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At least 235 records · Page 13

Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities

Microorganisms frequently colonize surfaces within food production facilities. Detection of Listeria monocytogenes in this setting relies on culture-dependent methods, but the complex dynamics of bacterial interactions within these environments and their impact on pathogen detection remain largely unexplored. To address this challenge, we applied both 16S rRNA and shotgun quasimetagenomic (enriched microbiome) sequencing of swab culture enrichments from five seafood and seven dairy production environments. Utilizing 16S rRNA amplicon sequencing, we observed variability between 355 samples taken from these 12 production facilities and a distinctive microbiome for each environment. With shotgun quasimetagenomic sequencing, we were able to assemble L. monocytogenes metagenome-assembled genomes (MAGs) from 28 of the 32 culture-positive samples. We compared these MAGs to their corresponding whole-genome sequencing assemblies, which resulted in two polyphyletic clades consisting of L. monocytogenes lineages I and II with 13,195 and 25,556 single-nucleotide polymorphism sites, respectively. The remaining four MAGs did not produce sufficient genome coverage. To understand and establish limits for pathogen detection and subtyping using shotgun quasimetagenomics, these same data sets were downsampled in slilico to produce a titration series of abundances of L. monocytogenes and analyzed. Pathogen detection was achieved for all downsampled data sets, even those with only 3× genome coverage. This study contributes to the understanding of microbial diversity within food production environments and presents insights into the level of genome coverage needed in a metagenome sequencing data set to detect, subtype, and source track a foodborne pathogen.

59 BASIC BIOLOGICAL SCIENCES↗

Comparison of measurement techniques and sorption of radium-226 in low and high salinity aqueous samples

Human activities have the potential to redistribute radium (Ra) in the marine environment in a manner that may necessitate monitoring or management of subsequent human or environmental exposures. There is therefore a need to identify accurate and accessible techniques for Ra measurement in high salinity samples and to describe the distribution of Ra in estuarine and marine environments, but most efforts in these areas have focused on low salinity matrices. In addition, rapid and reliable measurements are crucial for time-sensitive samples such as short-lived isotopes or emergency situations. The objective of this study is to describe the limits of detection, cost, and relative ease for measurement of Ra in both low and high salinity aqueous samples via three analytical methods: liquid scintillation counting (LSC), high purity germanium (HPGe) gamma spectrometry, and inductively coupled plasma mass spectrometry (ICP-MS). To contextualize these measurements for real-world scenarios, the partitioning of 226 Ra to substrates relevant to the marine environment was also characterized. Although HPGe detection with solid phase extraction had the lowest limit of detection for low salinity samples (0.27 Bq L −1 ), poor 226 Ra recovery for high salinity samples and high materials costs make this method prohibitive for many users. Limits of detection for high salinity samples were lower for LSC (1.28 Bq L −1 ) than for ICP-MS without dilution (11.4 Bq L −1 ), but significant and unexpected degradation of the high salinity LSC standards was observed after six months. Furthermore, our preferred measurement method for high salinity Ra samples is ICP-MS with sample dilution as necessary to reduce matrix effects.

07 ISOTOPE AND RADIATION SOURCES↗

Metallicity beats sSFR: the connection between superluminous supernova host galaxy environments and the importance of metallicity for their production

ABSTRACT We analyse 33 Type I superluminous supernovae (SLSNe) taken from Zwicky Transient Facility (ZTF)’s Bright Transient Survey to investigate the local environments of their host galaxies. We use a spectroscopic sample of galaxies from the Sloan Digital Sky Survey (SDSS) to determine the large-scale environmental density of the host galaxy. Noting that SLSNe are generally found in galaxies with low stellar masses, high star formation rates (SFRs), and low metallicities, we find that SLSN hosts are also rarely found within high-density environments. Only $3\substack{+9 \\ -1}$ per cent of SLSN hosts were found in regions with two or more bright galaxies within 2 Mpc. For comparison, we generate a sample of 662 SDSS galaxies matched to the photometric properties of the SLSN hosts. This sample is also rarely found within high-density environments, suggesting that galaxies with properties required for SLSN production favour more isolated environments. Furthermore, we select galaxies within the IllustrisTNG simulation to match SLSN host galaxy properties in colour and stellar mass. We find that the fraction of simulated galaxies in high-density environments quantitatively match the observed SLSN hosts only if we restrict to simulated galaxies with metallicity 12 + log (O/H) ≤ 8.12. In contrast, limiting to only the highest specific star formation rate (sSFR) galaxies in the sample leads to an overabundance of SLSN hosts in high-density environments. Thus, our measurement of the environmental density of SLSN host galaxies appears to break the degeneracy between low metallicity and high sSFR as the driver for SLSN hosts and provides evidence that the most constraining factor on SLSN production is low metallicity.

79 ASTRONOMY AND ASTROPHYSICS↗

SDSS-IV MaNGA: the role of the environment in AGN triggering

ABSTRACT The large- and small-scale environments around optically-selected AGN host galaxies and a control sample of non-active galaxies in the MaNGA survey have been investigated in order to evaluate the importance of the environment in AGN triggering. Using the MaNGA integral field spectroscopy, we quantify non-circular motions of the ionized gas and detect an excess of radial gas motions in AGN hosts relative to control galaxies, not associated to AGN feedback and are most likely the result of tidal interactions, possibly associated with the triggering of the AGN. We find that the large-scale environments are similar for the AGN hosts and control galaxies in our sample and are biased towards lower large-scale densities and group virial masses, suggestive that the large-scale environment properties is only relevant to the AGN phenomenon in an indirect way, in the form, e.g. of the morphology-density relation. The small-scale environment, as measured by the frequency and luminosity of close neighbours, was also found to be similar for AGN and control galaxies. However, we find a correlation between the intensity of the non-circular gas motions in AGN hosts and the strength of the tidal field, while the control sample does not present such correlation. Also, AGN hosts with the most intense radial gas motions present larger tidal fields than their control galaxies. These findings indicate that at least a fraction of the AGN hosts in our sample have been triggered by tidal interactions with nearby galaxies.

Rembold, Sandro B.↗

Quasi-In-Situ Analysis of Electrode Top Atomic Layers via High-Sensitivity Low-Energy Ion Scattering and Potential-Controlled Sample Transfer

Electrocatalytic reactions involve interfacial interactions between the surfaces of electrodes and reactive species at an electrolyte interface. There are presently no universal or unambiguous methods to directly assay the active top atomic layer composition that influences the reactivity of these electrodes under relevant operating conditions. Low-energy ion scattering (LEIS) spectroscopy is a surface characterization technique that yields compositional analysis of the outermost atomic layer of a material, but it must be performed in ultrahigh vacuum (UHV). Application of LEIS measurements to electrochemical materials that are removed from ambient liquid-phase environments thus leaves an open question as to whether the surface that is transferred to UHV is truly the surface that manifested during the electrochemical reaction. Toward the goal of preserving the active surface state, we developed a sample transfer workflow for LEIS enabling air-free removal and drying of an electrode from an electrochemical cell while maintaining control of the potential using an auxiliary electrode. The potential-controlled emersion method was demonstrated to give distinct potential-dependent surface compositions for a Cu−Pd alloy relative to removal after uncontrolled return to open-circuit potential. A Cu-enriched surface was found at anodic potential and a Pd-enriched surface at cathodic potential, suggesting that the approach can be used to retain representative atomic configurations during transfer. Since adsorbates will often persist from the reaction environment, conventional sample pretreatment methods for removal, including atomic O and atomic H exposure, were also contrasted. Both methods were found to differ with results from incidental low-dose depth profiling by the LEIS primary ion source, which removes adventitious species and surface atoms during the course of repeated measurements. These depth profiles were found to be sensitive to sample history and thus qualitatively informative, despite the possible changes induced by ion damage. The results exhibit (i) the need for complete control over the polarization state of the sample at all times (no excursions to open circuit during transfer) and (ii) the utility of low-dose depth profiling to capture changes in the near-surface composition.

Alloys↗

Modeling the use of mobile modular gas samplers in near-field detection

The Wireless Independent Noble Gas Sampler (WINGS) is a mobile, modular gas sampling system designed for use in low infrastructure environments. In the case of a suspected underground nuclear explosion (UNE), WINGS units could be deployed to detect noble gases emanating from the suspected explosion site or identify gases originating from another source entering the local area from offsite. In conclusion, this work uses the atmospheric transport modeling tool inline WRF-HYSPLIT to test the effectiveness of WINGS units around a suspected UNE site as a function of sampler density and distance from the emission point of gases from a UNE.

Air sampling↗

Phase Transformation and Water Adsorption Behavior of As‐Deposited and Annealed Ru Metal Thin Films Prepared by Atomic Layer Deposition

ABSTRACT Surfaces play a central role in catalytic processes, and understanding the transformation of ruthenium metal into ruthenium oxide during annealing is essential for tailoring functional catalytic interfaces. In this study, we systematically investigate ≈22 nm thick Ru metal films deposited by atomic layer deposition (ALD) at 300°C, focusing on their chemical composition, structural evolution, and surface hydration behavior following post‐deposition annealing in air from 400 to 600°C. Lab‐based and synchrotron X‐ray photoelectron spectroscopy (XPS) reveal a gradual conversion from metallic Ru to fully oxidized Ru 4+ with increasing annealing temperature, accompanied by a corresponding increase in lattice oxygen. X‐ray diffraction (XRD) shows amorphous Ru oxide phases at 400°C and 500°C that evolve into crystalline RuO 2 at 600°C, while atomic force microscopy (AFM) indicates enhanced grain growth and surface roughening upon annealing. Ambient‐pressure XPS (AP‐XPS) under controlled H 2 O vapor environments (1–17 Torr) demonstrates that samples annealed at 400°C and 500°C exhibit initially high hydroxyl coverage that decreases with increasing water vapor pressure, concurrent with a rise in molecular H 2 O adsorption. In contrast, the crystalline RuO 2 surface formed at 600°C maintains stable hydroxylation and supports increased water uptake. Overall, this work provides fundamental insight into Ru oxide–H 2 O interactions and establishes design principles for engineering oxide surfaces optimized for electrocatalytic applications.

APXPS↗

Use of a Be-dome holder for texture and strain characterization of Li metal thin films via sin 2 (ψ) methodology

Residual strain in electrodeposited Li films may affect safety and performance in Li metal battery anodes, so it is important to understand how to detect residual strain in electrodeposited Li and the conditions under which it arises. To explore this Li films, electrodeposited onto Cu metal substrates, were prepared under an applied pressure of either 10 or 1000 kPa and subsequently tested for the presence or absence of residual strain via sin 2 (ψ) analysis. X-ray diffraction (XRD) analysis of Li films required preparation and examination within an inert environment; hence, a Be-dome sample holder was employed during XRD characterization. Results show that the Li film grown under 1000 kPa displayed a detectable presence of in-plane compressive strain (–0.066%), whereas the Li film grown under 10 kPa displayed no detectable in-plane strain. Here, the underlying Cu substrate revealed an in-plane residual strain near zero. Texture analysis via pole figure determination was also performed for both Li and Cu and revealed a mild fiber texture for Li metal and a strong bi-axial texture of the Cu substrate. Experimental details concerning sample preparation, alignment, and analysis of the particularly air-sensitive Li films have also been detailed. This work shows that Li metal exhibits residual strain when electrodeposited under compressive stress and that XRD can be used to quantify that strain.

36 MATERIALS SCIENCE↗

In Situ XAFS, XRD, and DFT Characterization of the Sulfur Adsorption Sites on Cu and Ce Exchanged Y Zeolites

Adsorptive desulfurization with Cu and Ce ion-exchanged Y zeolite (CuCeY) has proven to be an effective method for the removal of sulfur compounds from hydrocarbon fuels. In this study, Cu and Ce exchanged Y materials including CuY, CeY, and CuCeY were prepared and examined to investigate the mechanism behind the superior sulfur adsorption and selectivity of CuCeY. In situ conditions were used to study the materials as prepared for optimal desulfurization. X-ray diffraction (XRD) confirmed the absence of large well-ordered crystalline phases from metallic or oxide Cu and Ce after the reduction of the samples. The oxidation states and local environments of Cu and Ce were determined using X-ray adsorption fine structure (XAFS) analysis and correlated to theoretical findings obtained from density functional theory (DFT) calculations. XAFS data indicate the successful reduction of Cu species to Cu + and Cu o , and Ce to Ce 3+ . Analysis of XAFS spectra located Cu and Ce within the Y zeolite framework with Cu cations in the six-member ring sites and as small metallic Cu clusters. Ce cations were found to occupy both six-member ring and hexagonal prism sites. Furthermore, these results reveal the structure of CuCeY as prepared for desulfurization and provide insight into its superior sulfur adsorption performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems

The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Charge collection and electrical characterization of neutron irradiated silicon pad detectors for the CMS High Granularity Calorimeter

The replacement of the existing endcap calorimeter in the Compact Muon Solenoid (CMS) detector for the high-luminosity LHC (HL-LHC), scheduled for 2027, will be a high granularity calorimeter. It will provide detailed position, energy, and timing information on electromagnetic and hadronic showers in the immense pileup of the HL-LHC. The High Granularity Calorimeter (HGCAL) will use 120-, 200-, and 300-$\mu\textrm{m}$ thick silicon (Si) pad sensors as the main active material and will sustain 1-MeV neutron equivalent fluences up to about $10^{16}~\textrm{n}_\textrm{eq}\textrm{cm}^{-2}$. In order to address the performance degradation of the Si detectors caused by the intense radiation environment, irradiation campaigns of test diode samples from 8-inch and 6-inch wafers were performed in two reactors. Characterization of the electrical and charge collection properties after irradiation involved both bulk polarities for the three sensor thicknesses. Since the Si sensors will be operated at -30 $^\circ$C to reduce increasing bulk leakage current with fluence, the charge collection investigation of 30 irradiated samples was carried out with the infrared-TCT setup at -30 $^\circ$C. TCAD simulation results at the lower fluences are in close agreement with the experimental results and provide predictions of sensor performance for the lower fluence regions not covered by the experimental study. All investigated sensors display 60$\%$ or higher charge collection efficiency at their respective highest lifetime fluences when operated at 800 V, and display above 90$\%$ at the lowest fluence, at 600 V. The collected charge close to the fluence of $10^{16}~\textrm{n}_\textrm{eq}\textrm{cm}^{-2}$ exceeds 1 fC at voltages beyond 800 V.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Active matter shepherding and clustering in inhomogeneous environments

Here, we consider a mixture of active and passive run-and-tumble disks in an inhomogeneous environment where only half of the sample contains quenched disorder or pinning. The disks are initialized in a fully mixed state of uniform density. We identify several distinct dynamical phases as a function of motor force and pinning density. At high pinning densities and high motor forces, there is a two-step process initiated by a rapid accumulation of both active and passive disks in the pinned region, which produces a large density gradient in the system. This is followed by a slower species phase separation process where the inactive disks are shepherded by the active disks into the pin-free region, forming a nonclustered fluid and producing a more uniform density with species phase separation. For higher pinning densities and low motor forces, the dynamics becomes very slow and the system maintains a strong density gradient. For weaker pinning and large motor forces, a floating clustered state appears, and the time-averaged density of the system is uniform. We illustrate the appearance of these phases in a dynamic phase diagram.

97 MATHEMATICS AND COMPUTING↗

Mjölnir: a miniature triaxial rock deformation apparatus for 4D synchrotron X-ray microtomography

An X-ray transparent experimental triaxial rock deformation apparatus, here named 'Mjölnir', enables investigations of brittle-style rock deformation and failure, as well as coupled thermal, chemical and mechanical processes relevant to a range of Earth subsurface environments. Designed to operate with cylindrical samples up to 3.2 mm outside-diameter and up to 10 mm length, Mjölnir can attain up to 50 MPa confining pressure and in excess of 600 MPa axial load. The addition of heaters extends the experimental range to temperatures up to 140°C. Deployment of Mjolnir on synchrotron beamlines indicates that full 3D datasets may be acquired in a few seconds to a few minutes, meaning full 4D investigations of deformation processes can be undertaken. Mjölnir is constructed from readily available materials and components and complete technical drawings are included in the supporting information.

47 OTHER INSTRUMENTATION↗

Online Optimization for Networked Distributed Energy Resources With Time-Coupling Constraints

This paper proposes a Lyapunov optimization-based online distributed (LOOD) algorithmic framework for active distribution networks (ADNs) with numerous photovoltaic inverters and inverter air conditionings (IACs). In the proposed scheme, ADNs can track an active power setpoint reference at the substation in response to transmission-level requests while concurrently minimizing the social utility loss and ensuring the security of voltages. Conventional distributed optimization methods are rarely feasible to track the optimal solutions in fast variable environments using a fine-grained sampling interval where the underlying optimization problem evolves with the iterations of the algorithms. In contrast, based on the framework of online convex optimization (OCO), the developed approach uses a distributed algebraic update to compute the next round decisions relying on the current feedback of measurements. Notably, the time-coupling constraints of IACs are decoupled for online implementation with Lyapunov optimization technique. An incentive scheme is tailored to coordinate the customer-owned assets in lieu of the direct control from network operators. Optimality and convergency are characterized analytically. Finally, we corroborate the proposed method on a modified version of 33-node test feeder. Benchmark tests show that the proposed method is computationally and economically efficient, and outperforming existing algorithms.

active distribution networks↗

Spatially Resolved Characterisation of Low Mass Fraction Uranium Glass Working Reference Materials

Here, we present the results of a study to generate reference glasses that reflect an environment analogous to historic nuclear fallout samples of interest for post-detonation nuclear forensics. The glasses were generated by melting and then quenching SiO 2 , Al 2 O 3 and CaCO 3 powders. Two suites of glasses with three distinct U isotopic ratios were successfully made with enrichments in the 235 U isotope (~ natural [0.72%], ~ 53% and 94%), but the bulk elemental data showed heterogeneity (~ 10% RSD) with U mass fractions ranging from 331.47 to 373.63 μg g -1 . Spatially resolved U isotopic measurements were performed using three mass spectrometry techniques (secondary ion mass spectrometry-single stage accelerator mass spectrometry [SIMS-SSAMS], large geometry [LG] - SIMS, and laser ablation-inductively coupled plasma-mass spectrometry [LA-ICP-MS]) across five National Laboratories. The results showed good agreement with the bulk U isotopic data for the low, medium, and high U mass fractions. We conclude that despite elemental heterogeneity, these samples can serve as useful working reference materials for spatially resolved nuclear fallout analyses, as well as for other related spatially resolved analyses.

36 MATERIALS SCIENCE↗

Five draft genome assemblies from Bacillaceae isolated from a degraded wetland environment

Abstract We isolated 5 Bacillaceae from a degraded wetland environment and sequenced their genomes using Illumina NextSeq. Here, we report draft genome sequences of Bacillus velezensus-SC119, Priestia megaterium-SC120, Bacillus zhangzhouensis-SC123, Bacillus pumilis-SC124, and Bacillus idriensis-SC127. The genomes range between 3,657,353 and 5,772,725 base pairs with %GC between 37.62% and 46.38%. Introduction Wetland environments play critical roles in the terrestrial carbon and water cycles and microbial communities are key players in healthy ecosystem function. Endospore forming bacteria in the Bacillaceae family are metabolically and genomically diverse soil heterotrophs that influence plant health, carbon and nitrogen cycling, and often produce diverse natural products that influence other bacterial and non-bacterial species in their environment (1). We collected two soil samples on January 19, 2023 from 42°43'12.7"N 73°45'01.4"W. One was highly hydrated and within a patch of invasive common reeds (Phragmites sp.) and the other was near the base of an Eastern cottonwood tree (Populus deltoides). Bacillus pumilis strain SC124 was isolated from the soil from near the cottonwood tree, while Bacillus velezensis strain SC119, Priestia megaterium strain SC120, Bacillus zhangzhouensis strain SC123, Bacillus idriensis strain SC127 and were isolated from the marshy soil.

isolate, wetlands, genome announcement↗

Charge Compensation by Iodine Covalent Bonding in Lead Iodide Perovskite Materials

Metal halide perovskite materials (MHPs) are a family of next-generation semiconductors that are enabling low-cost, high-performance solar cells and optoelectronic devices. The most-used halogen in MHPs, iodine, can supplement its octet by covalent bonding resulting in atomic charges intermediate to I− and I0. Here, we examine theoretically stabilized defects of iodine using density functional theory (DFT); defect formation enthalpies and iodine Bader charges which illustrate how MHPs adapt to stoichiometry changes. Experimentally, X-ray photoelectron spectroscopy (XPS) is used to identify perovskite defects and their relative binding energies, and validate the predicted chemical environments of iodine defects. Examining MHP samples with excess iodine compared with near stoichiometric samples, we discern additional spectral intensity in the I 3d5/2 XPS data arising from defects, and support the presence of iodine trimers. I 3d5/2 defect peak areas reveal a ratio of 2:1, matching the number of atoms at the ends and middle of the trimer, whereas their binding energies agree with calculated Bader charges. Results suggest the iodine trimer is the preferred structural motif for incorporation of excess iodine into the perovskite lattice. Understanding these easily formed photoactive defects and how to identify their presence is essential for stabilizing MHPs against photodecomposition.

36 MATERIALS SCIENCE↗

The Demographics, Stellar Populations, and Star Formation Histories of Fast Radio Burst Host Galaxies: Implications for the Progenitors

We present a comprehensive catalog of observations and stellar population properties for 23 highly secure host galaxies of fast radio bursts (FRBs). Our sample comprises 6 repeating FRBs and 17 apparent nonrepeaters. We present 82 new photometric and 8 new spectroscopic observations of these hosts. Using stellar population synthesis modeling and employing nonparametric star formation histories (SFHs), we find that FRB hosts have a median stellar mass of ≈10 9.9 M ⊙ , mass-weighted age ≈5.1 Gyr, and ongoing star formation rate ≈1.3 M ⊙ yr -1 but span wide ranges in all properties. Classifying the hosts by degree of star formation, we find that 87% (20 of 23 hosts) are star-forming, two are transitioning, and one is quiescent. The majority trace the star-forming main sequence of galaxies, but at least three FRBs in our sample originate in less-active environments (two nonrepeaters and one repeater). Across all modeled properties, we find no statistically significant distinction between the hosts of repeaters and nonrepeaters. However, the hosts of repeating FRBs generally extend to lower stellar masses, and the hosts of nonrepeaters arise in more optically luminous galaxies. While four of the galaxies with the clearest and most prolonged rises in their SFHs all host repeating FRBs, demonstrating heightened star formation activity in the last ≲100 Myr, one nonrepeating host shows this SFH as well. Our results support progenitor models with short delay channels (i.e., magnetars formed via core-collapse supernova) for most FRBs, but the presence of some FRBs in less-active environments suggests a fraction form through more delayed channels.

79 ASTRONOMY AND ASTROPHYSICS↗