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At least 1,459 records · Page 81

Assessments of epistemic uncertainty using Gaussian stochastic weight averaging for fluid-flow regression

Here, we use Gaussian stochastic weight averaging (SWAG) to assess the epistemic uncertainty associated with neural-network-based function approximation relevant to fluid flows. SWAG approximates a posterior Gaussian distribution of each weight, given training data, and a constant learning rate. Having access to this distribution, it is able to create multiple models with various combinations of sampled weights, which can be used to obtain ensemble predictions. The average of such an ensemble can be regarded as the 'mean estimation', whereas its standard deviation can be used to construct 'confidence intervals', which enable us to perform uncertainty quantification (UQ) with regard to the training process of neural networks. We utilize representative neural-network-based function approximation tasks for the following cases: (i) a two-dimensional circular-cylinder wake; (ii) the DayMET dataset (maximum daily temperature in North America); (iii) a three-dimensional square-cylinder wake; and (iv) urban flow, to assess the generalizability of the present idea for a wide range of complex datasets. SWAG-based UQ can be applied regardless of the network architecture, and therefore, we demonstrate the applicability of the method for two types of neural networks: (i) global field reconstruction from sparse sensors by combining convolutional neural network (CNN) and multi-layer perceptron (MLP); and (ii) far-field state estimation from sectional data with two-dimensional CNN. We find that SWAG can obtain physically-interpretable confidence-interval estimates from the perspective of epistemic uncertainty. This capability supports its use for a wide range of problems in science and engineering.

97 MATHEMATICS AND COMPUTING↗

Characterization of the procoagulant phenotype of amniotic fluid across gestation in rhesus macaques and humans

Background: Amniotic fluid (AF) plays a key role in fetal development, yet the evolving composition of AF and its effects of hemostasis and thrombosis are poorly understood. Objectives: Here, we aim to determine how the evolving molecular composition of AF relates to its procoagulant properties. Methods: We analyzed the proteomes, lipidomes and procoagulant properties of AF obtained by amniocentesis from rhesus macaque and human pregnancies at gestational-age matched timepoints. Results When added to human plasma, both rhesus and human AF accelerated clotting time and fibrin generation. We identified proteomic modules associated with clotting time and enriched for coagulation-related pathways. Proteins known to be involved in hemostasis were highly correlated with each other and their intensity of expression varied across gestation in both rhesus and humans. Inhibition of contact pathway did not affect the procoagulant effect of AF. Blocking tissue factor pathway inhibitor reversed the ability of AF to block the generation of FXa. The prothrombinase activity of AF was inhibited by phospholipid inhibitors. The levels of phosphatidylserine in AF were inversely correlated with clotting time. AF promoted platelet activation and secretion in plasma. Conclusions: The addition of AF to plasma enhances coagulation in a manner dependent on phospholipids as well as the presence of proteases and other proteins that directly regulate coagulation. We describe a correlation between clotting time and expression of coagulation proteins and phosphatidylserine in both rhesus and human AF, supporting the use rhesus models for future studies of AF biology.

amniotic fluid↗

Protective effects of pulmonary epithelial lining fluid on oxidative stress and DNA single-strand breaks caused by ultrafine carbon black, ferrous sulphate and organic extract of diesel exhaust particles

Pulmonary epithelial lining fluid (ELF) is the first substance to make contact with inhaled particulate matter (PM) and interacts chemically with PM components. The objective of this study was to determine the role of ELF in oxidative stress, DNA damage and the production of proinflammatory cytokines following physicochemical exposure to PM. Ultrafine carbon black (ufCB, 15 nm; a model carbonaceous core), ferrous sulphate (FeSO{sub 4}; a model transition metal) and a diesel exhaust particle (DEP) extract (a model organic compound) were used to examine the acellular oxidative potential of synthetic ELF and non-ELF systems. We compared the effects of exposure to ufCB, FeSO{sub 4} and DEP extract on human alveolar epithelial Type II (A549) cells to determine the levels of oxidative stress, DNA single-strand breaks and interleukin-8 (IL-8) production in ELF and non-ELF systems. The effects of ufCB and FeSO{sub 4} on the acellular oxidative potential, cellular oxidative stress and DNA single-strand breakage were mitigated significantly by the addition of ELF, whereas there was no decrease following treatment with the DEP extract. There was no significant effect on IL-8 production following exposure to samples that were suspended in ELF/non-ELF systems. The results of the present study indicate that ELF plays an important role in the initial defence against PM in the pulmonary environment. Experimental components, such as ufCB and FeSO{sub 4}, induced the production of oxidative stress and led to DNA single-strand breaks, which were moderately prevented by the addition of ELF. These findings suggest that ELF plays a protective role against PM-driven oxidative stress and DNA damage. -- Highlights: ► To determine the role of ELF in ROS, DNA damage and IL-8 after exposure to PM. ► ufCB, FeSO{sub 4} and DEP extract were used to examine the protective effects of ELF. ► PM-driven oxidative stress and DNA single-strand breakage were mitigated by ELF. ► The findings suggest that ELF has a protective role against PM. ► The synthetic ELF system could reduce the use of animals in PM-driven ROS testing.

60 APPLIED LIFE SCIENCES↗

Cellular uptake of lead in the blood-cerebrospinal fluid barrier: Novel roles of Connexin 43 hemichannel and its down-regulations via Erk phosphorylation

As the structural basis of blood-cerebrospinal fluid barrier (BCB), epithelial cells in the choroid plexus (CP) are targets for lead (Pb). Pb is known to accumulate in the CP; however, the mechanism of Pb uptake in the choroidal epithelial cells remains unknown. Recently, hemichannels of Connexin 43 (Cx43), the most ubiquitously expressed gap junction proteins in the CP, were found to be important pathways for many substances. This study was designed to investigate the roles of Cx43 in Pb uptake in the epithelial cells. Autometallography was used to outline Pb's subcellular location, and the characteristics of Pb transport into CP cells, including concentration- and time-dependence were analyzed by atomic absorption spectroscopy. Knockdown/overexpression of Cx43 with transient siRNA/plasmids transfections before Pb exposure diminished/increased the Pb accumulation. In the Z310 cell-based doxycycline-inducible Cx43 expression cell line (iZCx43), doxycycline induced a significant increase (3-fold) in Pb uptake, corresponding to the increased Cx43 levels. Activation of Cx43 hemichannels by reduced serum conditions caused an increase of Pb concentrations. Cx43-induced Pb uptake was attenuated after blockage of Cx43 hemichannels with its inhibitor, carbenoxolone. Additionally, down-regulation of Cx43 protein levels by Pb exposure paralleled cellular Pb concentrations in the time study. Concomitantly, expressions of phosphor-Src and phosphor-Erk were both significantly increased by Pb. However, inactivation of Erk, not Src pathway, reversed Pb-induced downregulation of Cx43. Taken together, these data establish that Pb can accumulate in the BCB and validate the role of Cx43 hemichannel in Pb uptake and its regulations through Erk phosphorylation. - Highlights: • Pb is sequestrated in choroid plexus both in vivo and in vitro. • Cx43 knockdown/overexpression prevents/increases Pb accumulations. • Cx43 hemichannels are required for Pb uptake. • Pb-induced Erk activation causes reduction of Cx43.

60 APPLIED LIFE SCIENCES↗

High vacuum measurements and calibrations, molecular flow fluid transient effects

High vacuum pressure measurements and calibrations below 1 × 10 -8 Torr are problematic. Specifically, measurement accuracies change drastically for vacuum gauges when pressures are suddenly lowered in vacuum systems. How can gauges perform like this? A brief system description is first required to answer this question. Calibrations were performed using a vacuum calibration chamber with attached vacuum gauges. To control chamber pressures, vacuum pumps decreased the chamber pressure while nitrogen tanks increased the chamber pressure. By balancing these opposing pressures, equilibrium in the chamber was maintained at selected set point pressures to perform calibrations. When pressures were suddenly decreased during set point adjustments, a sudden rush of gas from the chamber also caused a surge of gas from the gauges to decrease the pressures in those gauges. Gauge pressures did not return to equilibrium as fast as chamber pressures due to the sparse distribution of gas molecules in the system. This disparity in the rate of pressure changes caused the pressures in different gauges to be different than expected. This discovery was experimentally proven to show that different gauge designs return to equilibrium at different rates, and that gauge accuracies vary for different gauge designs due to fluid transients in molecular flow.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Integration of the Biot–Gassmann Fluid Substitution Method and Machine Learning-Based Velocity–Stress Relationship for Estimating In Situ Stresses

Recent advancements have shown that in situ stresses can be reliably estimated through an integrated machine/deep learning (ML/DL)-based framework, which relies on models trained and validated using true triaxial ultrasonic velocity (TUV) experimental data that involve measurements of ultrasonic velocity in saturated rocks under varying stress configurations. However, when the goal is to interpret lower frequency measurements, it may be more appropriate to run experiments on dry rocks and then obtain Biot–Gassmann-derived equivalent saturated velocities (low-frequency approximation) and employ these quantities for training ML/DL models to predict in situ stress. Whether the dispersion effect of frequency on the velocity–stress relationship substantially impacts in situ stress prediction is an important and unresolved question. This work presents an enhancement of ML/DL-based workflow by training and implementing ML/DL models using equivalent saturated acoustic velocities (low-frequency) obtained by applying Biot–Gassmann fluid substitution on the ultrasonic velocities of dry cores. The models were trained on TUV data sets derived from three subsurface cores extracted from the geothermal well 16B(78)-32 at the Utah FORGE site. Each core was subjected to 75 unique stress configurations for velocity measurement in the dry state. The ML/DL trained on the TUV data set with equivalent saturated velocities demonstrated promising performance to predict in situ stress in subsurface geological rocks using velocity–stress relationships with R 2 of 0.86, 0.971, and 0.975 and root mean squared error (RMSE) of 2.59, 1.92, and 1.80 for validation/testing phases of vertical, minimum horizontal, and maximum horizontal stress models, respectively. Additionally, interpretation and explanation by Shapley additive explanations (SHAP) analysis further improved scientific validation and model reliability for estimating in situ stresses.

colloids↗

Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp novicida

Francisella tularensis causes the zoonosis tularemia in humans and is one of the most virulent bacterial pathogens. We utilized a global proteomic approach to characterize protein changes in bronchoalveolar lavage fluid from mice exposed to one of three organisms, F. tularensis ssp. novicida, an avirulent mutant of F. tularensis ssp. novicida (F.t. novicida-ΔmglA); and Pseudomonas aeruginosa. The composition of BALF proteins was altered following infection, including proteins involved in neutrophil activation, oxidative stress and inflammatory responses. Components of the innate immune response were induced including the acute phase response and the complement system, however the timing of their induction varied. Francisella tularensis ssp. novicida infected mice do not appear to have an effective innate immune response in the first hours of infection, however within 24 hours they show an upregulation of innate immune response proteins. This delayed response is in contrast to P. aeruginosa infected animals which show an early innate immune response. Likewise, F.t. novicida-ΔmglA infection initiates an early innate immune response, however this response is dimished by 24 hours. Finally, this study identifies several candidate biomarkers, including Chitinase 3-like-1 (CHI3L1 or YKL-40) and peroxiredoxin 1, that are associated with F. tularensis ssp. novicida but not P. aeruginosa infection.

59 BASIC BIOLOGICAL SCIENCES↗

Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease

Acute Lyme disease results from transmission of and infection by the bacterium Borrelia burgdorferi following a tick bite. During acute infection, bacteria can disseminate to the central nervous system (CNS) leading to the development of Lyme meningitis. Here we have analyzed pooled cerebrospinal fluid (CSF) allowing for a deep view into the proteome for a cohort of patients with early-disseminated Lyme disease and CSF inflammation leading to the identification of proteins that reflect host responses, which are distinct for subjects with acute Lyme disease. Additionally, we analyzed individual patient samples and quantified changes in protein abundance employing label-free quantitative mass spectrometry based methods. The measured changes in protein abundances reflect the impact of acute Lyme disease on the CNS as presented in CSF. We have identified 89 proteins that differ significantly in abundance in patients with acute Lyme disease. A number of the differentially abundant proteins have been found to be localized to brain synapse and thus constitute important leads for better understanding of the neurological consequence of disseminated Lyme disease.

Borreliosis, Lyme Megingitis↗

Statistical Inference Over Persistent Homology Predicts Fluid Flow in Porous Media

Here, we statistically infer fluid flow and transport properties of porous materials based on their geometry and connectivity, without the need for detailed We summarize structure by persistent homology and then determines the similarity of structures using image analysis and statistics. Longer term, this may enable quick and automated categorization of rocks into known archetypes. We first compute persistent homology of binarized 3D images of material subvolume samples. The persistence parameter is the signed Euclidean distance from inferred material interfaces, which captures the distribution of sizes of pores and grains. Each persistence diagram is converted into an image vector. Here, we infer structural similarity by calculating image similarity. For each image vector, we compute principal components to extract features. We fit statistical models to features estimates material permeability, tortuosity, and anisotropy. We develop a Structural SIMilarity index to determine statistical representative elementary volumes.

36 MATERIALS SCIENCE↗

From Fluid Flow to Coupled Processes in Fractured Rock: Recent Advances and New Frontiers

Abstract Quantitative predictions of natural and induced phenomena in fractured rock is one of the great challenges in the Earth and Energy Sciences with far‐reaching economic and environmental impacts. Fractures occupy a very small volume of a subsurface formation but often dominate fluid flow, solute transport and mechanical deformation behavior. They play a central role in CO 2 sequestration, nuclear waste disposal, hydrogen storage, geothermal energy production, nuclear nonproliferation, and hydrocarbon extraction. These applications require predictions of fracture‐dependent quantities of interest such as CO 2 leakage rate, hydrocarbon production, radionuclide plume migration, and seismicity; to be useful, these predictions must account for uncertainty inherent in subsurface systems. Here, we review recent advances in fractured rock research covering field‐ and laboratory‐scale experimentation, numerical simulations, and uncertainty quantification. We discuss how these have greatly improved the fundamental understanding of fractures and one's ability to predict flow and transport in fractured systems. Dedicated field sites provide quantitative measurements of fracture flow that can be used to identify dominant coupled processes and to validate models. Laboratory‐scale experiments fill critical knowledge gaps by providing direct observations and measurements of fracture geometry and flow under controlled conditions that cannot be obtained in the field. Physics‐based simulation of flow and transport provide a bridge in understanding between controlled simple laboratory experiments and the massively complex field‐scale fracture systems. Finally, we review the use of machine learning‐based emulators to rapidly investigate different fracture property scenarios and accelerate physics‐based models by orders of magnitude to enable uncertainty quantification and near real‐time analysis.

58 GEOSCIENCES↗

Extended harmonic mapping connects the equations in classical, statistical, fluid, quantum physics and general relativity

Abstract One potential pathway to find an ultimate rule governing our universe is to hunt for a connection among the fundamental equations in physics. Recently, Ren et al. reported that the harmonic maps with potential introduced by Duan, named extended harmonic mapping (EHM), connect the equations of general relativity, chaos and quantum mechanics via a universal geodesic equation. The equation, expressed as Euler–Lagrange equations on the Riemannian manifold, was obtained from the principle of least action. Here, we further demonstrate that more than ten fundamental equations, including that of classical mechanics, fluid physics, statistical physics, astrophysics, quantum physics and general relativity, can be connected by the same universal geodesic equation. The connection sketches a family tree of the physics equations, and their intrinsic connections reflect an alternative ultimate rule of our universe, i.e. , the principle of least action on a Finsler manifold.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter

We report a novel technical approach for subcritical fluid extraction (SFE) for organic matter characterization in complex matrices such as soil. The custom platform combines on-line SFE with micro-solid phase extraction, nano liquid chromatography (LC), electrospray ionization and Fourier transform mass spectrometry (SFE-LC-FTMS). We demonstrated the utility of SFE-LC-FTMS, including results from both Orbitrap and FTICR MS, for analysis of complex mixtures of organic compounds in a solid matrix by characterizing soil organic matter in peat, a high-carbon soil. For example, in a single experiment, >6000 molecular formulas can be assigned based upon FTICR MS data from 1–50 μL of soil samples (roughly 1–50 mg of soil, dependent on soil density), nearly twice that typically obtained from direct infusion liquid solvent extraction (LSE) from an order of magnitude larger volume of the same soil. The detected species consisted predominately of lipid-like, lignin-like and protein-like compounds, based on their O/C and H/C ratios, with predominantly CHO and CHONP molecular compositions. These results clearly demonstrate that SFE has the potential to effectively extract a variety of molecular species and could become an important member of a suite of extraction methods for studying SOM and other natural organic matter. This is especially true when comprehensive coverage, minimal sample volumes, and high sensitivity are required, or when the presence of organic solvent residue in residual soil is problematic. Lastly, the SFE based extraction protocol could potentially enable spatially resolved characterization of organic matter in soil with a resolution of ~1 mm3 to facilitate studies probing the spatial heterogeneity of soil.

54 ENVIRONMENTAL SCIENCES↗

Neutron field parameter measurements on the JET tokamak by means of super-heated fluid detectors

The neutron field parameters (fluence and energy distribution) at a specific location outside the JET Torus Hall have been measured by means of super-heated fluid detectors (or 'bubble detectors') in combination with an independent, time-of-flight, technique. The bubble detector assemblies were placed at the end of a vertical line of sight at about 16 m from the tokamak mid plane. Spatial distributions of the neutron fluence along the radial and toroidal directions have been obtained using two-dimensional arrays of bubble detectors. Using a set of three bubble detector spectrometers the neutron energy distribution was determined over a broad energy range, from about 10 keV to above 10 MeV, with an energy resolution of about 30% at 2.5 MeV. The very broad energy response allowed for the identification of energy features far from the main fusion component (around 2.45 MeV for deuterium discharges).

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Computational fluid dynamics and frequency-dependent finite-difference time-domain method coupling for the interaction between microwaves and plasma in rocket plumes

Under certain conditions during rocket flights, ionized exhaust plumes from solid rocket motors may interfere with radio frequency transmissions. To understand the relevant physical processes involved in this phenomenon and establish a prediction process for in-flight attenuation levels, we attempted to measure microwave attenuation caused by rocket exhaust plumes in a sea-level static firing test for a full-scale solid propellant rocket motor. The microwave attenuation level was calculated by a coupling simulation of the inviscid-frozen-flow computational fluid dynamics of an exhaust plume and detailed analysis of microwave transmissions by applying a frequency-dependent finite-difference time-domain method with the Drude dispersion model. The calculated microwave attenuation level agreed well with the experimental results, except in the case of interference downstream the Mach disk in the exhaust plume. It was concluded that the coupling estimation method based on the physics of the frozen plasma flow with Drude dispersion would be suitable for actual flight conditions, although the mixing and afterburning in the plume should be considered depending on the flow condition.

42 ENGINEERING↗

Verification of electromagnetic fluid-kinetic hybrid electron model in global gyrokinetic particle simulation

The fluid-kinetic hybrid electron model is verified in global gyrokinetic particle simulation of linear electromagnetic drift-Alfvenic instabilities in tokamak. In particular, we have recovered the {beta}-stabilization of the ion temperature gradient mode, transition to collisionless trapped electron mode, and the onset of kinetic ballooning mode as {beta}{sub e} (ratio of electron kinetic pressure to magnetic pressure) increases.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Quantum fluid model of coherent stimulated radiation by a dense relativistic cold electron beam

Using a quantum fluid model, the linear dispersion relation for FEL pumped by a short wavelength laser wiggler is deduced. Subsequently, a new quantum corrected resonance condition is obtained. It is shown that, in the limit of low energy electron beam and low frequency pump, the quantum recoil effect can be neglected, recovering the classical FEL resonance condition, k{sub s}=4k{sub w}γ{sup 2}. On the other hand, for short wavelength and high energy electron beam, the quantum recoil effect becomes strong and the resonance condition turns into k{sub s}=2√(k{sub w}/λ{sub c})γ{sup 3/2}, with λ{sub c} being the reduced Compton wavelength. As a result, a set of nonlinear coupled equations, which describes the quantum FEL dynamics as a three-wave interaction, is obtained. Neglecting wave propagation effects, this set of equations is solved numerically and results are presented.

43 PARTICLE ACCELERATORS↗

Statistical thermodynamics for a self-gravitating fluid of rotating particles

Systems with long-range interactions (those which decay at large distances as r{sup -l}, with l≥d, where d is the dimensionality of the considered space), like gravitational or charged ones, present difficulties when treated by conventional statistical mechanics perturbation methods. In this work a self-gravitating fluid of rotating spherical particles is considered. The corresponding inter-particle potential model is a long-ranged one and was obtained from the application of the Newtonian limit to the Kerr metric. This potential has been expressed as a finite sum of hard-core Yukawa potentials. This new potential mimics the original long-ranged one and can be treated with conventional statistical mechanics methods. The first-order mean spherical approximation is applied to this potential to obtain the thermodynamic response functions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Properties of the Lennard-Jones dimeric fluid in two dimensions: An integral equation study

The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗