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At least 1,189 records · Page 66

Peak selection matters in Principal Component Analysis: A case study of syntrophic microbes

In situ liquid time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique to address surface characterization of living biofilms in hydrated conditions. Principal component analysis (PCA) is an important tool to process a large amount of data and interpret the information from ToF-SIMS spectra. However, ToF-SIMS data analysis is still a great challenge in complicated bacterial biofilms, because many interference peaks from the medium may result in inaccurate interpretation of ToF-SIMS spectral analysis. In this study, two syntrophic Geobacter populations were investigated using in situ liquid ToF-SIMS to reveal the biofilm surface changes between them as due to direct interspecies electron transfer (DIET). Peak overlay is an effective strategy to eliminate the matrix effects in handling complex ToF-SIMS data and was used to accomplish peak selection in this work. Both all peak and selected peak spectral PCA showed a distinctive separation among different samples. However, medium samples occupied high scores values in all peak PCA compared with the selected peak PCA, suggesting a strong interference from the medium as the matrix effect. Amino acids and lipids contributed significantly in separating all samples in selected peak PCA, which indicated that surface membrane components such as pili and proteins are important in the co-cultured Geobacter community compared to controls such as the single population planktonic cells and biofilms, respectively. Additionally, the spectral PCA results of high intensity and high resolution data obtained from liquid ToF-SIMS were compared. Selected peak PCA obtained nice separation among samples in both data sets; however, the high resolution data showed better separation between co-culture planktonics and co-culture aggregates, confirming that the higher mass accuracy is useful in analysis of microbial samples. Furthermore, amino acid and water cluster as an important media for microbial metabolite were selected for a more focused selected peak PCA comparison. Consistent scores and loadings plots were achieved. In conclusion, we show that peak selection is critical for acquiring effective microbial information and interpretation of syntrophic Geobacter using spectral data from in situ liquid ToF-SIMS.

spectral overlay, peak selection, matrix effect, P↗

Diffusive Properties of UNESE Core Samples via Continuously Monitored Mass Spectroscopy

The transport properties of porous geological media are of fundamental importance when modeling the migration of chemical and radiological species in subterranean systems. Due to their relatively high mobility, short-lived noble gas species are of particular interest as detection of these species at the surface is a tell-tale indicator of recent nuclear activity. However, determining the diffusivity of these species is challenging due to their inert and transparent nature, requiring chemically insensitive techniques, such as mass spectroscopy, to quantify noble gas concentrations. The work described herein details recent advances in the methodology for determining diffusivity on porous media and results obtained on samples relevant to the UNESE project.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Ultrasonic/Sonic Driller/Corer (USDC) as a Subsurface Sampler and Sensors Platform for Planetary Exploration Applications

The search for existing or past life in the Universe is one of the most important objectives of NASA's mission. For this purpose, effective instruments that can sample and conduct in-situ astrobiology analysis are being developed. In support of this objective, a series of novel mechanisms that are driven by an Ultrasonic/Sonic actuator have been developed to probe and sample rocks, ice and soil. This mechanism is driven by an ultrasonic piezoelectric actuator that impacts a bit at sonic frequencies through the use of an intermediate free-mass. Ultrasonic/Sonic Driller/Corer (USDC) devices were made that can produce both core and powdered cuttings, operate as a sounder to emit elastic waves and serve as a platform for sensors. For planetary exploration, this mechanism has the important advantage of requiring low axial force, virtually no torque, and can be duty cycled for operation at low average power. The advantage of requiring low axial load allows overcoming a major limitation of planetary sampling in low gravity environments or when operating from lightweight robots and rovers. The ability to operate at duty cycling with low average power produces a minimum temperature rise allowing for control of the sample integrity and preventing damage to potential biological markers in the acquired sample. The development of the USDC is being pursued on various fronts ranging from analytical modeling to mechanisms improvements while considering a wide range of potential applications. While developing the analytical capability to predict and optimize its performance, efforts are made to enhance its capability to drill at higher power and high speed. Taking advantage of the fact that the bit does not require rotation, sensors (e.g., thermocouple and fiberoptics) were integrated into the bit to examine the borehole during drilling. The sounding effect of the drill was used to emit elastic waves in order to evaluate the surface characteristics of rocks. Since the USDC is driven by piezoelectric actuation mechanism it can designed to operate at extreme temperature environments from very cold as on Titan and Europa to very hot as on Venus. In this paper, a review of the latest development and applications of the USDC will be given.

sampling↗

Polysaccharide-based liquid storage and transport media for non-refrigerated preservation of bacterial pathogens

The preservation of biological samples for an extended time period of days to weeks after initial collection is important for the identification, screening, and characterization of bacterial pathogens. Traditionally, preservation relies on cold-chain infrastructure; however, in many situations this is impractical or not possible. Thus, our goal was to develop alternative bacterial sample preservation and transport media that are effective without refrigeration or external instrumentation. The viability, nucleic acid stability, and protein stability of Bacillus anthracis Sterne 34F2, Francisella novicida U112, Staphylococcus aureus ATCC 43300, and Yersinia pestis KIM D27 (pgm-) was assessed for up to 28 days. Xanthan gum (XG) prepared in PBS with L-cysteine maintained more viable F . novicida U112 cells at elevated temperature (40°C) compared to commercial reagents and buffers. Viability was maintained for all four bacteria in XG with 0.9 mM L-cysteine across a temperature range of 22–40°C. Interestingly, increasing the concentration to 9 mM L-cysteine resulted in the rapid death of S . aureus . This could be advantageous when collecting samples in the built environment where there is the potential for Staphylococcus collection and stabilization rather than other organisms of interest. F . novicida and S . aureus DNA were stable for up to 45 days upon storage at 22°C or 40°C, and direct analysis by real-time qPCR, without DNA extraction, was possible in the XG formulations. XG was not compatible with proteomic analysis via LC-MS/MS due to the high amount of residual Xanthomonas campestris proteins present in XG. Our results demonstrate that polysaccharide-based formulations, specifically XG with L-cysteine, maintain bacterial viability and nucleic acid integrity for an array of both Gram-negative and Gram-positive bacteria across ambient and elevated temperatures.

59 BASIC BIOLOGICAL SCIENCES↗

Preparation of novel BiVO4 nanofibers and their excellent adsorptive properties

Highlights: • Monoclinic BiVO{sub 4} nanofibers were obtained by two-step synthesis method. • BiVO{sub 4} nanofibers possessed highly effective adsorptive properties. • BiVO{sub 4} nanofibers showed higher specific surface area. • EG and NaOH promoted the formation of BiVO{sub 4} nanofibers. - Abstract: The novel BiVO{sub 4} nanofibers were firstly obtained by two-step synthesis method. Characterized by X-ray diffractometer (XRD) and scanning electron microscopy (SEM), the samples were shown to be nanofibers with monoclinic phase. The ethylene glycol (EG) and NaOH solution played an important role on their formation. Taking rhodamine B (RhB) as the removal object, the nanofibers exhibited the enhanced adsorptive activity compared with other samples. It may be due to the increase of the specific surface area, the acidic surface property of the BiVO{sub 4} nanofibers and the nature of the RhB dye. The formation mechanism of the special morphology was investigated and proposed. It is expected to provide some guidance for designing and preparing other materials for removal of organic pollutants.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Application of High-Spatial Resolution LA-MC-ICP-MS in Planetary Materials

High-precision stable and radiogenic isotopic measurements of planetary materials can help elucidate processes taking place during early Solar System formation, as well as during subsequent planetary differentiation. Laser Ablation Multi Collector Inductively Coupled Plasma Mass Spectrometry (LA-MC-ICP-MS) adds the valuable ability of preserving the spatial context of these isotopic measurements, by sampling small sample volumes (~10 – 60 um diameter) using a pulsed laser system. In the Center for Isotope Cosmochemistry and Geochronology (CICG) at NASA Johnson Space Center, these in-situ isotopic measurements are primarily made using the Applied SpectraTM iX-fs-Tandem LA-LIBS Instrument coupled to the Nu InstrumentsTM SP1700 MC-ICP-MS. The instrumental set-up also provides simultaneous Laser Induced Breakdown Spectroscopy (LIBS) measurements and the potential use of a low energy path with a collision/reaction cell for additional interference removal, though we focus here on the typical high-energy LA-MC-ICP-MS operation. We will provide examples of stable (e.g., Mg) and radiogenic (e.g., Lu-Hf) isotopic systems measured in planetary materials and their terrestrial analogs. The measurement of mass dependent Mg isotopic variations is an important tool for reconstructing processes such as evaporation and condensation of solids in the solar nebula. For early Solar System samples, Mg isotope measurements are also important for the short-lived (t1/2 = 0.7 Ma) Al-Mg chronometer. During laser ablation analyses, the measurement of the Al-Mg isotopic system is made in medium mass resolution (RP ~9500 at ~20% transmission) to limit interferences from 48Ti2+ and 48Ca2+ on 24Mg+, in addition to 52Cr2+ and 12C14N+ on 26Mg+. Measured in the mineral zircon, the 176Lu-176Hf decay system is often used for understanding the growth of continents on Earth, and is also a vital aid in deciphering early large-scale planetary differentiation processes, such as the crystallization of the lunar magma ocean, which is thought to be responsible for much of the Moon’s crust. Lu-Hf measurements are made in low resolution mode (RP <2000), with 10 ion masses (from 171Yb to 180Hf) measured simultaneously to facilitate corrections for isobaric interferences from 176Yb and 176Lu on 176Hf.

Jacob B Setera↗

Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein

The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses.

59 BASIC BIOLOGICAL SCIENCES↗

An efficient and cost-effective method for preparing transmission electron microscopy samples from powders

The preparation of transmission electron microcopy (TEM) samples from powders with particle sizes larger than ~100 nm poses a challenge. The existing methods are complicated and expensive, or have a low probability of success. Herein, we report a modified methodology for preparation of TEM samples from powders, which is efficient, cost-effective, and easy to perform. This method involves mixing powders with an epoxy on a piece of weighing paper, curing the powder–epoxy mixture to form a bulk material, grinding the bulk to obtain a thin foil, punching TEM discs from the foil, dimpling the discs, and ion milling the dimpled discs to electron transparency. Compared with the well established and robust grinding–dimpling–ion-milling method for TEM sample preparation for bulk materials, our modified approach for preparing TEM samples from powders only requires two additional simple steps. In this article, step-by-step procedures for our methodology are described in detail, and important strategies to ensure success are elucidated. Furthermore, our methodology has been applied successfully for preparing TEM samples with large thin areas and high quality for many different mechanically milled metallic powders.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Tank 14H Preliminary Cease Waste Removal Sample Analyses

Savannah River Mission Completion Waste Removal and Tank Closure requested that Savannah River National Laboratory perform characterization analyses of Tank 14H in support of closure activities, specifically preliminary cease waste removal. This report provides important characterization of the prepared filtrate and air-dried solids in the January 2026 Tank 14H sample, HTF-14-26-1,2,3,4,5,6, for I-129, Tc-99, Cs-137, and Sr-90. The results reported here were utilized by SRMC to declare preliminary cease waste removal for Tank 14H.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Mars Rover Sample Return: A sample collection and analysis strategy for exobiology

For reasons defined elsewhere it is reasonable to search for biological signatures, both chemical and morphological, of extinct life on Mars. Life on Earth requries the presence of liquid water, therefore, it is important to explore sites on Mars where standing bodies of water may have once existed. Outcrops of layered deposits within the Valles Marineris appear to be ancient lake beds. Because the outcrops are well exposed, relatively shallow core samples would be very informative. The most important biological signature to detect would be organics, microfossils, or larger stromato-like structures, although the presence of cherts, carbonates, clays, and shales would be significant. In spite of the limitations of current robotics and pattern recognition, and the limitations of rover power, computation, Earth communication bandwidth, and time delays, a partial scenario was developed to implement such a scientific investigation. The rover instrumentation and the procedures and decisions and IR spectrometer are described in detail. Preliminary results from a collaborative effort are described, which indicate the rover will be able to autonomously detect stratification, and hence will ease the interpretation burden and lead to greater scientific productivity during the rover's lifetime.

Sims, M. H.↗

Efficient end-to-end simulation of time-dependent coherent X-ray scattering experiments

Physical optics simulations for beamlines and experiments allow users to test experiment feasibility and optimize beamline settings ahead of beam time in order to optimize valuable beam time at synchrotron light sources like NSLS-II. Further, such simulations also help to develop and test experimental data processing methods and software in advance. The Synchrotron Radiation Workshop ( SRW ) software package supports such complex simulations. We demonstrate how recent developments in SRW significantly improve the efficiency of physical optics simulations, such as end-to-end simulations of time-dependent X-ray photon correlation spectroscopy experiments with partially coherent undulator radiation (UR). The molecular dynamics simulation code LAMMPS was chosen to model the sample: a solution of silica nanoparticles in water at room temperature. Real-space distributions of nanoparticles produced by LAMMPS were imported into SRW and used to simulate scattering patterns of partially coherent hard X-ray UR from such a sample at the detector. The partially coherent UR illuminating the sample can be represented by a set of orthogonal coherent modes obtained by simulation of emission and propagation of this radiation through the coherent hard X-ray (CHX) scattering beamline followed by a coherent-mode decomposition. GPU acceleration is added for several key functions of SRW used in propagation from sample to detector, further improving the speed of the calculations. The accuracy of this simulation is benchmarked by comparison with experimental data.

36 MATERIALS SCIENCE↗

Cooperative Robotics and the Search for Extraterrestrial Life

If we think tenuous abodes of life may be hiding in remote extraterrestrial environmental niches, and if we want to assess the biological status of a given locale or entire planet before sending humans (perhaps because of contamination concerns or other motivations) then we face the challenge of robotically exploring a large space efficiently and in enough detail to have confidence in our assessment of the biological status of the environment in question. On our present schedule of perhaps two or so missions per opportunity, we will likely need a different exploratory approach than singular stationary landers or singular rover missions or sample return, because there appear to be fundamental limitations in these mission profiles to-obtain the many samples we will likely need if we want to have confidence in assessing the biological status of an environment in which life could be hiding in remote environmental niches. Singular rover missions can potentially accommodate sampling over a fairly large area, but are still limited by range and can be a single point of failure. More importantly, such mission profiles have limited payload capabilities which are unlikely to meet the demanding requirements of life-detection. Sample return has the advantage of allowing sophisticated analysis of the sample, but also has the severe limitations associated with only being able to bring back a few samples. This presentation will suggest two cooperative robotic approaches for exploration that have the potential to overcome these difficulties and facilitate efficient and thorough life-detecting exploration of a large space. Given the two premises state above, it appears at least two fundamental challenges have to be met simultaneously: coverage of a large space and bringing to bear a sophisticated suite of detection and experimental payloads on any specific location in order to address a major challenge in looking for extraterrestrial life: namely, executing a wide variety of detection scenarios and in situ experiments in order to gather the required data for a confident assessment that life has been detected and to, more generally, cover a wide range of extraterrestrial life possibilities. Cooperative robotics ]ends itself to this kind of problem because cooperation among the combined capabilities of a variety of simple single function agents can give rise to fairly complex task execution such as the search for and detection of extraterrestrial life.

Lupisella, Mark L.↗

Cooperative Robotics and the Search for Extraterrestrial Life

If we think tenuous abodes of life may be hiding in remote extraterrestrial environmental niches, and if we want to assess the biological status of a given locale or entire planet before sending humans (perhaps because of contamination concerns or other motivations) then we face the challenge of robotically exploring a large space efficiently and in enough detail to have confidence in our assessment of the biological status of the environment in question. On our present schedule of perhaps two or so missions per opportunity, we will likely need a different exploratory approach than singular stationary landers or singular rover missions or sample return, because there appear to be fundamental limitations in these mission profiles to obtain the many samples we will likely need if we want to have confidence in assessing the biological status of an environment in which life could be hiding in remote environmental niches. Singular rover missions can potentially accommodate sampling over a fairly large area, but are still limited by range and can be a single point of failure. More importantly, such mission profiles have limited payload capabilities which are unlikely to meet the demanding requirements of life-detection. Sample return has the advantage of allowing sophisticated analysis of the sample, but also has the severe limitations associated with only being able to bring back a few samples. This presentation will suggest two cooperative robotic approaches for exploration that have the potential to overcome these difficulties and facilitate efficient and thorough life-detecting exploration of a large space. Given the two premises stated above, it appears at least two fundamental challenges have to be met simultaneously: (1) coverage of a large space and (2) bringing to bear a sophisticated suite of detection and experimental payloads on any specific location in order to address a major challenge in looking for extraterrestrial life: namely, executing a wide variety of detection scenarios and in situ experiments in order to gather the required data for a confident assessment that life has been detected and to, more generally, cover a wide range of extraterrestrial life possibilities. Cooperative robotics lends itself to this kind of problem because cooperation among the combined capabilities of a variety of simple single function agents can give rise to fairly complex task execution such as the search for and detection of extraterrestrial life.

Lupisella, M. L.↗

Realizing an Epitaxial Decorated Stanene with an Insulating Bandgap

The exploration of intriguing topological quantum physics in stanene has attracted enormous interest but is challenged by lacking desirable material samples. The successful fabrication of monolayer stanene on PbTe(111) films with low-temperature molecular beam epitaxy and thorough characterizations of its atomic and electronic structures are reported here. In situ angle-resolved photoemission spectroscopy together with first-principles calculations identify two hole bands of p xy orbital with a spin-orbit coupling induced band splitting and meanwhile reveal an automatic passivation of p z orbital of stanene. Importantly, material properties are tuned by substrate engineering, realizing a decorated stanene sample with truly insulating bulk on Sr-doped PbTe. In conclusion, this finding paves a road for studies of stanene-based topological quantum effects and electronics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A tungsten external heater for BX90 diamond anvil cells with a range up to 1700 K

Resistive heating of a sample in a diamond anvil cell (DAC) can generate a homogeneous temperature field across the sample chamber with reliable temperatures measured by a thermocouple. It is of importance in experiments aiming at exploring phase diagrams and quantifying thermoelastic properties of materials. Here, we present a ring-heater design developed for BX90 diamond anvil cells (DACs). Furthermore, it is made of a ring-shaped aluminum oxide holder hosting a tungsten wire coil inside and coupled with Ar + 2% H 2 gas to prevent oxidation during experiment. This modular plug-and-play design enables in situ studies of samples via x-ray diffraction up to a temperature of 1700 K. Temperature in the BX90 sample volume as measured through a thermocouple was calibrated using the melting point of gold. As an application of this design, we report the thermal expansion coefficient of MgO at 9.5(1) GPa.

47 OTHER INSTRUMENTATION↗

Implementation of a 1550-nm laser system for beam characterization at the Argonne Wakefield Accelerator

Accurately recording an electron bunch’s longitudinal profile is an important diagnostic for wakefield accelerators employing shaped bunches to increase transformer ratios. Electro-optic sampling of terahertz radiation from the bunch is an attractive approach due to its non-destructive nature. In preparation for future characterization experiments, the Argonne Wakefield Accelerator test facility has recently installed a 1550 nm laser system, including the necessary support systems to synchronize with the photoinjector laser system at 81.25 MHz. We report here on the initial installation and synchronization demonstrations.

Ody, Alexander [Argonne, PHY]↗

Evaluating the functional importance of secretive species: A case study of aquatic snake predators in isolated wetlands

Abstract Although the need to prioritize limited conservation resources has prompted increased interest in understanding the functional importance of species within ecosystems, species that are infrequently observed are often written off as being unimportant. In this study, we use aquatic snakes as a case study for examining the importance of secretive predators. Most snakes are extremely cryptic and secretive, traits that not only lead to the perception that they are rare, and of minor importance, but also impede attempts to quantify densities. We used high sampling effort and robust‐design capture–recapture analyses to estimate density of aquatic snakes inhabiting an isolated 5.4‐ha wetland in South Carolina, USA . We assessed snake diets and coupled field measurements of growth rates with laboratory‐derived data on mass conversion efficiency to estimate prey consumption by snakes over a 1‐year period. We found a peak density 171 snakes ha −1 of wetland habitat, corresponding to a standing biomass of 7.77 kg ha −1 . We calculated that snakes within the wetland consumed a total of over 200 kg (>55 000 individuals) of amphibian prey annually, translating into >150 000 kJ ha −1 of energy flow from secondary to tertiary consumers within the wetland food web. Further, because many amphibians are primarily terrestrial as adults and are consumed by aquatic snakes only when they return to wetlands to breed, snakes can be responsible for substantial transfer of energy and biomass between terrestrial and aquatic habitats. Our study is one of the first comprehensive evaluations of the importance of snakes as predators and underscores the need to consider snakes in initiatives aimed at preserving overall ecosystem integrity.

Willson, J. D.↗

Long-Term Monitoring the Damage Performance of Multilayer Dielectric Grating Samples Residing Inside the Compressor Chamber of the OMEGA EP Laser

Understanding of the laser-induced damage threshold and impact of air–vacuum cycling of the optical components in short-pulse laser systems is of fundamental importance. We report the results of a damage-testing campaign that monitored representative pulse compression grating samples that were positioned inside the OMEGA EP grating compressor vacuum chamber during normal operation and routinely damage tested on every quarterly vent for a period of about 10 years. Here, the evolution of their damage resistance under 10-ps and 100-ps pulse lengths are associated with a significant degradation of the laser-induced damage thresholds, which is comparatively larger at 100 ps, is described.

42 ENGINEERING↗