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At least 1,063 records · Page 59

Bioactivity Profiling of Chemical Mixtures for Hazard Characterization

Abstract The assessment and regulation of chemical toxicity to protect human health and the environment are done one chemical at a time and seldom at environmentally relevant concentrations. However, chemicals are found in the environment as mixtures, and their toxicity is largely unknown. Understanding the hazard posed by chemicals within the mixture is critical to enforce protective measures. Here, we demonstrate the application of bioactivity profiling of environmental water samples using the sentinel and ecotoxicology model species Daphnia to reveal the biomolecular response induced by exposure to real-world mixtures. We exposed a Daphnia strain to 30 sampled waters of the Chaobai River and measured the gene expression response profiles. Using a multiblock correlation analysis, we establish correlations between chemical mixtures identified in 30 water samples with gene expression patterns induced by these chemical mixtures. We identified 80 metabolic pathways putatively activated by mixtures of inorganic ions, heavy metals, polycyclic aromatic hydrocarbons, industrial chemicals, and a set of biocides, pesticides, and pharmacologically active substances. Our data-driven approach discovered both known bioactivity signatures with previously described modes of action and new pathways linked to undiscovered potential hazards. This study demonstrates the feasibility of reducing the complexity of real-world mixture toxicity to characterize the biomolecular effects of a defined number of chemical components based on gene expression monitoring of the sentinel species Daphnia.

Engineering↗

Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling

Label-free quantitative proteomics has become an increasingly popular tool for profiling global protein abundances. However, one major weakness is the potential performance drift of the LC-MS platform over time, which in turn limits its utility for analyzing large-scale sample sets. To address this, in this work we introduce an experimental and data analysis scheme based on a block-design with common controls within each block for enabling LC-MS-based large-scale label-free quantification. In this scheme, a large number of samples (e.g., >100 samples) are analyzed in smaller, and more manageable blocks, minimizing instrument drift and variability within a block. Furthermore, each designated block also contains common controls (or reference) samples for normalization within and across blocks. We demonstrated the effectiveness of this method by profiling the proteome response of human macrophage THP-1 cells to 11 engineered nanomaterials (ENMs) at two different doses. A total of 116 samples were analyzed in six blocks, yielding an average coverage of 4500 proteins per sample. The data revealed consistent quantification of proteins across all six blocks, as shown by highly stable quantification of house-keeping proteins in all samples and high levels of quantification correlation among samples from different blocks. The data also demonstrated that label-free quantification is robust and accurate enough to quantify even very subtle abundance changes as well as large fold-changes without potential ratio compression as often encountered with isobaric labeling. Our streamlined workflow is easy to implement and can be readily adapted to other large cohort studies for reproducible label-free proteome quantification.

59 BASIC BIOLOGICAL SCIENCES↗

Enhance Low Level Temperature and Moisture Profiles Through Combining NUCAPS, ABI Observations, and RTMA Analysis

Thermodynamic information from low levels in the atmosphere is crucial for operational weather forecasts and meteorological researchers. The NOAA Unique Combined Atmospheric Processing System (NUCAPS) sounding products have been proven beneficial to fill the data gap between synoptic radiosonde observations (RAOBs). However, compared with the upper troposphere, the accuracy of NUCAPS soundings in the low levels still needs improvement. In this study, a deep neural network (DNN) is applied to fuse multiple data sources to enhance the NUCAPS temperature and moisture profiles in the lower atmosphere. The network is developed by combining satellite observations, including NUCAPS sounding retrievals and high resolution geostationary satellite observations from the Advanced Baseline Imager, and surface analysis from the Real-Time Mesoscale Analysis (RTMA) as inputs, while collocated soundings from ECMWF re-analysis version 5 are used as the benchmark for the training. The performance of the model is evaluated by using the independent testing data set, data from a different year, as well as collocated RAOBs, showing improvement to the temperature and moisture profiles by reducing the root-mean-squared-error (RMSE) by more than 30% in the lower atmosphere (from 700 hPa to surface) in both clear sky and partially cloudy conditions. A convective event from June 18, 2017 is presented to illustrate the application of the enhanced low level soundings on high impact weather events. The enhanced soundings from fused data capture the large surface-based convective available potential energy structures in the preconvection environment, which is very useful for severe storm nowcasting and forecasting applications.

54 ENVIRONMENTAL SCIENCES↗

Modeling Profiles of Micrometeorological Variables in a Tropical Premontane Rainforest Using Multi-Layered CLM (CLM-ML)

This study updates the multi-layered Community Land Model (CLM-ml) for hillslopes and compares predictions from against observations collected in tropical montane rainforest, Costa Rica. Modifications are made in order to capture a wider array of vertical leaf area distributions, predict CO 2 profiles, account for soil respiration, and adjust wind forcings for difficult topographic settings. Test results indicate that the modified multi-layer CLM model can successfully replicate the shape of various micrometeorological profiles (humidity, CO 2 , temperature, and wind speed) under the canopy. In the single-layer models (CLM4.5 and CLM5), excessive day-to-night differences in leaf temperature and leaf wetness were originally noted, but CLM-ml significantly improved these issues, decreasing the amplitudes of diurnal cycles by 67% and 47%. Sub-canopy considerations, such as canopy shapes and turbulent transfer parameters, also played a significant role in model performance. More importantly, unlike single layer models, the results that CLM-ml produces can be compared to variables measured within the canopy to provide far more detailed diagnostic information. Further observations and model developments, aimed at reflecting surface heterogeneity, will be necessary to adequately capture the complexity and the features of the tropical montane rainforest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Maritime Aerosol and CCN Profiles Derived From Ship₋Based Measurements Over Eastern North Pacific During MAGIC

Atmospheric aerosols are widely recognized to give rise to a substantial radiative forcing to the climate by scattering and absorbing radiation and by modifying the microphysical, lifetime, and radiative properties of clouds. During the Marine ARM GPCI Investigation of Clouds (MAGIC) over the Eastern North Pacific (ENP), the ship-based measured cloud condensation nuclei (CCN) concentration at 0.2% supersaturation (N CCN,0.2 ) and condensation nuclei concentration (N CN ) had mean values of 116.7 and 219.4 cm ⁻3 , with the highest concentrations found closest to LA due to an increase in aerosol sources. Moving westward, both N CCN,0.2 and N CN gradually decreased until stabilizing near 100 cm ⁻3 and 200 cm ⁻3 , respectively. Using the methods proposed by Ghan and Collins (2004), https://doi.org/10.1175/1520-0426(2004)021<0387:uoisdt>2.0.co;2 and Ghan et al. (2006), https://doi.org/10.1029/2004jd005752, N CCN,0.2 profiles are retrieved using the surface measured N CCN,0.2 as a constraint. For coupled conditions, correlations between the retrieved N CCN,0.2 profiles and cloud-droplet number concentration (N C ) increase from 0.26 at the surface to 0.38 near cloud base, particularly true for non-drizzling clouds. Although the correlations are lower than expected, the percentage increase (46.2%) is encouraging. Finally, the relationships between cloud breakup (CB) and the stratocumulus to cumulus transition (SCT) with environmental conditions and associated aerosols are also studied. The decreased N CN trend east of CB is mainly caused by precipitation scavenging, while the increased N CN trend west of CB is strongly associated with the increased surface wind speed and fewer drizzle events. A further study is needed using high-resolution models to simulate these events.

54 ENVIRONMENTAL SCIENCES↗

Turbulence Structures in the Very Stable Boundary Layer Under the Influence of Wind Profile Distortion

Abstract In very stable boundary layers (VSBL), a “cocktail” of submeso motions routinely result in elevated mean wind speed maxima above the ground, acting as a new source of turbulence generation. This new source of turbulent kinetic energy enhances turbulent mixing and causes mean wind profile distortion (WPD). As a results, this transient distortion in the wind profile adjusts the classical log‐law. Addressing how WPD‐induced turbulence regulates flow structures, turbulent fluxes, and transitions in stability regimes across layers remains a challenge. Eddy covariance data measured at four levels on a 62‐m tower are employed to address these questions. It is shown that the WPD initiates large turbulent eddies that penetrate downward, leading to enhanced vertical mixing and comparable turbulent transport efficiencies across layers. As a consequence, turbulence intensity and fluxes are increased. As the WPD is intensified, turbulent fluxes and turbulent flux transport caused by large eddies are also enhanced, leading to a transition from very stable to weakly stable regimes. Due to the influence of WPD‐induced large eddies, the large‐eddy turbulent Prandtl number does not deviate appreciably from unity and the partitioning between turbulent kinetic and potential energies is linearly related to the gradient Richardson number.

Meteorology & Atmospheric Sciences↗

Evaluation of Monin‐Obukhov Similarity Theory Wind Profiles in Convective Storm Environments and Cold Pools at the ARM Southern Great Plains Atmospheric Observatory

Monin-Obukhov similarity theory (MOST) is widely used in numerical weather prediction to model surface fluxes of momentum, heat, and water vapor. However, MOST is based on assumptions of steady state and horizontally homogeneous turbulence that can lead to prediction errors in and around convective storms. To understand the nature of these errors, we used wind and eddy covariance flux measurements from the Atmospheric Radiation Measurement Southern Great Plains Atmospheric Observatory to evaluate MOST wind profiles in fair-weather and convective storm environments, specifically those of mesoscale convective systems and ordinary thunderstorms. MOST wind profiles agreed well with observations in fair-weather cases, while in convective storm cases the theory systematically overestimated shear in cold pools after gust front passage. Surface layer stability was found to be important in assessing MOST within convective storm environments. The overestimation of wind shear in cold pools suggests the role of non-local fluxes in transferring momentum downward. We discuss reasons for differences and agreement with past studies, and conclude with recommendations to improve prediction of surface winds and fluxes in convective storm simulations.

58 GEOSCIENCES↗

Metabolic capabilities mute positive response to direct and indirect impacts of warming throughout the soil profile

Increasing global temperatures are predicted to stimulate soil microbial respiration. The direct and indirect impacts of warming on soil microbes, nevertheless, remain unclear. This is particularly true for understudied subsoil microbes. Here, we show that 4.5 years of whole-profile soil warming in a temperate mixed forest results in altered microbial community composition and metabolism in surface soils, partly due to carbon limitation. However, microbial communities in the subsoil responded differently to warming than in the surface. Throughout the soil profile—but to a greater extent in the subsoil—physiologic and genomic measurements show that phylogenetically different microbes could utilize complex organic compounds, dampening the effect of altered resource availability induced by warming. We find subsoil microbes had 20% lower carbon use efficiencies and 47% lower growth rates compared to surface soils, which constrain microbial communities. Collectively, our results show that unlike in surface soils, elevated microbial respiration in subsoils may continue without microbial community change in the near-term.

54 ENVIRONMENTAL SCIENCES↗

PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements

Multidimensional measurements using state-of-the-art separations and mass spectrometry provide advantages in untargeted metabolomics analyses for studying biological and environmental bio-chemical processes. However, the lack of rapid analytical methods and robust algorithms for these heterogeneous data has limited its application. Here, we develop and evaluate a sensitive and high-throughput analytical and computational workflow to enable accurate metabolite profiling. Our workflow combines liquid chromatography, ion mobility spectrometry and data-independent acquisition mass spectrometry with PeakDecoder, a machine learning-based algorithm that learns to distinguish true co-elution and co-mobility from raw data and calculates metabolite identification error rates. We apply PeakDecoder for metabolite profiling of various engineered strains of Aspergillus pseudoterreus, Aspergillus niger, Pseudomonas putida and Rhodosporidium toruloides. Results, validated manually and against selected reaction monitoring and gas-chromatography platforms, show that 2683 features could be confidently annotated and quantified across 116 microbial sample runs using a library built from 64 standards.

59 BASIC BIOLOGICAL SCIENCES↗

Extracting band edge profiles at semiconductor heterostructures from hard-x-ray core-level photoelectron spectra

Hard-x-ray photoelectron spectroscopy (HAXPES) is a valuable source of information on band-edge profiles deep inside semiconductor thin films and heterojunctions. However, extracting this information requires robust and physically meaningful decomposition of spectra into contributions from individual atomic planes. We present an approach that utilizes the physical requirements of a monotonic dependence of the built-in electrostatic potential on depth and continuity of the potential function and its derivatives. These constraints enable efficient extraction of band-edge profiles and allow one to capture details of the electronic structure, including determination of the signs and magnitudes of the band bending as well as the valence band offsets. The utility of this approach to generate quantitative insight into the electronic structure of complex materials is illustrated for epitaxial SrTiO 3 on intrinsic Si(001).

97 MATHEMATICS AND COMPUTING↗

Understanding the structure and composition of recalcitrant oligosaccharides in hydrolysate using high-throughput biotin-based glycome profiling and mass spectrometry

Novel Immunological and Mass Spectrometry Methods for Comprehensive Analysis of Recalcitrant Oligosaccharides in AFEX Pretreated Corn Stover. Lignocellulosic biomass is a sustainable alternative to fossil fuel and is extensively used for developing bio-based technologies to produce products such as food, feed, fuel, and chemicals. The key to these technologies is to develop cost competitive processes to convert complex carbohydrates present in plant cell wall to simple sugars such as glucose, xylose, and arabinose. Since lignocellulosic biomass is highly recalcitrant, it must undergo a combination of thermochemical treatment such as Ammonia Fiber Expansion (AFEX), dilute acid (DA), Ionic Liquid (IL) and biological treatment such as enzyme hydrolysis and microbial fermentation to produce desired products. However, when using commercial fungal enzymes during hydrolysis, only 75–85% of the soluble sugars generated are monomeric sugars, while the remaining 15–25% are soluble recalcitrant oligosaccharides that cannot be easily utilized by microorganisms. Previously, we successfully separated and purified the soluble recalcitrant oligosaccharides using a combination of charcoal and celite-based separation followed by size exclusion chromatography and studies their inhibitory properties on enzymes. We discovered that the oligosaccharides with higher degree of polymerization (DP) containing methylated uronic acid substitutions were more recalcitrant towards commercial enzyme mixtures than lower DP and neutral oligosaccharides. Here, we report the use of several complementary techniques that include glycome profiling using plant biomass glycan specific monoclonal antibodies (mAbs) to characterize sugar linkages in plant cell walls and enzymatic hydrolysate, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) using structurally-informative diagnostic peaks offered by negative ion post-secondary decay spectra, gas chromatography followed by mass spectrometry (GC–MS) to characterize oligosaccharide sugar linkages with and without derivatization. Since oligosaccharides (DP 4–20) are small, it is challenging to mobilize these molecules for mAbs binding and characterization. To overcome this problem, we have applied a new biotin-coupling based oligosaccharide immobilization method that successfully tagged most of the low DP soluble oligosaccharides on to a micro-plate surface followed by specific linkage analysis using mAbs in a high-throughput system. This new approach will help develop more advanced versions of future high throughput glycome profiling methods that can be used to separate and characterize oligosaccharides present in biomarkers for diagnostic applications.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring toroidal anvil profiles for larger sample volumes above 4 Mbar

Abstract With the advent of toroidal and double-stage diamond anvil cells (DACs), pressures between 4 and 10 Mbar can be achieved under static compression, however, the ability to explore diverse sample assemblies is limited on these micron-scale anvils. Adapting the toroidal DAC to support larger sample volumes offers expanded capabilities in physics, chemistry, and planetary science: including, characterizing materials in soft pressure media to multi-megabar pressures, synthesizing novel phases, and probing planetary assemblages at the interior pressures and temperatures of super-Earths and sub-Neptunes. Here we have continued the exploration of larger toroidal DAC profiles by iteratively testing various torus and shoulder depths with central culet diameters in the 30–50 µm range. We present a 30 µm culet profile that reached a maximum pressure of 414(1) GPa based on a Pt scale. The 300 K equations of state fit to our P–V data collected on gold and rhenium are compatible with extrapolated hydrostatic equations of state within 1% up to 4 Mbar. This work validates the performance of these large-culet toroidal anvils to > 4 Mbar and provides a promising foundation to develop toroidal DACs for diverse sample loading and laser heating.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Accelerating detector simulations with Celeritas: Profiling and performance optimizations

Celeritas is a GPU-optimized Monte Carlo (MC) particle transport code designed to meet the growing computational demands of next-generation high energy physics (HEP) experiments. It provides efficient simulation of electromagnetic (EM) physics processes in complex geometries with magnetic fields, detector hit scoring, and seamless integration into Geant4-driven applications to offload EM physics to GPUs. Recent efforts have focused on performance optimizations and expanding profiling capabilities. This paper presents some key advancements, including the integration of the Perfetto system profiling tool for detailed performance analysis and the development of track-sorting methods to improve computational efficiency.

Lund, Amanda [Argonne National Laboratory (ANL)]↗

Inferred UV fluence focal-spot profiles from soft x-ray pinhole-camera measurements on OMEGA

A method was developed with laser-irradiated Au planar foils to characterize the focal spot of UV laser beams on target at full energy from soft x-ray emission. A pinhole camera with a back-thinned charge-coupled–device detector and filtration with thin Be and Al foil filters provides images of the x-ray emission at photon energies <2 keV. This method requires a careful measurement of the relation between the applied UV fluence and the x-ray signal, which can be described by a power-law dependence. The measured exponent γ ~ 2 provides a dynamic range of ~25 for the inferred UV fluence. UV fluence profiles of selected beams were measured for 100-ps and 1-ns laser pulses and were compared to directly measured profiles from an UV equivalent-target-plane diagnostic. The inferred spot size and super-Gaussian order from the x-ray technique agree within several percent with the values measured with the direct UV measurements.

47 OTHER INSTRUMENTATION↗

Multi-layering of SU-8 exhibits distinct geometrical transitions from circular to planarized profiles

The negative tone photoresist SU-8 permits the creation of micrometer-scale structures by optical lithography. It is also the most used photoresist in soft lithography for the fast-prototyping of microfluidic devices. Despite its importance, the effect of capillary forces on SU-8 multi-layering onto topographical features has not been thoroughly studied. In particular, the profile of the added layer has not been examined in detail. The overlaying process exhibits a set of distinct behaviors, or regimes, depending on the relative thickness of the overlay and the underlying rectangular pattern. We demonstrate how capillary effects control the profile of multi-layer microchannels in a predictable manner. We derive a simple static model to describe the evolution of the overlay as a function of dimensionless geometric parameters. Our study provides a critical understanding of the parameters that govern multi-layer spin coating.

Sauzade, Martin↗

Verification of an improved equation-free projective integration method for neoclassical plasma-profile evolution in tokamak geometry

A brute-force, long-time gyrokinetic simulation of plasma profile evolution in magnetic fusion devices is not desirable due to large computational resource requirements and a possible accumulation of numerical error. The equation-free projective integration method of Keverekidis et al. [Commun. Math. Sci. 1(4), 715–762 (2003)] is one of the outstanding candidates in projecting micro-scale simulations to a longer timescale. However, its application to tokamak plasma has not been fruitful due to the appearance of spurious transient oscillations in the lifting process, which are present when the kinetic simulations are initialized with a simplified model distribution function and which make the kinetic simulations to deviate from the desired paths. In this work, a kinetically informed lifting algorithm is added to the equation-free projective integration method, which is then verified in the electrostatic gyrokinetic particle-in-cell code XGCa [R. Hager and C. S. Chang, Phys. Plasmas 23, 042503 (2016)] for a neoclassical ion heat transport problem with adiabatic electrons. This new lifting operator is demonstrated to control spurious transients, enabling an over four-times reduction in the overall computing time in the time-evolution of the ion temperature profile in an axisymmetric toroidal plasma. Further reduction in the computing time is found to be limited due to the stability properties of the linear least squares projective integrator.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Flattening of the tokamak current profile by a fast magnetic reconnection with implications for the solar corona

During tokamak disruptions, the profile of the net parallel current is observed to flatten on a time scale that is so fast that it must be due to a fast magnetic reconnection. After a fast magnetic reconnection has broken magnetic surfaces, a single magnetic field line covers an entire volume and not just a magnetic surface. The current profile, given by K &#x2261; &#x3BC; 0 j | | / B , relaxes to a constant within that volume by Alfven waves propagating along the chaotic magnetic field lines. The time scale for this relaxation determines the commonly observed disruption phenomena of a current spike and a sudden drop in the plasma internal inductance. An efficient method for studying this relaxation is derived, which allows a better understanding of the information encoded in the current spike and the associated sudden drop in the plasma internal inductance. Implications for coronal heating are also discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Characterization of injection and confinement improvement through impurity induced profile modifications on the Wendelstein 7-X stellarator

Pulsed injections of boron carbide granules into Wendelstein 7-X stellarator (W7-X) plasmas transiently increase the plasma stored energy and core ion temperatures above the reference W7-X experimental programs by up to 30%. In a series of 4 MW electron cyclotron resonance heating experiments, the PPPL Probe Mounted Powder Injector provided 50 ms bursts of 100 μm granules every 350 ms at estimated quantities ranging from approximately 1 mg/pulse to over 30 mg/pulse. For each injection, the stored energy was observed to initially drop and the radiated power transiently increased, while the radial electron density profile rose at the edge as material was assimilated. Once the injected boron carbide was fully absorbed, the density rise transitioned to the core while the stored energy increased above the previous baseline level by an amount linearly correlated with the injection quantity. During the injection, the ion temperature gradient steepened with peak core ion temperatures observed to increase from a nominal 1.7 keV to over 2.6 keV for the largest injection amounts. Enhanced performance is accompanied by a reversal of the radial electric field at ρ < 0.3, indicating that the core transport has switched to the ion root. These observations are suggestive of a change in transport and provide further evidence that externally induced profile modifications provide a possible path to enhanced W7-X performance metrics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗