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At least 991 records · Page 55

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.

42 ENGINEERING↗

Large-momentum effective theory’s asymptotic extrapolation vs the inverse problem

Large-momentum effective theory is a physics-guided systematic expansion to calculate light-cone parton distributions, including collinear (PDFs) and transverse-momentum-dependent ones, at any fixed momentum fraction 𝑥 within a range of [𝑥 min , 𝑥 max ]. It theoretically solves the ill-posed inverse problem that afflicts other theoretical approaches to collinear PDFs, such as short-distance factorizations. Recently, Dutrieux et al. raised practical concerns about whether current or even future lattice data will have sufficient precision in the subasymptotic correlation region to support an error-controlled extrapolation—and if not, whether it becomes an inverse problem where the relevant uncertainties cannot be properly quantified. While we agree that not all current lattice data have the desired precision to qualify for an asymptotic extrapolation, some calculations do, and more are expected in the future. We comment on the analysis and results in Dutrieux et al. and argue that a physics-based systematic extrapolation still provides the most reliable error estimates, even when the data quality is not ideal. In contrast, reframing the long-distance asymptotic extrapolation as a data-driven-only inverse problem with ad hoc mathematical conditioning could lead to unnecessarily conservative errors.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A new method for measuring refractory corrosion of ceramics in glass

Abstract Nuclear waste glass vitrification furnaces are lined with refractory ceramic blocks to contain the molten glass. The refractory liner is susceptible to corrosion and has a finite service lifetime. For this reason, predicting the refractory corrosion in contact with molten glass is integral to estimating melter service lifetime. Standardized laboratory tests varying time and temperature are commonly performed to estimate refractory material loss as a function of glass composition. These data are time and resource‐intensive to collect and are susceptible to considerable measurement error. In order to accelerate glass formulation and design for nuclear waste vitrification, methods are needed to increase laboratory‐scale throughput while maintaining data quality. In this work, a method to remove the residual glass from a corroded coupon using hydrofluoric acid is presented that accelerates the throughput of sample analysis while simultaneously facilitating more accurate measurements.

Amoroso, Jake W. [Savannah River National Laborato↗

CyanoCyc cyanobacterial web portal

CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial research and biotechnology communities. The 277 annotated cyanobacterial genomes currently in CyanoCyc are supplemented with computational inferences including predicted metabolic pathways, operons, protein complexes, and orthologs; and with data imported from external databases, such as protein features and Gene Ontology (GO) terms imported from UniProt. Five of the genome databases have undergone manual curation with input from more than a dozen cyanobacteria experts to correct errors and integrate information from more than 1,765 published articles. CyanoCyc has bioinformatics tools that encompass genome, metabolic pathway and regulatory informatics; omics data analysis; and comparative analyses, including visualizations of multiple genomes aligned at orthologous genes, and comparisons of metabolic networks for multiple organisms. CyanoCyc is a high-quality, reliable knowledgebase that accelerates scientists’ work by enabling users to quickly find accurate information using its powerful set of search tools, to understand gene function through expert mini-reviews with citations, to acquire information quickly using its interactive visualization tools, and to inform better decision-making for fundamental and applied research.

59 BASIC BIOLOGICAL SCIENCES↗

High-Resolution Scanning Coded-Mask-Based X-ray Multi-Contrast Imaging and Tomography

Near-field X-ray speckle tracking has been used in phase-contrast imaging and tomography as an emerging technique, providing higher contrast images than traditional absorption radiography. Most reported methods use sandpaper or membrane filters as speckle generators and digital image cross-correlation for phase reconstruction, which has either limited resolution or requires a large number of position scanning steps. Recently, we have proposed a novel coded-mask-based multi-contrast imaging (CMMI) technique for single-shot measurement with superior performance in efficiency and resolution compared with other single-shot methods. We present here a scanning CMMI method for the ultimate imaging resolution and phase sensitivity by using a coded mask as a high-contrast speckle generator, the flexible scanning mode, the adaption of advanced maximum-likelihood optimization to scanning data, and the multi-resolution analysis. Scanning CMMI can outperform other speckle-based imaging methods, such as X-ray speckle vector tracking, providing higher quality absorption, phase, and dark-field images with fewer scanning steps. Scanning CMMI is also successfully demonstrated in multi-contrast tomography, showing great potentials in high-resolution full-field imaging applications, such as in vivo biomedical imaging.

Qiao, Zhi (ORCID:0000000233928732)↗

Some experiences using wind-tunnel models in active control studies

A status report and review of wind tunnel model experimental techniques that have been developed to study and validate the use of active control technology for the minimization of aeroelastic response are presented. Modeling techniques, test procedures, and data analysis methods used in three model studies are described. The studies include flutter mode suppression on a delta-wing model, flutter mode suppression and ride quality control on a 1/30-size model of the B-52 CCV airplane, and an active lift distribution control system on a 1/22 size C-5A model.

Doggett, R. V., Jr.↗

Cycles till failure of silver-zinc cells with completing failures modes: Preliminary data analysis

One hundred and twenty nine cells were run through charge-discharge cycles until failure. The experiment design was a variant of a central composite factorial in five factors. Preliminary data analysis consisted of response surface estimation of life. Batteries fail under two basic modes; a low voltage condition and an internal shorting condition. A competing failure modes analysis using maximum likelihood estimation for the extreme value life distribution was performed. Extensive diagnostics such as residual plotting and probability plotting were employed to verify data quality and choice of model.

Sidik, S. M.↗

Lidar measurements of stratospheric ozone and intercomparisons and validation

A ground-based, high power differential absorption lidar (DIAL) system has been implemented to make long term, precise measurements or stratospheric ozone concentration profiles from about 20- to 50-km altitude. This lidar is located at an elevation of 2300 m in the San Gabriel Mountains, Southern California, and has been in operation since January 1988. Evaluation of the results obtained from this system has been provided through an intercomparison campaign, carried out during October/November 1988, and through long term comparison with SAGE II satellite measurements. This paper describes the implementation of the system and its operation, including the procedures for data analysis. Examples of ozone profiles measured, and intercomparisons with measurements made by other instruments, are presented; they show that the lidar is capable of producing high quality ozone measurements up to at least 45-km altitude.

Mcdermid, I. Stuart↗

An expert system/ion trap mass spectrometry approach for life support systems monitoring

Efforts to develop sensor and control system technology to monitor air quality for life support have resulted in the development and preliminary testing of a concept based on expert systems and ion trap mass spectrometry (ITMS). An ITMS instrument provides the capability to identify and quantitate a large number of suspected contaminants at trace levels through the use of a variety of multidimensional experiments. An expert system provides specialized knowledge for control, analysis, and decision making. The system is intended for real-time, on-line, autonomous monitoring of air quality. The key characteristics of the system, performance data and analytical capabilities of the ITMS instrument, the design and operation of the expert system, and results from preliminary testing of the system for trace contaminant monitoring are described.

Palmer, Peter T.↗

SpaceOps 1992: Proceedings of the Second International Symposium on Ground Data Systems for Space Mission Operations

The Second International Symposium featured 135 oral presentations in these 12 categories: Future Missions and Operations; System-Level Architectures; Mission-Specific Systems; Mission and Science Planning and Sequencing; Mission Control; Operations Automation and Emerging Technologies; Data Acquisition; Navigation; Operations Support Services; Engineering Data Analysis of Space Vehicle and Ground Systems; Telemetry Processing, Mission Data Management, and Data Archiving; and Operations Management. Topics focused on improvements in the productivity, effectiveness, efficiency, and quality of mission operations, ground systems, and data acquisition. Also emphasized were accomplishments in management of human factors; use of information systems to improve data retrieval, reporting, and archiving; design and implementation of logistics support for mission operations; and the use of telescience and teleoperations.

Source record↗

Analysis of Particle Image Velocimetry (PIV) Data for Acoustic Velocity Measurements

Acoustic velocity measurements were taken using Particle Image Velocimetry (PIV) in a Normal Incidence Tube configuration at various frequency, phase, and amplitude levels. This report presents the results of the PIV analysis and data reduction portions of the test and details the processing that was done. Estimates of lower measurement sensitivity levels were determined based on PIV image quality, correlation, and noise level parameters used in the test. Comparison of measurements with linear acoustic theory are presented. The onset of nonlinear, harmonic frequency acoustic levels were also studied for various decibel and frequency levels ranging from 90 to 132 dB and 500 to 3000 Hz, respectively.

Blackshire, James L.↗

On the Assessment and Uncertainty of Atmospheric Trace Gas Burden Measurements with High Resolution Infrared Solar Occultation Spectra from Space by the ATMOS Experiment

The Atmospheric Trace Molecule Spectroscopy (ATMOS) instrument is a high resolution Fourier transform spectrometer that measures atmospheric composition from low Earth orbit with infrared solar occultation sounding in the limb geometry. Following an initial flight in 1985, ATMOS participated in the Atmospheric Laboratory for Applications and Science (ATLAS) 1, 2, and 3 Space Shuttle missions in 1992, 1993, and 1994 yielding a total of 440 occultation measurements over a nine year period. The suite of more than thirty atmospheric trace gases profiled includes CO2, O3, N2O, CH4, H2O, NO, NO2, HNO3, HCl, HF, ClONO2, CCl3F, CCl2F2, CHF2Cl, and N2O5. The analysis method has been revised throughout the mission years culminating in the 'version 2' data set. The spectroscopic error analysis is described in the context of supporting the precision estimates reported with the profiles; in addition, systematic uncertainties assessed from the quality of the spectroscopic database are described and tabulated for comparisons with other experiments.

Abrams, M. C.↗

Improvement of the TOPEX and Jason Orbit Time Series: Precision Orbit Determination, Calibration, Validation and Improvement Through the Combined Reduction and Analysis of GPS, SLR, DORIS and Altimeter Data

Orbit error is a major component in the overall error budget of all altimeter satellite missions. Jason-I is no exception and a 1 cm radial orbit accuracy goal has been set, which represents a factor of two improvement over what is currently being achieved for TOPEX/Poseidon (TP). Our current analysis suggests this goal has been met and even improved upon, but the challenge is to be able to continually achieve this high accuracy, verify the performance and characterize and quantify the remaining errors over the lifetime of the mission. The computation, verification and error characterization of such high accuracy orbits requires the reduction and analysis of all available tracking data (GPS, SLR, DORIS and altimeter). Current analysis also indicates the history of TP orbits can be further improved employing new solution strategies developed and tested on Jason-I. Our research focuses on the calibration, validation and improvement of orbit accuracies using all available tracking data including altimetry. We will compute and distribute well centered Jason orbits with an accuracy of better than 1-cm in the radial component. In addition to the orbits themselves, a characterization of the orbit error will be distributed and accumulated as a time series of orbit performance metrics to track anomalies and trends. The long time series of orbit error characterization will enable a better understanding of the remaining orbit errors and its impact on the altimeter data analysis. As part of this research effort we are also significantly improving the current level of TP orbit accuracy, re-computing new high-accuracy TP orbits from the beginning of the TP mission and continuing into the future (as long as TP is healthy). Our funded research effort will result in a complete and consistent time series of improved orbits for both TP and Jason, significantly benefiting the long time series of altimeter data analysis and the TP/Jason dual mission. The resultant high accuracy orbits and the characterization of their error will allow further improvements to the accuracy and overall quality of the altimeter measurement time series making possible further strides in radar altimeter remote sensing.

Luthcke, Scott B.↗

Paradigm Shift in Data Content and Informatics Infrastructure Required for Generalized Constitutive Modeling of Materials Behavior

Materials property information such as composition and thermophysical/mechanical properties abound in the literature. Oftentimes, however, the corresponding response curves from which these data are determined are missing or at the very least difficult to retrieve. Further, the paradigm for collecting materials property information has historically centered on (1) properties for materials comparison/selection purposes and (2) input requirements for conventional design/analysis methods. However, just as not all materials are alike or equal, neither are all constitutive models (and thus design/ analysis methods) equal; each model typically has its own specific and often unique required materials parameters, some directly measurable and others indirectly measurable. Therefore, the type and extent of materials information routinely collected is not always sufficient to meet the current, much less future, needs of the materials modeling community. Informatics has been defined as the science concerned with gathering, manipulating, storing, retrieving, and classifying recorded information. A key aspect of informatics is its focus on understanding problems and applying information technology as needed to address those problems. The primary objective of this article is to highlight the need for a paradigm shift in materials data collection, analysis, and dissemination so as to maximize the impact on both practitioners and researchers. Our hope is to identify and articulate what constitutes "sufficient" data content (i.e., quality and quantity) for developing, characterizing, and validating sophisticated nonlinear time- and history-dependent (hereditary) constitutive models. Likewise, the informatics infrastructure required for handling the potentially massive amounts of materials data will be discussed.

Arnold, S. M.↗

How Does Mediterranean Basin's Atmosphere Become Weak Moisture Source During Negative Phase of NAO: Use of AIRS, AMSR, TOVS, & TRMM Satellite Datasets Over Last Two NAO Cycles to Examine Governing Controls on E-P

The Mediterranean Sea is a noted 'concentration" basin in that it almost continuously exhibits positive evaporation minus precipitation (E - P ) properties -- throughout the four seasons and from one year to the next. Nonetheless, according to the ECMWF Era-40 48-year (1958-2005) climate reanalysis dataset, for various phases of the North Atlantic Oscillation (NAO) when the pressure gradient between Portugal and Iceland becomes either very relaxed (large negative NAO-Index) or in transition (small positive or negative NAO-Index), the atmospheric moisture source properties of the basin become weak, at times even reversed for several months (i.e., negative E - P). This behavior poses numerous questions concerning how and why these events occur. Moreover, it begs the question of what it would take for the basin to reach its tipping point in which P would exceed E throughout the rainy season (some six months) on an annually persistent basis -- and the sea would possibly transform to a recurring "dilution" basin. This talk investigates these questions by: (1) establishing over a period from 1979 to present, based on detailed analyses of satellite retrieval products from a combination of NASA-AQUA, NOAA-LEO, NASA/JAXA Scatterometer, and NASA-TRMM platforms, plus additional specialized satellite data products and ancillary meteorological datasets, the actual observation-based behavior of E - P, (2) diagnosing the salient physical and meteorological mechanisms that lead to the weaker E - P events during the analysis period, partly based on analyzing surface and upper air data at discrete stations in the western and eastern Mediterranean -- while at the same time evaluating the quality of the ERA-40 data over this same time period, (3) conducting GCM and high-resolution regional modeling experiments to determine if perturbed but realistic meteorological background conditions could maintain Mediterranean as a "dilution" basin through the October to March rainy season on annually recurring basis, and (4) investigating how such conditions might modify important internal and external climatic processes known to be closely related to the dynamical, thermal, and hydrological properties of the basin (e.g., drought frequency over Iberian peninsula, rainfall accumulation within Sahel, alteration of Levantine branch of east-west aligned open thermohaline cell, and modification of warm-salty intermediate flow through Gibraltar straight into North Atlantic).

Smith, Eric A.↗

Guide to Flow Measurement for Electric Propulsion Systems

In electric propulsion (EP) systems, accurate measurement of the propellant mass flow rate of gas or liquid to the thruster and external cathode is a key input in the calculation of thruster efficiency and specific impulse. Although such measurements are often achieved with commercial mass flow controllers and meters integrated into propellant feed systems, the variability in potential propellant options and flow requirements amongst the spectrum of EP power regimes and devices complicates meter selection, integration, and operation. At the direction of the Committee on Standards for Electric Propulsion Testing, a guide was jointly developed by members of the electric propulsion community to establish a unified document that contains the working principles, methods of implementation and analysis, and calibration techniques and recommendations on the use of mass flow meters in laboratory and spacecraft electric propulsion systems. The guide is applicable to EP devices of all types and power levels ranging from microthrusters to high-power ion engines and Hall effect thrusters. The establishment of a community standard on mass flow metering will help ensure the selection of the proper meter for each application. It will also improve the quality of system performance estimates by providing comprehensive information on the physical phenomena and systematic errors that must be accounted for during the analysis of flow measurement data. This paper will outline the standard methods and recommended practices described in the guide titled "Flow Measurement for Electric Propulsion Systems."

spacecraft electric propulsion (EP) systems↗

Recommended Practices in Thrust Measurements

Accurate, direct measurement of thrust or impulse is one of the most critical elements of electric thruster characterization, and one of the most difficult measurements to make. The American Institute of Aeronautics and Astronautics has started an initiative to develop standards for many important measurement processes in electric propulsion, including thrust measurements. This paper summarizes recommended practices for the design, calibration, and operation of pendulum thrust stands, which are widely recognized as the best approach for measuring micro N- to mN-level thrust and micro Ns-level impulse bits. The fundamentals of pendulum thrust stand operation are reviewed, along with its implementation in hanging pendulum, inverted pendulum, and torsional balance configurations. Methods of calibration and recommendations for calibration processes are presented. Sources of error are identified and methods for data processing and uncertainty analysis are discussed. This review is intended to be the first step toward a recommended practices document to help the community produce high quality thrust measurements.

microthrusters↗

Satellite Ocean Colour: Current Status and Future Perspective

Spectrally resolved water-leaving radiances (ocean colour) and inferred chlorophyll concentration are key to studying phytoplankton dynamics at seasonal and inter-annual scales, for a better understanding of the role of phytoplankton in marine biogeochemistry; the global carbon cycle; and the response of marine ecosystems to climate variability, change and feedback processes. Ocean colour data also have a critical role in operational observation systems monitoring coastal eutrophication, harmful algal blooms, and sediment plumes. The contiguous ocean-colour record reached 21 years in 2018; however, it is comprised of a number of one-off missions such that creating a consistent time-series of ocean-colour data requires merging of the individual sensors (including MERIS, Aqua-MODIS, SeaWiFS, VIIRS, and OLCI) with differing sensor characteristics, without introducing artefacts. By contrast, the next decade will see consistent observations from operational ocean colour series with sensors of similar design and with a replacement strategy. Also, by 2029 the record will start to be of sufficient duration to discriminate climate change impacts from natural variability, at least in some regions. This paper describes the current status and future prospects in the field of ocean colour focusing on large to medium resolution observations of oceans and coastal seas. It reviews the user requirements in terms of products and uncertainty characteristics and then describes features of current and future satellite ocean-colour sensors, both operational and innovative. The key role of in situ validation and calibration is highlighted as are ground segments that process the data received from the ocean-colour sensors and deliver analysis-ready products to end-users. Example applications of the ocean-colour data are presented, focusing on the climate data record and operational applications including water quality and assimilation into numerical models. Current capacity building and training activities pertinent to ocean colour are described and finally a summary of future perspectives is provided.

ocean colour↗