This study presents an approach to lock O-acetyl groups by introducing trideuteroacetyl and propionyl substituents onto free hydroxyls of RG-I or partially acetylated RG-I. By combining matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS and electrospray ionization (ESI) MS with MS/MS or tandem mass spectrometry (MSn), we devised a way to determine the monosaccharide sequence in the oligomer and the precise positions of O-acetyl groups in partially acetylated RG-I. This method enables the study of the regiospecificity of recombinant pectin O-acetyltransferases and can be applied to other oligosaccharides to determine acyl positions.

O-acetylation↗
DOE OSTI2020

Radioactive Source Localization via Bayesian Particle Filter

In the event of a misplaced radioactive source or other emergency situation, measuring a radiation field, mapping its distribution, and determining a source location are essential tasks to ameliorating the situation. However, radiation fields may be extremely hazardous to human surveyors and minimizing received radiation doses is just as essential. Robots appear to be a potential solution to these problems. Beyond simply measuring radiation, the robot's computer processing capabilities offer a way to apply complex data analysis methods to radiation measurements in real-time. Methods which predict likely source locations can then feed this information into other processes, potentially improving path planning and enabling more efficient measurements. Given a robot mounted with a gamma-ray detector, can we: develop a methodology to account for detector performance across a wide range of source angles, distances, and photon energies? operate an autonomously navigating robot to effectively survey and characterize an area of interest? implement a data analysis method, conventionally used in measurements of motion, for source localization purposes? An open-source TurtleBot 3 robot, running Robot Operating System (ROS) on Ubuntu 16.04 LTS, was fitted with a Kromek GR1{sup R} Cadmium Zinc Telluride (CZT) solid-state gamma-ray detector. As a part of ROS, the packages OpenSlam, gmapping, and amcl were used to perform Simultaneous Localization and Mapping (SLAM), determining the robot's position and mapping the surrounding area. Data was acquired via Lidar mounted on top the TurtleBot 3. Detector Calibration Fit: The equation was fit to 365 counts of various energies, distances, and angles. A MATLAB{sup R} program was written to simulate measurements taken a robot on a random walk, with count data and positions discretized into finite element pixels. Using this program, a sample of 100 runs was performed on a map with a simulated source at the center, with a total of 200 of 2 pixels each. Similarly, multiple runs of the filter were performed on recorded robot measurement data. In both simulation and real tests, when corrected for errors (particles placed outside of bounds or on the robot, and simulation-specific errors), corresponding t-tests of predicted x and y-coordinates were within a 95% confidence interval of the actual position. For the real trial, these positions are slightly skewed right in the x-axis as the robot remained mainly to the left side of the source within the sample area. These simulations demonstrate potential validity for the usage of a particle filter as method of radioactive source localization. In the future, true real-time implementation and data fusion may further augment the performance of the robot to localize lost sources. Additionally, identification of multiple sources, determination of source types, and usage of a collimator are areas to potentially be explored.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2026

High-precision phase control of an optical lattice with up to 50 dB noise suppression

An optical lattice is a periodic light crystal constructed from the standing-wave interference patterns of laser beams. It can be used to store and manipulate quantum degenerate atoms and is an ideal platform for the quantum simulation of many-body physics. A principal feature is that optical lattices are flexible and possess a variety of multidimensional geometries with modifiable band structure. An even richer landscape emerges when control functions can be applied to the lattice by modulation of the position or amplitude with Floquet driving. However, the desire of realizing high-modulation bandwidths while preserving extreme lattice stability has been difficult to achieve. In this paper, we demonstrate an effective solution that consists of overlapping two counterpropagating lattice beams and controlling the phase and intensity of each with independent acousto-optic modulators. Our phase controller mixes sampled light from both lattice beams with a common optical reference. This dual heterodyne locking method allows exquisite determination of the lattice position, while also removing parasitic phase noise accrued as the beams travel along separate paths. Here, we report up to 50 dB suppression in lattice phase noise in the 0.1–1 Hz band, along with significant suppression spanning more than 4 decades of frequency. The absolute phase diffusion of the lattice position is only 10 Å when integrated over 10 s. This method permits precise, high-bandwidth modulation (greater than 50 kHz) of the optical lattice intensity and phase. We demonstrate the efficacy of this approach by executing intricate time-varying phase profiles for atom interferometry.

Atom interferometry↗
DOE OSTI2020

Validation of pooling strategies of clinical COVID-19 samples for more efficient diagnostic testing

Pooling of COVID-19 clinical samples can offer significant reduction in reagents, time, and labor needed to test large numbers of clinical samples. Especially for testing asymptomatic and return-towork/ school cases, where the prevalence of COVID-19 may be relatively low, large groups of clinical samples can be classified as negative with a single test, with no need to test every sample individually. LANL has performed validation for two different pooling strategies to assess diagnostic assay sensitivity in pooled samples compared to the clinical positive sample alone. (1) Pooling study - Determine diagnostic assay sensitivity in pooled samples with ratios of 1:5, 1:10, 1:20, and 1:30 positive to negative clinical samples. (2) Reloading study - Determine diagnostic assay sensitivity in reloading of multiple clinical samples through a Qiagen column in 5x, 10, and 20x sample volumes (1 positive plus 4, 9, and 19 negative samples).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Determining the three-dimensional atomic structure of an amorphous solid

Amorphous solids such as glass, plastics and amorphous thin films are ubiquitous in our daily life and have broad applications ranging from telecommunications to electronics and solar cells 1-4 . However, owing to the lack of long-range order, the three-dimensional (3D) atomic structure of amorphous solids has so far eluded direct experimental determination 5-15 . Here we develop an atomic electron tomography reconstruction method to experimentally determine the 3D atomic positions of an amorphous solid. Using a multi-component glass-forming alloy as proof of principle, we quantitatively characterize the short- and medium-range order of the 3D atomic arrangement. We observe that, although the 3D atomic packing of the short-range order is geometrically disordered, some short-range-order structures connect with each other to form crystal-like superclusters and give rise to medium-range order. We identify four types of crystal-like medium-range order-face-centred cubic, hexagonal close-packed, body-centred cubic and simple cubic-coexisting in the amorphous sample, showing translational but not orientational order. These observations provide direct experimental evidence to support the general framework of the efficient cluster packing model for metallic glasses 10,12-14,16 . Finally, we expect that this work will pave the way for the determination of the 3D structure of a wide range of amorphous solids, which could transform our fundamental understanding of non-crystalline materials and related phenomena.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Lattice Relaxations in Bixbyite‐Structured Rare‐Earth Sesquioxides

This report examines atomic relaxations in rare‐earth sesquioxides with the cubic bixbyite crystal structure. In particular, the experimentally determined unit cell atom positions in bixbyite compounds are compared to “ideal” bixbyite atom positions, where the concept of ideality is based on similarities between the bixbyite and fluorite crystal structures. Analyses indicate that all rare‐earth sesquioxide compounds deviate from ideality in similar ways and that there is a trend wherein the magnitudes of these atomic deviations decrease with increasing cationic size. The deviations from an ideal, fluorite‐like structure produce highly distorted coordination polyhedra and variations in metal‐oxygen bond lengths. A modified bond valence sum analysis revealed that the first nearest neighbor cation‐anion bond length variations lead to large (20%) variations in cation‐anion bond strength. This report also provides a qualitative analysis regarding the accuracy of atomic relaxed deviation parameters, based on x‐ray diffraction measurements. The analysis indicates that uncertainties in the accuracy of measured oxygen relaxed deviation parameters in bixbyite sesquioxides are likely much greater than the published uncertainties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump

The multidrug efflux pumps of Gram-negative bacteria are a class of complexes that span the periplasm, coupling both the inner and outer membranes to expel toxic molecules. The best-characterized example of these tripartite pumps is the AcrAB-TolC complex of Escherichia coli. However, how the complex interacts with the peptidoglycan (PG) cell wall, which is anchored to the outer membrane (OM) by Braun’s lipoprotein (Lpp), is still largely unknown. In this work, we present molecular dynamics simulations of a complete, atomistic model of the AcrAB-TolC complex with the inner membrane, OM, and PG layers all present. We find that the PG localizes to the junction of AcrA and TolC, in agreement with recent cryo-tomography data. Free-energy calculations reveal that the positioning of PG is determined by the length and conformation of multiple Lpp copies anchoring it to the OM. The distance between the PG and OM measured in cryo-electron microscopy images of wild-type E. coli also agrees with the simulation-derived spacing. Finally, sequence analysis of AcrA suggests a conserved role for interactions with PG in the assembly and stabilization of efflux pumps, one that may extend to other trans-envelope complexes as well.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Time-domain Brillouin scattering theory for probe light and acoustic beams propagating at an angle and acousto-optic interaction at material interfaces

A theory has been developed to interpret time-domain Brillouin scattering (TDBS) experiments involving coherent acoustic pulse (CAP) and light pulse beams propagating at an angle to each other. It predicts the influence of the directivity pattern of their acousto-optic interaction on TDBS signals when heterodyne detection of acoustically scattered light is in backward direction to incident light. The theory reveals relationships between the carrier frequency, amplitude and duration of acoustically induced ”wave packets” in light transient reflectivity signals, and factors such as CAP duration, widths of light and sound beams, and their interaction angle. It describes the transient dynamics of these wave packets when the light and CAP encounter material interfaces, and how the light scattering by the incident CAP transforms into scattering by the reflected and transmitted CAPs. The theory suggests that single-point TDBS experiments can determine not only depth positions of buried interfaces but also their local inclinations/orientations.

42 ENGINEERING↗