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At least 1,009 records · Page 56

Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae

Klebsiella pneumoniae is a major threat to public health, causing significant morbidity and mortality worldwide. The emergence of highly drug-resistant strains is particularly concerning. There has been a recognition and division of Klebsiella pneumoniae into three distinct phylogenetic groups: Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. K. variicola and K. quasipneumoniae have often been described as opportunistic pathogens that have less virulence in humans than K. pneumoniae does. We recently sequenced the genomes of 1,777 extended-spectrum-beta-lactamase (ESBL)-producing K. pneumoniae isolates recovered from human infections and discovered that 28 strains were phylogenetically related to K. variicola and K. quasipneumoniae. Whole-genome sequencing of 95 additional non-ESBL-producing K. pneumoniae isolates recovered from patients found 12 K. quasipneumoniae strains. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis initially identified all patient isolates as K. pneumoniae, suggesting a potential pitfall in conventional clinical microbiology laboratory identification methods. Whole-genome sequence analysis revealed extensive sharing of core gene content and plasmid replicons among the Klebsiella species. For the first time, strains of both K. variicola and K. quasipneumoniae were found to carry the Klebsiella pneumoniae carbapenemase (KPC) gene, while another K. variicola strain was found to carry the New Delhi metallo-beta-lactamase 1 (NDM-1) gene. K. variicola and K. quasipneumoniae infections were not less virulent than K. pneumoniae infections, as assessed by in-hospital mortality and infection type. We also discovered evidence of homologous recombination in one K. variicola strain, as well as one strain from a novel Klebsiella species, which challenge the current understanding of interrelationships between clades of Klebsiella.

59 BASIC BIOLOGICAL SCIENCES↗

Effect of the size of experimental channels of the lead slowing-down spectrometer SVZ-100 (Institute for Nuclear Research, Moscow) on the moderation constant

Lead slowing-down (LSD) spectrometers have a low energy resolution (about 30%), but their luminosity is 10{sup 3} to 10{sup 4} times higher than that of time-of-flight (TOF) spectrometers. A high luminosity of LSD spectrometers makes it possible to use them to measure neutron cross section for samples of mass about several micrograms. These features specify a niche for the application of LSD spectrometers in measuring neutron cross sections for elements hardly available in macroscopic amounts-in particular, for actinides. A mathematical simulation of the parameters of SVZ-100 LSD spectrometer of the Institute for Nuclear Research (INR, Moscow) is performed in the present study on the basis of the MCNPX code. It is found that the moderation constant, which is the main parameter of LSD spectrometers, is highly sensitive to the size and shape of detecting volumes in calculations and, hence, to the real size of experimental channels of the LSD spectrometer.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Modern trends in methods of charged particle identification at high energies

The survey is devoted to methods of charged particle identification at high energies that are based on measurements of the angle of Cherenkov radiation (ring imaging Cherenkov counters — RICH), of time of flight (TOF) and propagation (TOP), and of ionization energy loss (dE / dx ). As an example, some operating spectrometers are considered (LHCb, ALICE, COMPASS, Belle, and BaBar) together with proposed ones (Belle-2 and PANDA) in which new achievements of recent years are introduced.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Spallation neutron source GNEIS

A brief description of the spallation pulsed neutron source and neutron TOF spectrometer GNEIS based on the 1 GeV proton synchrocyclotron of PNPI in Gatchina is presented. The main parameters of the GNEIS are given in comparison with the analogous world-class facilities. The experimental capabilities of the GNEIS are demonstrated by the examples of some nuclear physics and applied research experiments carried out during four decades of its operation.

43 PARTICLE ACCELERATORS↗

Ion Chromatography and Combustion Ion Chromatography Analysis of Fuel Cell Effluent Water During Open Circuit Voltage

Open circuit voltage tests were conducted on sixteen 3M Ionomer and eight Nafion™ NR211 membranes. Lifetime distributions were determined, and ion chromatography (IC) techniques were used to measure fluoride, sulfate, trifluoro acetate, and oxalate ions. Combustion Ion Chromatography (CIC) was used to determine the total organic fluoride (TOF) associated with water soluble membrane degradation fragments. The ratio of these products relative to the fluoride release rates were used to infer the likely degradation mechanism for each membrane. Peroxide attack at the sulfonic acid side chain was determined to be the least relevant reaction pathway while the long-proposed polymer chain end unzipping appears to be the dominant mechanism. Abstraction of the tertiary fluorine in the NR211 backbone and side chain is evident by organic fluoride release rates higher than can be explained by unzipping alone.

25 ENERGY STORAGE↗

Solvent Oligomerization during SEI Formation on Model Systems for Li-Ion Battery Anodes

We report the results of electrochemical quartz crystal microbalance (EQCM), and matrix assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectrometry (MS) measurements along with detailed calculations examining the formation of the solid electrolyte interphase (SEI) on battery anode electrodes. EQCM analysis of Au and Sn surfaces in propylene carbonate (PC) and a 1:1 mixture of ethylene carbonate and dimethyl carbonate (EC:DMC) showed major irreversible mass uptake by the electrode surface especially during the first five cycles between +2 and 0.1 V vs. Li/Li+. MALDI-MS on emersed electrodes showed that long chain (m/z = 3000 on PC) oligomerized species were present on Au surfaces in PC and EC:DMC solvents, where oligomerized species formed in PC solutions showed higher mass ratios. The repeating units of the oligomer, visible as oscillations in the MALDI-MS, vary with the type of the solvent and electrode material. Sn surfaces initially showed formation of long chain polymers, but this material was not in evidence on electrode emersed after five cycles, which likely arises as a consequence of the catalytic involvement of Sn in decomposition of initially formed species. Density functional theory (DFT) calculations of cyclic solvent molecules suggested a radical initiated polymerization mechanism and predict oligomer subunits consistent with the experimental results.

25 ENERGY STORAGE↗

Structure of a Rhamnogalacturonan Fragment from Apple Pectin: Implications for Pectin Architecture

A commercial apple pectin was sequentially digested with the cloned enzymes endopolygalacturonase, galactanase, arabinofuranosidase, xylogalacturonase, and rhamnogalacturonan hydrolase. The rhamnogalacturonan hydrolase-generated oligosaccharides were separated by ultrafiltration, anion exchange, and size-exclusion chromatography. Fractions from the ion exchange chromatography were pooled, lyophilized, and screened by MALDI-TOF MS. An oligosaccharide (RGP14P3) was identified and its structure, α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A- ( 1 → 2 ) - α -L-Rha p - ( 1 → 4 ) - α -D-Gal p A, determined by 1D and 2D NMR spectrometry. This oligosaccharide probably represents a direct connection between homogalacturonan and rhamnogalacturonan in pectin. Alternatively, it could indicate that the nonreducing end of rhamnogalacturonan starts with a galacturonic acid residue.

Wu, Xiangmei↗

Vertical Profiles of Aerosol Composition over Beijing, China: Analysis of In Situ Aircraft Measurements

Aerosol samples were collected over Beijing, China, during several flights in November 2011. Aerosol composition of nonrefractory submicron particles (NR-PM 1 ) was measured by an Aerodyne compact time-of-flight aerosol mass spectrometer (C-ToF-AMS). This measurement on the aircraft provided vertical distribution of aerosol species over Beijing, including sulfate (SO 4 ), nitrate (NO 3 ), ammonium (NH4), chloride (Chl), and organic aerosols [OA; hydrocarbon-like OA (HOA) and oxygenated OA (OOA)]. The observations showed that aerosol compositions varied drastically with altitude, especially near the top of the planetary boundary layer (PBL). On average, organics (34%) and nitrate (32%) were dominant components in the PBL, followed by ammonium (15%), sulfate (14%), and chloride (4%); in the free troposphere (FT), sulfate (34%) and organics (28%) were dominant components, followed by ammonium (20%), nitrate (19%), and chloride (1%). The dominant OA species was primarily HOA in the PBL but changed to OOA in the FT. For sulfate, nitrate, and ammonium, the sulfate mass fraction increased from the PBL to the FT, nitrate mass fraction decreased, and ammonium remained relatively constant. Analysis of the sulfate-to-nitrate molar ratio further indicated that this ratio was usually less than one in the FT but larger than one in the PBL. Further analysis revealed that the vertical aerosol composition profiles were influenced by complex processes, including PBL structure, regional transportation, emission variation, and the aging process of aerosols and gaseous precursors during vertical diffusion.

54 ENVIRONMENTAL SCIENCES↗

Data for Evaluation of Strategies to Narrow the Product Chain-Length Distribution of Microbially Synthesized Free Fatty Acids

The dominant strategy for tailoring the chain-length distribution of free fatty acids (FFA) synthesized by heterologous hosts is expression of a selective acyl-acyl carrier protein (ACP) thioesterase. However, few of these enzymes can generate a precise (greater than 90% of a desired chain-length) product distribution when expressed in a microbial or plant host. The presence of alternative chain-lengths can complicate purification in situations where blends of fatty acids are not desired. We report the assessment of several strategies for improving the dodecanoyl-ACP thioesterase from the California bay laurel to exhibit more selective production of medium-chain free fatty acids to near exclusivity. We demonstrated that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) was an effective library screening technique for identification of thioesterase variants with favorable shifts in chain-length specificity. This strategy proved to be a more effective screening technique than several rational approaches discussed herein. With this data, we isolated four thioesterase variants which exhibited a more selective FFA distribution over wildtype when expressed in the fatty acid accumulating E. coli strain, RL08. We then combined mutations from the MALDI isolates to generate BTE-MMD19, a thioesterase variant capable of producing free fatty acids consisting of 90% of C12 products. Of the four mutations which conferred a specificity shift, we noted that three affected the shape of the binding pocket, while one occurred on the positively charged acyl carrier protein landing pad. Finally, we fused the maltose binding protein (MBP) from E. coli to the N – terminus of BTE-MMD19 to improve enzyme solubility and achieve a titer of 1.9 g per L of twelve-carbon fatty acids in a shake flask.

Conversion↗

Design of Cherenkov bars for the optical part of the time-of-flight detector in Geant4

We present the results of studies devoted to the development and optimization of the optical part of a high precision time-of-flight (TOF) detector for the Large Hadron Collider (LHC). This work was motivated by a proposal to use such a detector in conjunction with a silicon detector to tag and measure protons from interactions of the type p + p → p + X + p, where the two outgoing protons are scattered in the very forward directions. The fast timing detector uses fused silica (quartz) bars that emit Cherenkov radiation as a relativistic particle passes through and the emitted Cherenkov photons are detected by, for instance, a micro-channel plate multi-anode Photomultiplier Tube (MCP-PMT). Several possible designs are implemented in Geant4 and studied for timing optimization as a function of the arrival time, and the number of Cherenkov photons reaching the photo-sensor.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Hemicellulose and starch citrate chitosan foam adsorbents for removal of arsenic and other heavy metals from contaminated water

Arsenic and other heavy metal contaminants in water are a significant global health threat. In this study, low-cost, sulfur-free, sustainable, water-insoluble materials with heavy metal remediation properties were produced from renewable resources such as starch, xylan, citric acid, and chitosan. Synthesized starch citrate-chitosan (SCC) foam and xylan citrate-chitosan (XCC) foam were flexible, porous, and elastic. The foams’ arsenic uptake in water was significantly greater than five different commercial metal remediating agents. The mercury and lead uptakes with the synthesized foams were similar to the performance of a commercial sulfur-based product, SorbaTech 450 (ST450). However, the cadmium and selenium uptakes were comparatively lower. The complexation of arsenic with oxygen and nitrogen of the SCC foam was shown with time-of-flight secondary ion mass spectrometry (TOF-SIMS). The XCC foam was also shown to adsorb potassium iodide (KI) at a similar rate to sodium chloride. This may be used to remediate water contaminated with radioactive materials, such as iodine 131.

Materials Science↗

Meteorological Conditions and Atmospheric Components Concentration in Urban Sites in Knoxville, USA. 2024

This dataset, which contains five csv files, reports several meteorological conditions such as temperature, wind speed, solar radiation, and net radiation measured in Cumberland Estates Park (CEP) and Socially Equal Energy Efficient Development (SEEED) sites in Knoxville, Tennessee, USA. Also, hourly concentration of particulate matter (PM) with different aerodynamic diameter and inorganic gases such as ozone and nitrogen dioxide measured in the two are included in this dataset. The concentrations of PM and inorganic gases were monitored using the MODULAIR, a low-cost sensor equipped with a solar power module. The measurement of the concentration of biogenic and anthropogenic volatile organic compounds (VOCs) of the two sites was determined using a High-Resolution Proton Transfer Reaction Time of Flight Mass Spectrometer (PTR-ToF-MS). The VOCs were collected using miniature canister (400 mL) equipped with female RAVEqc valve to 1/4” male compression fitting and an integrated passive air sampling kit. This work is a part of a larger study which investigates the impact of soil moisture and plant evapotranspiration on ambient temperature and relative humidity in several city parks in Knoxville, Tennessee.

54 ENVIRONMENTAL SCIENCES↗

MAGNETRON SPUTTERING OF Nb3Sn FOR SRF CAVITIES

Nb3Sn is a potential candidate for surface material of SRF cavities since it can enable the cavity to operate at higher temperatures with high quality factor and at an increased accelerating gradient. Nb-Sn films were deposited using magnetron sputtering of individual Nb and Sn targets onto Nb and sapphire substrates. The as-deposited films were annealed at 1200 °C for 3 hours. The films were characterized for their structure by X-ray Diffraction (XRD), morphology by Field Emission Scanning Electron Microscopy (FESEM), and composition by Energy Dispersive X-ray Spectroscopy (EDS) and Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS). The surface resistivity was measured down to cryogenic temperature to determine the superconducting transition temperature and its width. The composition of the multilayered films was controlled by varying the thickness of the Nb and Sn layers. The films showed crystalline Nb3Sn phases with Tc up to 17.6 K.

Eremeev, G.↗

AI-driven neutrino diagnostics and radiation-hard beam instrumentation for next-generation neutrino experiments

The Long Baseline Neutrino Facility (LBNF) at Fermilab will deliver a high-intensity, multi-megawatt neutrino beam to the Deep Underground Neutrino Experiment (DUNE), enabling precision tests of the three-neutrino paradigm, CP violation searches, neutrino mass ordering determination, and supernova neutrino studies. To accelerate DUNE’s physics reach and ensure robust beam operations, we propose an integrated AI-driven framework with real-time diagnostics and radiation-hardened instrumentation. At its core is a Real-Time Beam Integrity Monitor using a physics-informed Digital Twin. By reconstructing pion phase space from muon profiles and exploiting magnetic horn optic linearity, it enables spill-by-spill beam correction and flux stabilization. By using this approach, flux-related systematics could be reduced from 5% to 1%, potentially accelerating the discovery of CP violations by four to six years. Complementing this, a US–Japan R&D effort will deploy a LAPPD-based muon monitor in the NuMI beamline. ToF measurements can be acquired with picosecond precision using this radiation-hard system, enhancing sensitivity to horn chromatic effects. Simulations confirm strong response to these effects. ML models predict beam quality and horn current to sub-percent accuracy from muon data, enhancing anomaly detection and stability. This scalable, AI-enabled strategy improves beam fidelity, reduces systematics, and sets a new standard for high-power accelerator operations.

Ganguly, Sudeshna [Fermilab] (ORCID:00000003163482↗

NeuNorm

NeuNorm is a scipp-based Python library for neutron imaging normalization and time-of-flight (TOF) data processing at Oak Ridge National Laboratory imaging facilities (MARS at HFIR and VENUS at SNS). NeuNorm 2.0 is a complete, scipp-based rewrite of the original NeuNorm normalization library, adding HDF5 output, automatic uncertainty propagation, and TOF/event-mode processing.

Zhang, Chen [Oak Ridge National Laboratory (ORNL),↗

Cleareye In-Ground and In-Concrete DIV Inspections: FY11 Final Report

This report summarizes the results of a series of feasibility testing studies for in-ground and in-concrete imaging/detection technologies including radar imaging and acoustic time-of flight method. The objectives of this project are: (1) Design Information Verification (DIV) Tools for In-Concrete Inspections - To determine the feasibility of using holographic radar imaging (HRI), radar imaging, and acoustic time-of-flight (TOF) non-destructive evaluation technologies to detect, locate and identify pipes and voids embedded in standard-density and high-density concrete walls that typify those the IAEA will need to verify during field inspections; (2) DIV Tools for In-Ground Inspections - To determine the feasibility of using HRI and radar imaging non-destructive evaluation technologies to detect, locate, and identify objects buried at various depths made of various materials (metal, plastic, wood, and concrete) and representing geometries that typify those the IAEA will need to verify during field inspections; and (3) Based on the results of the studies, recommend the next steps needed to realize fieldable tools for in-concrete and in-ground inspections (including detection of deeply buried polyvinyl chloride [PVC] pipes) that employ the technologies shown to be feasible.

09 BIOMASS FUELS↗

Developing Laser-Induced Re-Collision Electron Self-Diffraction (Brief summary of accomplishments)

Our principal goal was the experimental demonstration of Laser-Induced Electron Diffraction (LIED). Key steps along the development of this experimental technique have been accomplished and reported in the publications listed in this brief report. We started with measuring 3D electron momenta spectra in aligned nitrogen and oxygen molecules. Chakra Maharjan (Ph.D. student of Lew Cocke) was a lead researcher on this project. Although Chakra succeeded in obtaining those spectra, we were scooped by the publication of identical results in Science by the NRC Ottawa group. Our results were never published as a refereed article, but became a part of Chakra's Ph.D. dissertation. That Science paper was the first experimental demonstration of Laser-Induced Electron Diffraction (LIED). Chakra also worked on wavelength dependence of 3D ATI spectra of atoms and molecules using tunable OPA pulses. Another Ph.D. student, Maia Magrakvelidze (her GRA was funded by the grant), started working on COLTRIMS experiments using OPA pulses (1800 nm wavelength). After some initial experiments it became apparent that COLTRIMS did not yield sufficient count rates of electrons in the high-energy part of the spectrum to see diffraction signatures with acceptable statistics (unfavorable scaling of the electron yield with laser wavelength was partly to blame). Nevertheless, Maia managed to use COLTRIMS and OPA to measure the angular dependence of the tunneling ionization rate in D 2 molecules. Following the initial trial experiments, the decision was made to switch from COLTRIMS to VMI in order to increase the count rates by a factor of ~100, which may have given us a chance to see LIED. Research Associate Dr. Sankar De (his salary was funded by the grant), in collaboration with Matthias Kling's group (then at MPQ Garching), proceeded to design a special multi-electrode VMI spectrometer for capturing high-energy ATI electrons and to install it in place of COLTRIMS inside our experimental chamber. That apparatus was later used for the first demonstration of field-free orientation in CO using two-color laser pulses as well as for a series of other experiments, such as pump-probe studies of molecular dynamics with few-cycle laser pulses, control of electron localization in dissociating hydrogen molecules using two-color laser pulses, and ATI spectra of Xe ionized by two-color laser pulses. In parallel, Dipanwita Ray (Ph.D. student of Lew Cocke) worked on measuring angle-resolved ATI spectra of noble gases using a stereo-ATI phasemeter as a TOF electron spectrometer. She observed the angular diffraction structures in 3D ATI spectra of Ar, Kr and Xe, which were interpreted in terms of the Quantitative Rescattering theory newly developed by C.D. Lin. We also attempted to use a much more powerful OPA (five times more energy per pulse than the one we had at JRML) available at the Advanced Laser Light Source (ALLS) in Montreal to observe LIED. Two visits to ALLS by the PI, Igor Litvinyuk, and one visit by the PI's Ph.D. student (Irina Bocharova) were funded by the grant. Though we failed to observe LIED (the repetition rate of the ALLS OPA was too low at only 100 Hz), this international collaboration resulted in several publications on other related subjects, such as the wavelength dependence of laser Coulomb explosion of hydrogen, the wavelength dependence of non-sequential double ionization of neon and argon, the demonstration of charge-resonance enhanced ionization in CO 2 , and the study of non-elastic scattering processes in H 2 }. Theoretical efforts to account for the hydrogen Coulomb explosion experiment resulted in another paper by Maia Magrakvelidze as lead author. Although for various reasons we failed to achieve our main goal of observing LIED, we salute the recent success in this endeavor by Lou DiMauro's group (with theoretical support from our KSU colleague C.D. Lin) published in Nature, which validates our approach.

08 HYDROGEN↗

Experiments with the LECO Pegasus® Gas Chromatograph/ Time-of-Flight Mass Spectrometer Phase 1: Fast GC Separations and Comparison of the GC/TOF-MS with Conventional Quadrupole GC/MS and Fast Quadrupole GC/MS

Conventional analysis by gas chromatography/quadrupole mass spectrometry (GC/MS) can be time-consuming (30 – 60 minutes) and prone to interferences. The use of fast gas chromatography coupled with time-of-flight mass spectrometry (GC/TOF-MS) offers the advantages of faster (13 min) analysis times, improved GC resolution afforded by the use of narrower (0.1– 0.18 mm i.d.) columns, and improved mass resolution and data acquisition speed provided by the TOF-MS. In addition, GC/TOF-MS offers the promise of better detection limits than quadrupole GC/MS, while still providing the full mass spectral data which offers an additional level of confidence in analyte identification.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗