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At least 1,495 records · Page 83
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

STEPS: A Grid Search Methodology for Optimized Peptide Identification Filtering of MS/MS Database Search Results

For bottom-up proteomics there are a wide variety of database searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection - referred to as STEPS - utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2023

Analytical estimation of the signal to noise ratio efficiency in axion dark matter searches using a Savitzky-Golay filter

The signal to noise ratio efficiency ϵ SNR in axion dark matter searches has been estimated using large-statistic simulation data reflecting the background information and the expected axion signal power obtained from a real experiment. This usually requires a lot of computing time even with the assistance of powerful computing resources. Employing a Savitzky-Golay filter for background subtraction, in this work, we estimated a fully analytical ϵ SNR without relying on large-statistic simulation data, but only with an arbitrary axion mass and the relevant signal shape information. Hence, our work can provide ϵ SNR using minimal computing time and resources prior to the acquisition of experimental data, without the detailed information that has to be obtained from real experiments. Axion haloscope searches have been observing the coincidence that the frequency independent scale factor ξ is approximately consistent with the ϵ SNR . This was confirmed analytically in this work, when the window length of the Savitzky-Golay filter is reasonably wide enough, i.e., at least 5 times the signal window.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

A Novel Technique Using a Protection Filter During Fibrin Sheath Removal for Implanted Venous Access Device Dysfunction

With the increased use of implanted venous access devices (IVADs) for continuous long-term venous access, several techniques such as percutaneous endovascular fibrin sheath removal, have been described, to maintain catheter function. Most standard techniques do not capture the stripped fibrin sheath, which is subsequently released in the pulmonary circulation and may lead to symptomatic pulmonary embolism. The presented case describes an endovascular technique which includes stripping, capture, and removal of fibrin sheath using a novel filter device. A 64-year-old woman presented with IVAD dysfunction. Stripping was performed using a co-axial snare to the filter to capture the fibrin sheath. The captured fragment was subsequently removed for visual and pathological verification. No immediate complication was observed and the patient was discharged the day of the procedure.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Application of a data assimilation method via an ensemble Kalman filter to reactive urea hydrolysis transport modeling

With growing importance of water resources in the world, remediations of anthropogenic contaminations due to reactive solute transport become even more important. A good understanding of reactive rate parameters such as kinetic parameters is the key to accurately predicting reactive solute transport processes and designing corresponding remediation schemes. For modeling reactive solute transport, it is very difficult to estimate chemical reaction rate parameters due to complex processes of chemical reactions and limited available data. To find a method to get the reactive rate parameters for the reactive urea hydrolysis transport modeling and obtain more accurate prediction for the chemical concentrations, we developed a data assimilation method based on an ensemble Kalman filter (EnKF) method to calibrate reactive rate parameters for modeling urea hydrolysis transport in a synthetic one-dimensional column at laboratory scale and to update modeling prediction. We applied a constrained EnKF method to pose constraints to the updated reactive rate parameters and the predicted solute concentrations based on their physical meanings after the data assimilation calibration. From the study results we concluded that we could efficiently improve the chemical reactive rate parameters with the data assimilation method via the EnKF, and at the same time we could improve solute concentration prediction. The more data we assimilated, the more accurate the reactive rate parameters and concentration prediction. The filter divergence problem was also solved in this study.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Numerical analysis of a time discretized method for nonlinear filtering problem with Lévy process observations

Abstract In this paper, we consider a nonlinear filtering model with observations driven by correlated Wiener processes and point processes. We first derive a Zakai equation whose solution is an unnormalized probability density function of the filter solution. Then, we apply a splitting-up technique to decompose the Zakai equation into three stochastic differential equations, based on which we construct a splitting-up approximate solution and prove its half-order convergence. Furthermore, we apply a finite difference method to construct a time semi-discrete approximate solution to the splitting-up system and prove its half-order convergence to the exact solution of the Zakai equation. Finally, we present some numerical experiments to demonstrate the theoretical analysis.

Mathematics↗
DOE OSTI2019

Wave-Vector Filtering Effect in a Novel Magnetic Nanostructure with Zero Average Magnetic Field

We report a theoretical investigation on wave-vector filtering (WVF) effect in a magnetic nanostructure, which can be experimentally realized by depositing ferromagnetic (FM) stripes on the surface of GaAs/Al{sub x}Ga{sub 1-x}As heterostructure. An appreciable WVF effect appears in this nanosystem. The WVF efficiency is associated with structural parameters of magnetic nanostructure. Therefore, such a device can be employed as a momentum filter for nanoelectronics device applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Reduction of amplified spontaneous emission noise using a statistical signal adaptive filter

This paper proposes a statistical signal adaptive filter (SSAF) based on adaptive total variation to reduce amplified spontaneous emission (ASE) noise in optical amplifiers, e.g. erbium doped fiber amplifiers. Non-return-to-zero on–off keying signal to noise ratio (SNR) is degraded by ASE noise. However, this can be improved by squeezing ASE using the proposed SSAF after photodetection to effectively remove the noise by analyzing the signal movement statistically. We obtained 4-dB SNR gain by reducing ASE beat noise compared with not applying SSAF. Simultaneous optical bandpass filter and SSAF application reduced the 2-dB power penalty for a 20-km optical link more than when only SSAF was used.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Effect of Addition of Other Acids into Butyric Acid on Selective Leaching of Zinc from Basic Oxygen Steelmaking Filter Cake

The selective leaching of zinc over iron from basic oxygen steelmaking (BOS) filter cake was investigated using mixtures of butyric acid with acetic and/or propionic acid, HCl, or H{sub 2}SO{sub 4}. The main focus was to assess the effects of other acids on the zinc and iron leaching in butyric acid. The results show that slight reduction of zinc leaching and increase in iron leaching may take place with addition of acetic and propionic acids, causing a minor decrease in the selectivity of zinc leaching over iron. Intermittent addition of H{sub 2}SO{sub 4} and HCl was required to control the pH to be not less than that of pure butyric acid solution. Overall, an excellent selectivity can be maintained with the butyric acid–other acid mixtures. The results demonstrate the feasibility to use raw butyric acid without purification or waste butyric acid containing other impurity acids for leaching of zinc from the BOS filter cake to be recycled. Using high content of H{sub 2}SO{sub 4} in leaching is not recommended because it has a more detrimental effect on the selectivity of zinc leaching and may cause deposition of CaSO{sub 4} in the leaching residue which may increase the SO{sub 2} or CO{sub 2} emission in later high-temperature recycling processes.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Effect of Coil Current on the Properties of Hydrogenated DLC Coatings Fabricated by Filtered Cathodic Vacuum Arc Technique

We successfully prepared hydrogenated DLC (a-C:H) with a thickness higher than 25 μm on stainless steel using a filtered cathode vacuum arc (FCVA) technique. The structural and mechanical properties of DLC were systematically analyzed using different methods such as x-ray photoelectron spectroscopy, Raman spectroscopy, scanning electron microscopy, Vickers hardness, nanohardness, and friction and wear tests. The effect of coil current on the arc voltage, ion current, and mechanical properties of resultant films was systematically investigated. The novelty of this study is the fabrication of DLC with Vickers hardness higher than 1500 HV, in the meanwhile with the thickness higher than 30 μm through varying the coil current with FCVA technique. The results indicated that the ion current, deposition rate, friction coefficient, and Vickers hardness of DLC were significantly affected by the magnetic field inside the filtered duct.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Nanoparticle treated stainless steel filters for metal vapor sequestration

The ability to sequester vapor phase radioactive compounds during industrial processes reduces the exposure of workers and the environment to dangerous radioactive materials. Nanomaterials have a lot of potential in this area because they typically demonstrate size- and shape-dependent properties with higher reactivity than bulk. This is due to the increased surface area-to-volume ratio and quantum size effects. In this report, we developed a gold nanomaterial-treated stainless steel filter, namely wools and coupons, that can be efficiently used for zinc vapor sequestration. Without nanoparticle modification, stainless steel coupons do not react or alloy with Zn. Gold nanomaterials were grown onto various stainless steel filters using solution chemistry that is amenable to scaling up. Materials were characterized by electron microscopy, inductively coupled plasma mass spectroscopy and dynamic light scattering before and after exposure to zinc vapors. X-ray diffraction, high-resolution transmission electron microscopy, energy dispersive x-ray spectroscopy mapping and ultraviolet-visible spectroscopy confirm the formation of gold-zinc alloys after Zn vapor exposure. Furthermore, the effect of surface topography on nanoparticle morphology, size and loading density were also investigated, and stainless steel surface defects were found to have an impact on the Au NP growth and subsequently Zn sequestration.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Measurements of effective actinides neutron capture cross sections in a cadmium-filtered epithermal neutron spectrum

In this work, a total of 20 actinide samples were irradiated in the Advanced Test Reactor (ATR) at Idaho National Laboratory (INL): 233 U (1), 235 U (1), 236 U (1), 238 U (1), 237 Np (2), 239 Pu (1), 240 Pu (1), 242 Pu (2), 244 Pu (2), 241 Am (2), 243 Am (2), 244 Cm (2), and 248 Cm (2). The samples were loaded in a basket containing a 1.1-mm thick cadmium filter. The presence of the filter drastically changes the neutron spectrum in the samples and accentuates the reaction rates in the resonance region. Isotopic ratios were determined using Multi-Collector Inductively Coupled Plasma Mass Spectrometry (MC-ICP-MS) that allowed inferring effective capture cross sections. Detailed best-estimate MCNP models of the experiment using ENDF/B-VII.0 nuclear data were developed to calculate the effective neutron cross sections and, subsequently, compare them with the cross sections inferred from experimental results.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering

Single-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge of current methods is their inability to identify and provide accurate quantitative information for low abundance proteins. Herein, we describe an ion mobility-enhanced mass spectrometry acquisition and peptide identification method, TIFF (Transferring Identification based on FAIMS Filtering), to improve the sensitivity and accuracy of label-free scProteomics. TIFF extends the ion accumulation times for peptide ions by filtering out singly charged ions. The peptide identities are assigned by a three-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells with >1,100 proteins consistently identified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during lipopolysaccharide stimulation and identified time-dependent proteome changes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Development and validation of an enhanced filtered drag model for simulating gas-solid fluidization of Geldart A particles in all flow regimes

Coarse-grid two-fluid simulation of gas-solid fluidized bed reactors based on the kinetic theory of granular flow exhibits a significant dependence on drag models, especially for Geldart A particles. Many drag models are available in the literature, which have been reported to work for different systems. This work focused on the evaluation of an enhanced filtered drag model along with other different drag models derived from different methods for three-dimensional two-fluid model simulations of gas-solid fluidized beds of Geldart A particles covering a broad range of fluidization regimes, including bubbling fluidization, turbulent fluidization, fast fluidization, and dilute phase transport regimes. Eight drag models were selected, which included five heterogeneous drag models and three homogeneous drag models. Comparison with the available experimental data demonstrates the need for modification of homogeneous drag models to account for the effect of mesoscale structures (i.e., bubbles and clusters). The enhanced filtered drag model and energy-minimization multi-scale (EMMS) drag models were found to achieve superior predictions in all fluidization regimes, while the other drag models were only capable of predicting certain fluidization regimes. Finally, the results of this work provide a guideline for choosing appropriate drag models for simulating Geldart A particles and suggestions on developing more reliable and general drag models applicable in all flow regimes.

42 ENGINEERING↗
DOE OSTI2026

A filter-dependent granular temperature model from large-scale CFD-DEM data

The computational study of strongly-coupled, gas–solid flows at scales relevant to most environmental and engineering applications requires the use of ‘coarse-grained’ methodologies such as the two-fluid model, particle-in-cell approach or the multiphase Reynolds Averaged Navier–Stokes equations. While these strategies enable computations at desirable length- and time-scales, they rely heavily on models to capture important flow physics that occur at scales smaller than the mesh. To date, the models that do exist are based on a limited set of flow conditions, such as very dilute particle phase. To this end, we leverage a large-scale repository of CFD-DEM data to develop filter-size dependent models for the mean variance in particle volume fraction, a quantity commonly used to assess the degree of clustering, and the granular temperature, a key quantity for accurately predicting gas–solid flows. In conclusion, because of its filter-size dependence, the granular temperature model can be directly translated to coarse-grained approaches and tied directly to grid size.

AMReX↗
DOE OSTI2017

Analyte-induced spectral filtering in femtosecond transient absorption spectroscopy

Here, we discuss the influence of spectral filtering by samples in femtosecond transient absorption measurements. Commercial instruments for transient absorption spectroscopy (TA) have become increasingly available to scientists in recent years and TA is becoming an established technique to measure the dynamics of photoexcited systems. Furthermore, we show that absorption of the excitation pulse by the sample can severely alter the spectrum and consequently the temporal pulse shape. This “spectral self-filtering” effect can lead to systematic errors and misinterpretation of data, most notably in concentration dependent measurements. Finally, the combination of narrow absorption peaks in the sample with ultrafast broadband excitation pulses is especially prone to this effect.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A filtering strategy for the numerical convergence of radiation transport through purely absorbing particle clouds

Radiation transport through particle clouds plays a major role in many engineering applications. Here in this paper, we study this problem by means of solving the radiative transport equation (RTE) on a Eulerian continuous domain. The particle clouds are generated through direct numerical simulation of Navier-Stokes equations coupled with Lagrangian particle transport at different Stokes numbers. We confirm the earlier observation noted in the literature that the solution to the RTE on Eulerian mesh diverges when the Eulerian mesh size is of the order of the particle diameter. This observation is often called the homogenization error stemming from relegation of number density onto the Eulerian domain. In order to circumvent this divergence problem, we propose a filtering strategy that spreads the information of the particles to the neighboring cells in a way that the representation of the particles remains the same even when the mesh size is smaller than that of the particle size. We show through our simulations that our filtering strategy solves the issue of homogenization error for the cases where the Beer-Bouger law is valid.

42 ENGINEERING↗
DOE OSTI2017

Identification of the suitable leaf margin for liver stereotactic body radiotherapy with flattening filter-free beams

The purpose of this study is to identify the suitable leaf margin for liver stereotactic body radiotherapy (SBRT) with flattening filter-free (FFF) beams, as compared with that with flattening filter (FF) beams. SBRT treatment planning for 10 patients with liver cancer was performed using 10-MV FFF and FF beams obtained from a Varian TrueBeam (Varian Medical Systems, Palo Alto, CA) linear accelerator. Each plan was generated with the leaf margin to the planning target volume (PTV) ranging from −3 to 5 mm. The prescription dose at D95 (dose covering 95% of the volume) was 48 Gy in 4 fractions to the PTV. The following dosimetric parameters were evaluated quantitatively: homogeneity index (HI), conformity index (CI), gradient index (GI), the normal liver receiving a dose greater than or equal to 20 Gy (V20), and the mean normal liver dose. The HI for FFF and FF beams increased as the leaf margin decreased. The leaf margins that achieved the best CI and GI were 0.1 and −0.3 mm for FFF beams, and 0.1 and −0.9 mm for FF beams. The liver V20 and the mean liver dose reached their minimum values at leaf margins of −0.8 and 0.0 mm for FFF beams, and −0.8 and 0.0 mm for FF beams. The suitable leaf margin for SBRT planning did not differ significantly for FFF and FF beams. Our data showed that, for both FFF and FF beams, a leaf margin of 0 or −1 mm was optimal for liver SBRT planning in terms of both target coverage and normal tissue sparing.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Measurement of the absolute neutron beam polarization from a supermirror polarizer and the absolute efficiency of a neutron spin rotator for the NPDGamma experiment using a polarized 3 He neutron spin-filter

Accurately measuring the neutron beam polarization of a high flux, large area neutron beam is necessary for many neutron physics experiments. The Fundamental Neutron Physics Beamline (FnPB) at the Spallation Neutron Source (SNS) is a pulsed neutron beam that was polarized with a supermirror polarizer for the NPDGamma experiment. The polarized neutron beam had a flux of ~10 9 neutrons per second per cm 2 and a cross sectional area of 10 x 12 cm 2 . The polarization of this neutron beam and the efficiency of a RF neutron spin rotator installed downstream on this beam were measured by neutron transmission through a polarized 3 He neutron spin-filter. The pulsed nature of the SNS enabled us to employ an absolute measurement technique for both quantities which does not depend on accurate knowledge of the phase space of the neutron beam or the 3 He polarization in the spin filter and is therefore of interest for any experiments on slow neutron beams from pulsed neutron sources which require knowledge of the absolute value of the neutron polarization. The polarization and spin-reversal efficiency measured were done for the NPDGamma experiment, which measures the parity violating γ-ray angular distribution asymmetry with respect to the neutron spin direction in the capture of polarized neutrons on protons. Finally, the experimental technique, results, systematic effects, and applications to neutron capture targets are discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗