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At least 433 records · Page 24

COVID-19 biomarkers based on respiratory microbiome content

COVID-19 patient care management would greatly benefit from new tools that enable accurate assessment of disease severity and stage, potentially enabling a personalized medicine approach. Detection of the SARS-CoV-2 virus itself, or even quantitation of viral loads, is not sufficient for accurate assessment of disease state beyond diagnosis of infection [eg, doi:10.1093/cid/ciaa344]. Levels of usual suspect protein biomarkers associated with host response to infection [eg, C-reactive protein (CRP); cytokines like IL-6, TNF-alpha, and IL-10; complement proteins like C3a and C5a], and of individual blood cell types (eg, leukocytes, lymphocytes, and subsets thereof), show limited correlation with disease severity and stage, with high patient-to-patient and study-to-study variability [eg, doi:10.1093/cid/ciaa248]. High-dimensional panels of biomarkers should have greater predictive power and resilience to unavoidable sources of variability; however, their assembly from proteins and cell types is extremely difficult, due to technical limitations in analyte measurement, especially with regard to starting material requirements and detection sensitivity. Host response profiling through Next Generation Sequencing (NGS) of gene expression patterns (ie, RNA-Seq) is a promising approach, but at the time of this project there were only two publicly available datasets of relevance [doi:10.1093/cid/ciaa203, doi:10.1080/22221751.2020.1747363], and close inspection of them revealed that each had at least one major flaw that severely undermined its value in supporting robust analysis of host response to SARS-CoV- 2 infection. However, the first of these studies [doi:10.1093/cid/ciaa203] fortuitously collected NGS data not only from host cells, but also from bacteria present in bronchoalveolar lavage fluid (BALF) recovered from COVID-19 patients; and because the respiratory microbiome (in terms of bacterial species content) is far less complex than the human transcriptome, the NGS data collected were sufficient to provide coverage depth supporting robust analysis. Surprisingly, the authors of the study did not carry out a detailed analysis of these data and their potential for revealing important new information about COVID-19. Therefore, we carried out a meta-analysis of the dataset as a first step in evaluating the potential for profiling of respiratory microbiome dynamics as a means of accurately assessing COVID-19 disease state.

59 BASIC BIOLOGICAL SCIENCES↗

Design of Fiber Optic Sensors for Measuring Hydrodynamic Parameters

The science of optical hydrodynamics involves relating the optical properties to the fluid dynamic properties of a hydrodynamic system. Fiber-optic sensors are being designed for measuring the hydrodynamic parameters of various systems. As a flowing fluid makes an encounter with a flat surface, it forms a boundary layer near this surface. The region between the boundary layer and the flat plate contains information about parameters such as viscosity, compressibility, pressure, density, and velocity. An analytical model has been developed for examining the hydrodynamic parameters near the surface of a fiber-optic sensor. An analysis of the conservation of momentum, the continuity equation and the Navier-Stokes equation for compressible flow were used to develop expressions for the velocity and the density as a function of the distance along the flow and above the surface. When examining the flow near the surface, these expressions are used to estimate the sensitivity required to perform direct optical measurements and to derive the shear force for indirect optical measurements. The derivation of this result permits the incorporation of better design parameters for other fiber-based sensors. Future work includes analyzing the optical parametric designs of fiber-optic sensors, modeling sensors to utilize the parameters for hydrodynamics and applying different mixtures of hydrodynamic flow. Finally, the fabrication of fiber-optic sensors for hydrodynamic flow applications of the type described in this presentation could enhance aerospace, submarine, and medical technology.

Lyons, Donald R.↗

Immunoassay readout method using extrinsic Raman labels adsorbed on immunogold colloids

An immunoassay readout method based on surface-enhanced Raman scattering (SERS) is described. The method exploits the SERS-derived signal from reporter molecules that are coimmobilized with biospecific species on gold colloids. This concept is demonstrated in a dualanalyte sandwich assay, in which two different antibodies covalently bound to a solid substrate specifically capture two different antigens from an aqueous sample. The captured antigens in turn bind selectively to their corresponding detection antibodies. The detection antibodies are conjugated with gold colloids that are labeled with different Raman reporter molecules, which serve as extrinsic labels for each type of antibody. The presence of a specific antigen is established by the characteristic SERS spectrum of the reporter molecule. A near-infrared diode laser was used to excite efficiently the SERS signal while minimizing fluorescence interference. We show that, by using different labels with little spectral overlap, two different antigenic species can be detected simultaneously. The potential of this concept to function as a readout strategy for multiple analytes is briefly discussed.

NASA Program Advanced Human Support Technology↗

Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

Kallman, Tim↗

Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. This paper describes simple numerical experiments designed to examine some of these issues. Similar studies have been carried out previously in the context of solar UV lines by Gianetti et al. (2000); Savin & Laming (2002) and in the context of the iron M shell UTA in NGC 3783 by Netzer (2004).

Kallman, T.↗

Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn 011 many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

Kallman, Tim↗

Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. This talk describes simple numerical experiments designed to examine some of these issues.

Kallman, T.↗

Testing Photoionization Calculations Using Chandra X-ray Spectra

A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

Kallman, Tim↗

Development of efficient solar cells using combination of QSPR and DFT approaches

The awarded research project aimed to design and determine the effective organic dye-sensitizers from the ensemble of chromophores for the dye-sensitized solar cell (DSSC) and fullerene-derivatives (FDs) as acceptor for polymer solar cell (PSC) followed by explore the electron transfer mechanism using the combined quantitative structure-property relationship (QSPR) analysis in conjunction with density functional theory (DFT) and time-dependent DFT (TDDFT)-based calculations. Based on our proposal we have employed different in silico approaches to design photo-efficient organic dye-sensitizers for DSSCs and FDs as acceptor for PSCs with exhaustive screening methodology.

14 SOLAR ENERGY↗

Titan Ice and Dust Experiment (TIDE): Detection and Analysis of Compounds of Interest to Astrobiology in the Lower Atmosphere and Surface of Titan

The Titan Orbiter Aerorover Mission (TOAM) is a proposed concept for the Solar System Exploration Visions Mission, Titan Explorer, a follow-on to the Cassini-Huygens mission. TOAM would use a Titan polar orbiter and a lighter-than-air aerorover to investigate the surface and atmosphere of Titan. Astrobiology issues will be addressed though TOAM investigations including, for example: Distribution and composition of organics (atmospheric, aerosol, surface); Organic chemical processes, their chemical context and energy sources; and Seasonal variations and interactions of the atmosphere and surface. The TIDE instrument will perform in-situ analyses to obtain comprehensive and sensitive molecular and elemental assays of volatile organics in the atmosphere, oceans and surface. TIDE chemical analyses are conducted by a Gas Chromatograph-Ion Mobility Spectrometer (GC-IMS). This TIDE GC-IMS was a component of the mini-Cometary Ice and Dust Experiment (mini-CIDEX) developed for the chemical analysis of a cometary environment. Both the GC and helium IMS of mini-CIDEX have been further developed to better meet the analytical and operational requirements of the TOAM. application. A Micro-ElectroMechanical System (MEMS) GC and Mini-Cell helium IMS are under development to replace their respective mini-CIDEX components, providing similar or advanced analytical capabilities.

Kojiro, Daniel R.↗

Characterization of NU-LHT-4M Lunar Regolith Simulant Using Different Raman Configurations

As much as possible, structures to help sustain a long-term human presence on the moon will be constructed via in-situ resource utilization (ISRU) from lunar regolith. Various processes have been proposed to make lunar regolith-based construction materials, but one complication is that the lunar regolith is relatively complex in terms of composition and can vary quite significantly from one site to another. Some of these methods to make lunar regolith-based construction materials are quite sensitive to the composition and so in-situ methods for evaluating the composition of the lunar regolith could be critical. Various analytical instrumentation has been proposed for in-situ characterization of the composition of regolith on planetary bodies. Raman spectroscopy has been suggested and has some advantages over other in-situ techniques, such as potential for relatively high spatial resolution, direct determination of the mineralogy (while other methods may only infer the mineralogy), nondestructive analysis, relatively simple instrument configurations, and minimal sample preparation/handling. For example, Raman instrumentation has already been deployed in rover-based missions to Mars. Previously, we developed the Standoff Ultracompact Micro-Raman Sensor (SUCR), which is a portable Raman spectroscopy instrument capable to be integrated into a rover or onto a lander. Here, we present work on Raman spectroscopy measurements of NU-LHT-4M lunar simulant using three different Raman instruments with different configurations for collecting Raman data with the goal to explore the effect of these different configurations on the results, especially for use in a lunar environment.

Raman Spectroscopy↗

Numerical Investigation of Fluid Flow and Space Charge in Liquid Argon Time Projection Chamber (LArTPC) Detectors

Overview This project focused on developing a high-fidelity numerical framework to simulate the multiphysics environment within Liquid Argon Time Projection Chamber (LArTPC) detectors. The primary objective was to characterize the complex interplay between ion transport, background fluid dynamics, and electric field distortions—a critical factor for the calibration and sensitivity of next-generation High Energy Physics experiments, such as DUNE. Technical Achievements The research successfully yielded a hybrid numerical space-charge solver utilizing a Cell-Centered Finite Volume Method (FVM) for ion transport coupled with a Finite Element Method (FEM) for electric potential. Key accomplishments include: • Verification & Validation: The 3-D solver was rigorously verified against 1-D analytical solutions, demonstrating high numerical accuracy in predicting space-charge-induced field deviations. • Field Distortion Analysis: 3D simulations revealed that space charge effects introduce significant non-uniformities in the electric field. Critically, the research identified that background LAr flow velocities, when comparable to ion drift velocities, markedly exacerbate these distortions. • Technology Transfer: The resulting source code and comprehensive user manuals were successfully transferred to collaborators at Fermilab, providing a portable computational tool for the broader scientific community. Challenges and Future Directions While the space-charge solver achieved all performance metrics, the integrated fluid dynamics modeling encountered convergence challenges stemming from the extreme 200-fold disparity in length scales between the detector's 37 mm inlet pipes and the 8-meter global domain. To address this, the project has identified a clear technical pivot toward Hierarchical Geometric Adaptive Mesh Refinement (HG-AMR). By implementing an h-type refinement strategy with hanging nodes, future iterations of this solver will be capable of resolving localized high-gradient inlet flows without the prohibitive computational costs of regular grids. This advancement, combined with data-driven uncertainty quantification based on MicroBooNE-style calibration, will enable the precise modeling of detector responses in large-scale cryogenic environments where direct measurement remains difficult. Impact The computational tools developed under this award provide a foundation for enhancing the energy resolution and spatial reconstruction of noble liquid detectors. By bridging the gap between theoretical fluid dynamics and experimental field calibration, this work supports the DOE’s mission to advance the frontiers of neutrino physics and dark matter detection.

42 ENGINEERING↗

Mapping valence electron distributions with multipole density formalism using 4D-STEM

Recent advancement in aberration correction and detector technology opened a door to various applications using 4D-STEM, which yields a diffraction pattern for each scanning position within a crystal unit-cell in scanning transmission electron microscopy (STEM) and generates incredible amounts of data in momentum space. Currently 4D-STEM analysis relies on the center-of-mass of the diffraction patterns in electric field and charge density mapping. It only derives the total projected charge density and is limited to phase objects, e.g. extremely thin samples. Here, we propose a new analytical method to accurately map aspherical valence electron distributions with atom-centered multipolar functions formalism using the whole 4D-STEM dataset. We demonstrate that, with the full dynamical calculations for various sample thicknesses, the method is sensitive not only to the miniscule charge transfer, but also to the atomic site symmetry and aspherical electron orbitals. The process of the refinement is much more robust and reliable than quantitative convergent beam electron diffraction.

4D-STEM↗

Heat Transfer Analysis in Wire Bundles for Aerospace Vehicles

Design of wiring for aerospace vehicles relies on an understanding of "ampacity" which refers to the current carrying capacity of wires, either, individually or in wire bundles. Designers rely on standards to derate allowable current flow to prevent exceedance of wire temperature limits due to resistive heat dissipation within the wires or wire bundles. These standards often add considerable margin and are based on empirical data. Commercial providers are taking an aggressive approach to wire sizing which challenges the conventional wisdom of the established standards. Thermal modelling of wire bundles may offer significant mass reduction in a system if the technique can be generalized to produce reliable temperature predictions for arbitrary bundle configurations. Thermal analysis has been applied to the problem of wire bundles wherein any or all of the wires within the bundle may carry current. Wire bundles present analytical challenges because the heat transfer path from conductors internal to the bundle is tortuous, relying on internal radiation and thermal interface conductance to move the heat from within the bundle to the external jacket where it can be carried away by convective and radiative heat transfer. The problem is further complicated by the dependence of wire electrical resistivity on temperature. Reduced heat transfer out of the bundle leads to higher conductor temperatures and, hence, increased resistive heat dissipation. Development of a generalized wire bundle thermal model is presented and compared with test data. The steady state heat balance for a single wire is derived and extended to the bundle configuration. The generalized model includes the effects of temperature varying resistance, internal radiation and thermal interface conductance, external radiation and temperature varying convective relief from the free surface. The sensitivity of the response to uncertainties in key model parameters is explored using Monte Carlo analysis.

S L Rickman↗

Effects of non-thermal termolecular reactions on detonation development in hydrogen (H 2 )/methane (CH 4 ) - air mixtures

The binary fuel blend of H 2 /CH 4 is one of the most promising hydrogen-enriched hydrocarbon fuels in spark-ignition (SI) engines. Yet, the undesirable phenomenon of super-knock, which can severely and in-stantaneously damage an SI engine, limits its widespread adoption. Moreover, there is still a lack of con-sensus on the precise mechanism by which this phenomenon occurs i.e. via flame acceleration or spon-taneous ignition, despite numerous previous investigations. At the same time, recent studies [M. P. Burke, S. J. Klippenstein, Nat. Chem. 9 (2017) 1078 -1082, Y. Tao, A. W. Jasper, Y. Georgievskii, S. J. Klippenstein, R. Sivaramakrishnan, Proc. Combust. Inst. 38 (2021) 515-522] have demonstrated a high probability of occurrence of non-thermal reactions in premixed flames of such H 2 /CH 4 fuel blends with air due to the presence of non-trivial amounts of highly reactive radicals including H, O and OH apart from O 2 . The present study focuses on the evolution of an initial deflagration front to a detonation wave in H 2 /CH 4 - air mixtures under SI engine relevant conditions through fully resolved, constant volume 1D simulations with and without non-thermal reactivity. Non-thermal reactions were included in the macroscopic kinetics model as chemically termolecular reactions facilitated by the H + CH 3 and H + OH radical-radical recombination and the H + O 2 radical-molecule association reactions. Further, the nonthermal reactions result in a corresponding decrease in the reaction fluxes of the incipient recombination/association reactions. Therefore, an additional set of simulations were performed by applying corrections to the respective incipient recombination/association rate constants using the methodology demonstrated by Tao et al. [Y. Tao, A. W. Jasper, Y. Georgievskii, S. J. Klippenstein, R. Sivaramakrishnan, Proc. Combust. Inst. 38 (2021) 515-522]. Compared to the baseline case, the onset of spontaneous ignition in the end-gas region was observed to be delayed in the presence of non-thermal termolecular reactions. Concurrently, the developing detonation was observed to be significantly stronger. In contrast, applying corrections to the recombi-nation/association rate constants resulted in a completely different behavior. Specifically, detonation was observed to occur due to self acceleration of the primary flame in the absence of spontaneous ignition in the end-gas region. Sensitivity analysis was performed to quantify the effects of non-thermal reactions on the duration of heat release rate and thereby the mechanism of detonation formation. In addition, chemical explosive mode analysis (CEMA) was performed to identify the dominant species/reactions re-sponsible for the observed results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

New insights in the numerical reliability properties of existing Kalman filter implementations

The convergence properties of Kalman filter algorithms are investigated analytically. A theoretical error analysis is performed on four types of algorithms, as defined by Anderson and Moore (1979): (1) a conventional Kalman filter, (2) a square-root (SR) covariance filter, (3) the Chandrasekhar SR filter, and (4) an SR information filter. The derivations are given in detail, and numerical results for the flight-path reconstruction problem studied by Verhaegen (1987) are presented in tables and graphs. It is shown that error propagation in algorithms (1) and (2) is sensitive to the condition number of the innovation-signal covariance matrix and the spectral norm of the filter state-transition matrix, whereas other parameters are dominant in (3) and (4). Filter (2) is found to be the most reliable for the class of problems studied.

Verhaegen, M. H.↗

Sensitivity analysis of dynamic aeroelastic responses

This paper summarizes ongoing research on the sensitivity analysis of dynamic aeroelastic response of wings. Two approaches are being used to express the unsteady aerodynamic loads: (1) the frequency-domain approach, and (2) the state-space approach. The frequency-domain approach is demonstrated on a three-dimensional box wing and the state-space domain approach is demonstrated on a simple two-dimensional sectional model. Three different methods are used to find the sensitivities: (1) a purely finite difference approach, (2) a semi-analytical approach in which an analytical expression is used for calculating the sensitivity of an eigenvalue of the complex valued aeroelastic matrix, however, the derivatives of the components of the matrix are obtained using finite difference, and (3) a semi-analytic approach that differs from (2) in the sense that the sensitivity of the aerodynamic matrix is now obtained analytically. A good agreement is seen between the three sets of results. For the two-dimensional sectional model the results for the sensitivities of the flutter speed with respect to the various parameters are obtained.

Kapania, Rakesh K.↗

Advanced Stirling Convertor Heater Head Durability and Reliability Quantification

The National Aeronautics and Space Administration (NASA) has identified the high efficiency Advanced Stirling Radioisotope Generator (ASRG) as a candidate power source for long duration Science missions, such as lunar applications, Mars rovers, and deep space missions, that require reliable design lifetimes of up to 17 years. Resistance to creep deformation of the MarM-247 heater head (HH), a structurally critical component of the ASRG Advanced Stirling Convertor (ASC), under high temperatures (up to 850 C) is a key design driver for durability. Inherent uncertainties in the creep behavior of the thin-walled HH and the variations in the wall thickness, control temperature, and working gas pressure need to be accounted for in the life and reliability prediction. Due to the availability of very limited test data, assuring life and reliability of the HH is a challenging task. The NASA Glenn Research Center (GRC) has adopted an integrated approach combining available uniaxial MarM-247 material behavior testing, HH benchmark testing and advanced analysis in order to demonstrate the integrity, life and reliability of the HH under expected mission conditions. The proposed paper describes analytical aspects of the deterministic and probabilistic approaches and results. The deterministic approach involves development of the creep constitutive model for the MarM-247 (akin to the Oak Ridge National Laboratory master curve model used previously for Inconel 718 (Special Metals Corporation)) and nonlinear finite element analysis to predict the mean life. The probabilistic approach includes evaluation of the effect of design variable uncertainties in material creep behavior, geometry and operating conditions on life and reliability for the expected life. The sensitivity of the uncertainties in the design variables on the HH reliability is also quantified, and guidelines to improve reliability are discussed.

Krause, David L.↗