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At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Characterization of Lactobacilli Phage Endolysins and Their Functional Domains–Potential Live Biotherapeutic Testing Reagents

Phage endolysin-specific binding characteristics and killing activity support their potential use in biotechnological applications, including potency and purity testing of live biotherapeutic products (LBPs). LBPs contain live organisms, such as lactic acid bacteria (LAB), and are intended for use as drugs. Our approach uses the endolysin cell wall binding domains (CBD) for LBP potency assays and the endolysin killing activity for purity assays. CBDs of the following five lactobacilli phage lysins were characterized: CL1, Jlb1, Lj965, LL-H, and ΦJB. They exhibited different bindings to 27 LAB strains and were found to bind peptidoglycan or surface polymers. Flow cytometry based on CBD binding was used to enumerate viable counts of two strains in the mixture. CL1-lys, jlb1-lys, and ΦJB-lys and their enzymatic domains (EADs) exhibited cell wall digestive activity and lytic activity against LAB. Jlb1-EAD and ΦJB-EAD were more sensitive than their respective hololysins to buffer pH and NaCl changes. The ΦJB-EAD exhibited stronger lytic activity than ΦJB-lys, possibly due to ΦJB-CBD-mediated sequestration of ΦJB-lys by cell debris. CBD multiplex assays indicate that these proteins may be useful LBP potency reagents, and the lytic activity suggests that CL1-lys, jlb1-lys, and ΦJB-lys and their EADs are good candidates for LBP purity reagent development.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Full-Length ASFV B646L Gene Sequencing by Nanopore Offers a Simple and Rapid Approach for Identifying ASFV Genotypes

African swine fever (ASF) is an acute, highly hemorrhagic viral disease in domestic pigs and wild boars. The disease is caused by African swine fever virus, a double stranded DNA virus of the Asfarviridae family. ASF can be classified into 25 different genotypes, based on a 478 bp fragment corresponding to the C-terminal sequence of the B646L gene, which is highly conserved among strains and encodes the major capsid protein p72. The C-terminal end of p72 has been used as a PCR target for quick diagnosis of ASF, and its characterization remains the first approach for epidemiological tracking and identification of the origin of ASF in outbreak investigations. Recently, a new classification of ASF, based on the complete sequence of p72, reduced the 25 genotypes into only six genotypes; therefore, it is necessary to have the capability to sequence the full-length B646L gene (p72) in a rapid manner for quick genotype characterization. Here, we evaluate the use of an amplicon approach targeting the whole B646L gene, coupled with nanopore sequencing in a multiplex format using Flongle flow cells, as an easy, low cost, and rapid method for the characterization and genotyping of ASF in real-time.

Virology↗
DOE OSTI2021

SDSS-V Algorithms: Fast, Collision-free Trajectory Planning for Heavily Overlapping Robotic Fiber Positioners

Robotic fiber positioner (RFP) arrays are becoming heavily adopted in wide-field massively multiplexed spectroscopic survey instruments. RFP arrays decrease nightly operational overheads through rapid reconfiguration between fields and exposures. In comparison to similar instruments, SDSS-V has selected a very dense RFP packing scheme where any point in a field is typically accessible to three or more robots. This design provides flexibility in target assignment. However, the task of collisionless trajectory planning is especially challenging. We present two multiagent distributed control strategies that are highly efficient and computationally inexpensive for determining collision-free paths for RFPs in heavily overlapping workspaces. We demonstrate that a reconfiguration path between two arbitrary robot configurations can be efficiently found if a “folded” state, in which all robot arms are retracted and aligned in a lattice-like orientation, is inserted between the initial and final states. Although developed for SDSS-V, the approach we describe is generic and thus applicable to a wide range of RFP designs and layouts. Robotic fiber positioner technology continues to advance rapidly, and in the near future ultra-densely packed RFP designs may be feasible. Our algorithms are especially capable in routing paths in very crowded environments, where we see efficient results even in regimes significantly more crowded than the SDSS-V RFP design.

42 ENGINEERING↗
DOE OSTI2022

The Stability of Fiber Spectrographs in the Faint-source Regime

The use of optical fibers in astronomical instrumentation offers high-multiplex and light-gathering flexibility. However, with most previous fiber spectrographs optimized for large fields of view on modest-aperture telescopes, the performance of fibers in the context of faint targets on large telescopes remains largely untested. In this paper, we evaluate aspects of fiber stability, especially as they apply in the context of precision sky subtraction of faint sources at modest spectral resolution ($R$ ~ 3000). After introducing a framework for describing potential systematic errors, we use publicly available data from existing instruments, including instrumentation used by the fourth-generation Sloan Digital Sky Survey’s MaNGA project (MaNGA: Mapping Nearby Galaxies at Apache Point Observatory) and the Very Large Telescope’s FLAMES: Fiber Large Array Multi Element Spectrograph. We isolate sources of fiber systematics and estimate the observed amplitude of persistent residuals as well as stochastic noise contributions resulting from changing fiber stresses. Comparing these levels against their impact on various sky subtraction schemes demonstrates that 0.1% precision sky subtraction with fiber instruments is possible. As a demonstration, we show that the MaNGA instrument can deliver 0.2% residuals on bright near-IR sky lines with nonlocal sky subtraction, if pseudo-slit limitations are addressed by allocating 50% of its fibers to sky. We further highlight recently published deep exposures that achieved a 1$σ$ background level of 27.6 AB per square arc second, equivalent to a precision of 0.2% of the sky background continuum.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Measuring Fiber Positioning Accuracy and Throughput with Fiber Dithering for the Dark Energy Spectroscopic Instrument

Highly multiplexed, fiber-fed spectroscopy is enabling surveys of millions of stars and galaxies. The performance of these surveys depends on accurately positioning fibers in the focal plane to capture target light. We describe a technique to measure the positioning accuracy of fibers by dithering fibers slightly around their ideal locations. This approach also enables measurement of the total system throughput and point-spread function delivered to the focal plane. We then apply this technique to observations from the Dark Energy Survey Instrument (DESI), and demonstrate that DESI positions fibers to within 0farcs08 of their targets (5% of a fiber diameter) and achieves a system throughput within about 7% of expectations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Correcting Turbulence-induced Errors in Fiber Positioning for the Dark Energy Spectroscopic Instrument

Highly multiplexed, robotic, fiber-fed spectroscopic surveys are observing tens of millions of stars and galaxies. For many systems, accurate positioning relies on imaging the fibers in the focal plane and feeding that information back to the robotic positioners to correct their positions. Inhomogeneities and turbulence in the air between the focal plane and the imaging camera can affect the measured positions of fibers, limiting the accuracy with which fibers can be placed on targets. For the Dark Energy Spectroscopic Instrument, we dramatically reduced the effect of turbulence on measurements of positioner locations in the focal plane by taking advantage of stationary positioners and the correlation function of the turbulence. We were able to reduce positioning errors from 7.3 to 3.5 μm, speeding the survey by 1.6% under typical conditions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Deep Spectroscopy with DESI for Photometric Redshift Training and Calibration

Deep spectroscopic samples can improve photometric redshift (photo-z) estimates and reduce uncertainties on redshift distributions. Such improvements can increase the cosmological constraining power of large imaging-based experiments such as the Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST) and mitigate what may be a limiting systematic effect. We present results from the “DESI-Deep pilot” program, which was designed to assess the capability of the Dark Energy Spectroscopic Instrument (DESI) on the 4m Mayall telescope to measure redshifts of galaxies as faint as expected lensing samples for early LSST data (m i ≤ 24.5). We find that DESI is remarkably efficient at this task, with redshift success rates comparable to the results of observations from 10 m class telescopes with only ∼2 × longer integration time (rather than ∼8 × longer as would be expected from aperture-area scaling), while simultaneously achieving ∼30 times larger multiplexing. We also find that the signal-to-noise ratio of the spectra scales as expected for background-limited observations even for the longest exposure times (∼7 hr) and faintest targets in the program. These results demonstrate that DESI could provide the definitive redshift sample for the early years of LSST with a modest investment of observing time. Based upon the results of this program, we provide updated predictions for the time required to collect benchmark samples for photo-z training and calibration using a variety of spectroscopic facilities. Finally, we describe a potential “DESI-Deep” survey designed to train and calibrate photo-z’s for imaging experiments, and provide forecasts of its impact on cosmological inference.

Dey, Biprateep [University of Toronto; University ↗
DOE OSTI2021

The Stars of the HETDEX Survey. I. Radial Velocities and Metal-poor Stars from Low-resolution Stellar Spectra

The Hobby–Eberly Telescope Dark Energy Experiment (HETDEX) is an unbiased, massively multiplexed spectroscopic survey, designed to measure the expansion history of the universe through low-resolution ( R ~ 750) spectra of Ly α emitters. In its search for these galaxies, HETDEX will also observe a few times 10 5 stars. In this paper, we present the first stellar value-added catalog within the internal second data release of the HETDEX Survey (HDR2). The new catalog contains 120,571 low-resolution spectra for 98,736 unique stars between 10 < G < 22 spread across the HETDEX footprint at relatively high ( b ~ 60°) Galactic latitudes. With these spectra, we measure radial velocities (RVs) for ~42,000 unique FGK-type stars in the catalog and show that the HETDEX spectra are sufficient to constrain these RVs with a 1 σ precision of 28.0 km s -1 and bias of 3.5 km s -1 with respect to the Large Sky Area Multi-Object Fibre Spectroscopic Telescope surveys and 1 σ precision of 27.5 km s -1 and bias of 14.0 km s -1 compared to the Sloan Extension for Galactic Understanding and Exploration survey. Since these RVs are for faint ( G ≥ 16) stars, they will be complementary to Gaia. Using t-Distributed Stochastic Neighbor Embedding (tSNE), we also demonstrate that the HETDEX spectra can be used to determine a star’s T eff , and log g and its [Fe/H]. With the tSNE projection of the FGK-type stars with HETDEX spectra we also identify 416 new candidate metal-poor ([Fe/H] < -1 dex) stars for future study. These encouraging results illustrate the utility of future low-resolution stellar spectroscopic surveys.

Astronomy & Astrophysics↗
DOE OSTI2026

Probing the Environment around GW170817 with DESI: Insights on Galaxy Group Peculiar Velocities for Standard Siren Measurements

We present a new measurement of the Hubble constant, H 0 , following the gravitational-wave event GW170817 and Dark Energy Spectroscopic Instrument (DESI) observations. A standard siren measurement with a nearby (luminosity distance ∼40 Mpc) event such as GW170817 is typically sensitive to the peculiar motion of the host galaxy owing to local dynamics. Previous measurements from this event have taken advantage of peculiar velocity measurements of nearby galaxies, including a handful of objects in the galaxy group that the host of the event, NGC 4993, has been associated with. Still, the group’s properties and NGC 4993’s membership were debated. We present DESI observations of thousands of galaxies in the vicinity of NGC 4993, resulting in 39 group galaxies and a fivefold increase in galaxies compared to previous observations, with many contributing to a peculiar velocity measurement. Examining the local dynamics, our observations support the presence of a galaxy group of which NGC 4993 is a part with a halo mass of order ∼10 13 M ⊙ . Using peculiar velocity measurements from our fundamental plane galaxy observations, we find $H_0 = 70.9^{+6.4}_{-8.5}$ km s −1 Mpc −1 . In addition, using a peculiar velocity measurement for NGC 4993 from surface brightness fluctuations in Cosmicflows-4, we find $H_0 = 73.4^{+3.3}_{-3.9}$ km s −1 Mpc −1 . We study the impact of different galaxy selection criteria on the determination of the peculiar velocity and, in turn, on the H 0 measurement. Our results demonstrate the value of multiplexed spectroscopic observations for probing the local environments of gravitational-wave events used in standard siren measurements.

Amsellem, A. J. [Carnegie Mellon University, Pitts↗
DOE OSTI2022

The Design and Integrated Performance of SPT-3G

Abstract SPT-3G is the third survey receiver operating on the South Pole Telescope dedicated to high-resolution observations of the cosmic microwave background (CMB). Sensitive measurements of the temperature and polarization anisotropies of the CMB provide a powerful data set for constraining cosmology. Additionally, CMB surveys with arcminute-scale resolution are capable of detecting galaxy clusters, millimeter-wave bright galaxies, and a variety of transient phenomena. The SPT-3G instrument provides a significant improvement in mapping speed over its predecessors, SPT-SZ and SPTpol. The broadband optics design of the instrument achieves a 430 mm diameter image plane across observing bands of 95, 150, and 220 GHz, with 1.2′ FWHM beam response at 150 GHz. In the receiver, this image plane is populated with 2690 dual-polarization, trichroic pixels (∼16,000 detectors) read out using a 68× digital frequency-domain multiplexing readout system. In 2018, SPT-3G began a multiyear survey of 1500 deg 2 of the southern sky. We summarize the unique optical, cryogenic, detector, and readout technologies employed in SPT-3G, and we report on the integrated performance of the instrument.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Characterization of Low-mass Companions to Kepler Objects of Interest Observed with APOGEE-N

We report the characterization of 28 low-mass (0.02 M ⊙ ≤ M 2 ≤ 0.25 M ⊙ ) companions to Kepler objects of interest (KOIs), eight of which were previously designated confirmed planets. These objects were detected as transiting companions to Sunlike stars (G and F dwarfs) by the Kepler mission and are confirmed as single-lined spectroscopic binaries in the current work using the northern multiplexed Apache Point Observatory Galactic Evolution Experiment near-infrared spectrograph (APOGEE-N) as part of the third and fourth Sloan Digital Sky Surveys. We have observed hundreds of KOIs using APOGEE-N and collected a total of 43,175 spectra with a median of 19 visits and a median baseline of ~1.9 yr per target. We jointly model the Kepler photometry and APOGEE-N radial velocities to derive fundamental parameters for this subset of 28 transiting companions. The radii for most of these low-mass companions are overinflated (by ~10%) when compared to theoretical models. Tidally locked M dwarfs on short-period orbits show the largest amount of inflation, but inflation is also evident for companions that are well separated from the host star. We demonstrate that APOGEE-N data provide reliable radial velocities when compared to precise high-resolution spectrographs that enable detailed characterization of individual systems and the inference of orbital elements for faint (H > 12) KOIs. The data from the entire APOGEE-KOI program are public and present an opportunity to characterize an extensive subset of the binary population observed by Kepler.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

The Spectroscopic Stage-5 Experiment

The existence, properties, and dynamics of the dark sectors of our universe pose fundamental challenges to our current model of physics, and large-scale astronomical surveys may be our only hope to unravel these long-standing mysteries. In this white paper, we describe the science motivation, instrumentation, and survey plan for the next-generation spectroscopic observatory, the Stage-5 Spectroscopic Experiment (Spec-S5). Spec-S5 is a new all-sky spectroscopic instrument optimized to efficiently carry out cosmological surveys of unprecedented scale and precision. The baseline plan for Spec-S5 involves upgrading two existing 4-m telescopes to new 6-m wide-field facilities, each with a highly multiplexed spectroscopic instrument capable of simultaneously measuring the spectra of 13,000 astronomical targets. Spec-S5, which builds and improves on the hardware used for previous cosmology experiments, represents a cost-effective and rapid approach to realizing a more than 10$\times$ gain in spectroscopic capability compared to the current state-of-the-art represented by the Dark Energy Spectroscopic Instrument project (DESI). Spec-S5 will provide a critical scientific capability in the post-Rubin and post-DESI era for advancing cosmology, fundamental physics, and astrophysics in the 2030s.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

A New Inelastic Neutron Spectrometer HODACA

In this study, a new multiplex-type inelastic neutron scattering spectrometer, HOrizontally Defocusing Analyzer Concurrent data Acquisition spectrometer (HODACA), was recently developed and built at the C1-1 cold neutron beam port in the neutron source reactor JRR-3 at Japan Atomic Energy Agency. The spectrometer is suitable for dynamics measurements in the energy range of -1 meV ≲ ℏω ≲ 7 meV, catering to a broad array of research fields in physics and material science. HODACA combines 24 detectors and 132 pieces of analyzer crystals and has an estimated measurement efficiency that is 70 times greater than the existing conventional triple-axis spectrometer at the C1-1 beam port. The concept, design, specification, and results of commissioning experiments are described.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

Genomic DNA from each sample was prepared using the Wizard Genomic DNA Purification Kit (Promega) and after, DNA was quantified using the QuantiFluor ONE dsDNA System (Promega). Genomic DNA underwent shearing to ~200 bp fragments via sonication and the gDNA fragments were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Bead-based size selection was used to select ~200 bp fragments and the fragments then underwent a splinkerette PCR using a Tn5-enriching forward primer and custom reverse primers for multiplexing. A final bead-based size selection was used to select for the correct length DNA. DNA was sequenced at the University of Michigan Advanced Genomics Core using Illumina sequencing with a custom read primer reading the last 10 nt of the transposon. PhiX174 DNA spike was added to the run to ensure sufficient sequence diversity on the flow cell. Then, a custom index read primer and standard Illumina primer were used to sequence the index reads and PhiX174, respectively.

Keck, James L.↗
DOE OSTI2020

Design and performance of an in-vacuum, magnetic field mapping system for the Muon g-2 experiment

The E989 Muon g-2 experiment at Fermilab aims to measure the anomalous magnetic moment, a$_\mu$, of the muon with a precision of 140 parts-per-billion. This requires a precise measurement of both the anomalous spin precession frequency, $\omega_a$, and the average magnetic field in terms of the equivalent, free proton Larmor frequency, $\omega_p$. The measurement of $\omega_p$ with a total systematic uncertainty of 70 parts-per-billion involves a combination of various NMR probes. There are 378 probes in fixed locations constantly monitoring field drifts. A water-based probe provides the calibration in terms of $\omega_p$. A crucial element for the multi-step measurement of $\omega_p$ is the regular mapping of the magnetic field over the muon storage region. The former E821 experiment at Brookhaven employed an in-vacuum field mapping system equipped with 17 NMR probes, which was developed by the University of Heidelberg. We have refurbished and upgraded this system with new probes and electronics. The upgrades include a new communication scheme incorporating time-division multiplexing to separate the important NMR reference clock from the data communication. The addition digitization of the NMR signals replaced the hardware-implemented zero-crossing counting of the E821 system. The digitized signals offer new capabilities in the NMR frequency analysis and its related systematic uncertainties. While the mechanical systems that move the field mapper around the ring have been mostly refurbished, the motion control system was completely replaced with a custom-built electronics centered around a commercial Galil motion controller. Both the field mapping NMR system and its motion control were successfully commissioned at Fermilab and have been in reliable operation during the first data taking periods. This article provides details of the upgrades of the field mapper and its performance.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Fluid delivery manifolds and microfluidic systems

Embodiments of fluid distribution manifolds, cartridges, and microfluidic systems are described herein. Fluid distribution manifolds may include an insert member and a manifold base and may define a substantially closed channel within the manifold when the insert member is press-fit into the base. Cartridges described herein may allow for simultaneous electrical and fluidic interconnection with an electrical multiplex board and may be held in place using magnetic attraction.

42 ENGINEERING↗
DOE OSTI2020

Cyclic Prefix Direct Sequence Spread Spectrum Capacity Analysis

Cyclic Prefix Direct Sequence Spread Spectrum (CP-DSSS) is a novel waveform that has the potential to solve 5G objectives such as ultra reliable low latency communication (URLLC) and massive machine Type Communication (mMTC). This paper analyzes the capacity of the CP-DSSS waveform in comparison with Orthogonal Frequency Domain Multiplexing OFDM). CP-DSSS can be optimized to achieve the same capacity as OFDM when optimized by the water-filling algorithm. A significant advantage for CP-DSSS is that this capacity can be achieved with all symbols being transmitted with the same effective rate. As a result, stronger forward error correction codes can be used in a CP-DSSS implementation compared to an OFDM implementation with resource block constraints. In addition, the applicability of CP-DSSS as a waveform for a secondary network operating in the same frequency band as the primary network is discussed.

5G and Beyond Communications↗
DOE OSTI2020

CP-DSSS: An OFDM Compatible Variable Rate Modulation for 5G and Beyond

Cyclic prefix direct sequence spread spectrum (CPDSSS) is a recently proposed waveform that has been designed for coexistence with OFDM (orthogonal frequency division multiplexing) in the same or a pair of parallel networks. The first contribution of this paper is to present equations that reveal similarities and differences of CP-DSSS and OFDM. Furthermore, we show that the channel model of CP-DSSS reduces to that of a cyclic prefixed block-wise single carrier modulation (CP-SCM). However, unlike CP-SCM whose symbol rate is always equal to the transmission bandwidth, CP-DSSS can be adopted to any symbol rate equal to or smaller than the transmission bandwidth. This reduction in symbol rate allows CP-DSSS power spectral density to drop to an arbitrarily low level, hence, facilitates it coexistence as a secondary waveform in a network of primary users. The peak-to-average power ratio (PAPR) of CP-DSSS is also explored and a method for reducing it is proposed.

5G↗