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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Where Is the Provenance? Ethical Replicability and Reproducibility in GIScience and Its Critical Applications

As replicability and reproducibility (R&R) crises develop within emerging convergent inquiry, ethical use of provenance information is central to the establishment and preservation of trust in critical applications of GIScience and geospatial technologies. Today large volumes of geospatial data are generated at high velocity from satellite sensors and unmanned aircraft systems, citizen sensors, geolocation-based data services, global navigation satellite systems, and so on. The extensive use of these data for applications such as disaster and humanitarian response raises the issue of R&R from competing perspectives of location privacy and geospatial data quality. Although geospatial data can be integrated and linked with contextual information to identify individuals’ movements, steps taken to ensure privacy can complicate the multiuser development of high-quality geospatial workflows. Provenance information as digital records of historical (retrospective) and potential future (prospective) geospatial processes is often overlooked, misunderstood, or inadequately addressed. We explore the relationship between provenance information, location privacy, and geospatial data quality in the context of R&R with a focus on disaster analytics. Here, we argue that in the era of big data and deep learning, GIScientists and associated institutions bear greater responsibility both for geospatial workflow quality and for location privacy. Given vastly heterogenous computational landscapes, we provide practical recommendations for ethically driven provenance and R&R research and development within the GIScience community and beyond.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2015

Discrete restricted four-body problem: Existence of proof of equilibria and reproducibility of periodic orbits

We propose the discrete-time restricted four-body problem (d-R4BP), which approximates the orbits of the restricted four-body problem (R4BP). The d-R4BP is given as a special case of the discrete-time chain regularization of the general N-body problem published in Minesaki. Moreover, we analytically prove that the d-R4BP yields the correct orbits corresponding to the elliptic relative equilibrium solutions of the R4BP when the three primaries form an equilateral triangle at any time. Such orbits include the orbit of a relative equilibrium solution already discovered by Baltagiannis and Papadakis. Until the proof in this work, there has been no discrete analog that preserves the orbits of elliptic relative equilibrium solutions in the R4BP. For a long time interval, the d-R4BP can precisely compute some stable periodic orbits in the Sun–Jupiter–Trojan asteroid–spacecraft system that cannot necessarily be reproduced by other generic integrators.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

REPRODUCING THE OBSERVED ABUNDANCES IN RCB AND HdC STARS WITH POST-DOUBLE-DEGENERATE MERGER MODELS-CONSTRAINTS ON MERGER AND POST-MERGER SIMULATIONS AND PHYSICS PROCESSES

The R Coronae Borealis (RCB) stars are hydrogen-deficient, variable stars that are most likely the result of He-CO WD mergers. They display extremely low oxygen isotopic ratios, {sup 16}O/{sup 18}O {approx_equal} 1-10, {sup 12}C/{sup 13}C {>=} 100, and enhancements up to 2.6 dex in F and in s-process elements from Zn to La, compared to solar. These abundances provide stringent constraints on the physical processes during and after the double-degenerate merger. As shown previously, O-isotopic ratios observed in RCB stars cannot result from the dynamic double-degenerate merger phase, and we now investigate the role of the long-term one-dimensional spherical post-merger evolution and nucleosynthesis based on realistic hydrodynamic merger progenitor models. We adopt a model for extra envelope mixing to represent processes driven by rotation originating in the dynamical merger. Comprehensive nucleosynthesis post-processing simulations for these stellar evolution models reproduce, for the first time, the full range of the observed abundances for almost all the elements measured in RCB stars: {sup 16}O/{sup 18}O ratios between 9 and 15, C-isotopic ratios above 100, and {approx}1.4-2.35 dex F enhancements, along with enrichments in s-process elements. The nucleosynthesis processes in our models constrain the length and temperature in the dynamic merger shell-of-fire feature as well as the envelope mixing in the post-merger phase. s-process elements originate either in the shell-of-fire merger feature or during the post-merger evolution, but the contribution from the asymptotic giant branch progenitors is negligible. The post-merger envelope mixing must eventually cease {approx}10{sup 6} yr after the dynamic merger phase before the star enters the RCB phase.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

A Reproducible Approach of Preparing High-Quality Overdoped Bi 2 Sr 2 CaCu 2 O 8+ δ Single Crystals by Oxygen Annealing and Quenching Method

Here, we report a reproducible approach in preparing high-quality overdoped Bi 2 Sr 2 CaCu 2 O 8+δ (Bi2212) single crystals by annealing Bi2212 crystals in high oxygen pressure followed by a fast quenching. High-quality overdoped and heavily overdoped Bi2212 single crystals are obtained by controlling the annealing oxygen pressure. Furthermore, we find that, beyond a limit of oxygen pressure that can achieve most heavily overdoped Bi2212 with a T c ~63 K, the annealed Bi2212 begins to decompose. This accounts for the existence of the hole-doping limit and thus the T c limit in the heavily overdoped region of Bi2212 by the oxygen annealing process. Our results provide a reliable way in preparing high-quality overdoped and heavily overdoped Bi2212 crystals that are important for studies of the physical properties, electronic structure and superconductivity mechanism of the cuprate superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2011

Reproducing neutrino effects on the matter power spectrum through a degenerate Fermi gas approach

Modifications on the predictions about the matter power spectrum based on the hypothesis of a tiny contribution from a degenerate Fermi gas (DFG) test-fluid to some dominant cosmological scenario are investigated. Reporting about the systematic way of accounting for all the cosmological perturbations, through the Boltzmann equation we obtain the analytical results for density fluctuation, δ, and fluid velocity divergence, θ, of the DFG. Small contributions to the matter power spectrum are analytically obtained for the radiation-dominated background, through an ultra-relativistic approximation, and for the matter-dominated and Λ-dominated eras, through a non-relativistic approximation. The results can be numerically reproduced and compared with those of considering non-relativistic and ultra-relativistic neutrinos into the computation of the matter power spectrum. Lessons concerning the formation of large scale structures of a DFG are depicted, and consequent deviations from standard ΛCDM predictions for the matter power spectrum (with and without neutrinos) are quantified.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Towards more transparent and reproducible omics studies through a common metadata checklist and data publications

Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated high-throughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies omics studies are becoming increasingly prevalent yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research,. These three essential steps require consistent generation, capture, and distribution of the metadata. To ensure transparency, facilitate data harmonization, and maximize reproducibility and usability of life sciences studies, we propose a simple common omics metadata checklist. The proposed checklist is built on the rich ontologies and standards already in use by the life sciences community. The checklist will serve as a common denominator to guide experimental design, capture important parameters, and be used as a standard format for stand-alone data publications. This omics metadata checklist and data publications will create efficient linkages between omics data and knowledge-based life sciences innovation and importantly, allow for appropriate attribution to data generators and infrastructure science builders in the post-genomics era. We ask that the life sciences community test the proposed omics metadata checklist and data publications and provide feedback for their use and improvement.

Kolker, Eugene↗
DOE OSTI2024

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Reproducible radiation-damage processes in proteins irradiated by intense x-ray pulses

X-ray free-electron lasers have enabled femtosecond protein nanocrystallography, a novel method to determine the structure of proteins. It allows time-resolved imaging of nanocrystals that are too small for conventional crystallography. The short pulse duration helps in overcoming the detrimental effects of radiation damage because x rays are scattered before the sample has been significantly altered. It has been suggested that, fortuitously, the diffraction process self-terminates abruptly once radiation damage destroys the crystalline order. Our calculations show that high-intensity x-ray pulses indeed trigger a cascade of damage processes in ferredoxin crystals, a particular metalloprotein of interest. However, we found that the damage process is initially not completely random. Correlations exist among the protein monomers, so that Bragg diffraction still occurs in the damaged crystals, despite significant atomic displacements. Our results show that the damage process is reproducible to a certain degree, which is potentially beneficial for the orientation step in single-molecule imaging.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Derivation of a realistic forcing term to reproduce the turbulent characteristics of round jets on the centerline

Turbulence forcing techniques are often required in the numerical simulation of statistically stationary turbulent flows. However, the existing forcing techniques are not based on physics, but rather arbitrary numerical methods that sustain the turbulent kinetic energy. In this work, a forcing technique is devised to reproduce the centerline turbulent characteristics of round jets in a triply periodic box. It is derived from the Navier-Stokes equations by applying aReynolds decompositionwith themean velocity of the axisymmetric jet. The result is an anisotropic linear forcing term, which is intended to be used in a three-dimensional box to create turbulence. Four direct numerical simulations with different Re λ have been performed with these forcing terms. We report the budget of the terms in the kinetic energy equation is very close to the experimental measurement on the centerline. The anisotropy, kinetic energy k, and dissipation rate ε of the simulations are also comparable to experimental values. Finally, the kinetic energy spectrum in the axial direction, $\phi(κ_1)$, is presented. With appropriate normalizations, the spectrum agrees well with the round jet spectrum on its centerline.

42 ENGINEERING↗
DOE OSTI2018

Enhanced Control and Reproducibility of Non-Neutral Plasmas

The simultaneous control of the density and particle number of non-neutral plasmas confined in Penning-Malmberg traps is demonstrated. Control is achieved by setting the plasma’s density by applying a rotating electric field while simultaneously fixing its axial potential via evaporative cooling. This novel method is particularly useful for stabilizing positron plasmas, as the procedures used to collect positrons from radioactive sources typically yield plasmas with variable densities and particle numbers; it also simplifies optimization studies that require plasma parameter scans. The reproducibility achieved by applying this technique to the positron and electron plasmas used by the ALPHA antihydrogen experiment at CERN, combined with other developments, contributed to a 10-fold increase in the antiatom trapping rate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0–1 Å −1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q -range to <0.5 Å −1 , but within the limits of experimental uncertainties the major features of the consensus SANS data were also consistent with prediction for all five proteins measured in H 2 O and in D 2 O. Thus, a foundation set of consensus SAS profiles has been obtained for benchmarking scattering-profile prediction from atomic coordinates. Additionally, two sets of SAXS data measured at different facilities to q > 2.2 Å −1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

DataFed: Towards Reproducible Research via Federated Data Management

The increasingly collaborative, globalized nature of scientific research combined with the need to share data and the explosion in data volumes present an urgent need for a scientific data management system (SDMS). An SDMS presents a logical and holistic view of data that greatly simplifies and empowers data organization, curation, searching, sharing, dissemination, etc. We present DataFed - a lightweight, distributed SDMS that spans a federation of storage systems within a loosely-coupled network of scientific facilities. Unlike existing SDMS offerings, DataFed uses high-performance and scalable user management and data transfer technologies that simplify deployment, maintenance, and expansion of DataFed. DataFed provides web-based and command-line interfaces to manage data and integrate with complex scientific workflows. DataFed represents a step towards reproducible scientific research by enabling reliable staging of the correct data at the desired environment.

Stansberry, Dale↗
DOE OSTI2016

Device Engineering Towards Improved Tin Sulfide Solar Cell Performance and Performance Reproducibility

As novel absorber materials are developed and screened for their photovoltaic (PV) properties, the challenge remains to rapidly test promising candidates in high-performing PV devices. There is a need to engineer new compatible device architectures, including the development of novel transparent conductive oxides and buffer layers. Here, we consider the two approaches of a substrate-style and a superstrate-style device architecture for novel thin-film solar cells. We use tin sulfide as a test absorber material. Upon device engineering, we demonstrate new approaches to improve device performance and performance reproducibility.

14 SOLAR ENERGY↗
DOE OSTI2022

Simple steps to enable reproducibility: culture conditions affecting Chlamydomonas growth and elemental composition

Even subtle modifications in growth conditions elicit acclimation responses affecting the molecular and elemental makeup of organisms, both in the laboratory and in natural habitats. Here, we systematically explored the effect of temperature, pH, nutrient availability, culture density, and access to CO 2 and O 2 in laboratory-grown algal cultures on growth rate, the ionome, and the ability to accumulate Fe. We found algal cells accumulate Fe in alkaline conditions, even more so when excess Fe is present, coinciding with a reduced growth rate. Using a combination of Fe-specific dyes, X-ray fluorescence microscopy, and NanoSIMS, we show that the alkaline-accumulated Fe was intracellularly sequestered into acidocalcisomes, which are localized towards the periphery of the cells. At high photon flux densities, Zn and Ca specifically over-accumulate, while Zn alone accumulates at low temperatures. The impact of aeration was probed by reducing shaking speeds and changing vessel fill levels; the former increased the Cu quota of cultures, the latter resulted in a reduction in P, Ca, and Mn at low fill levels. Trace element quotas were also affected in the stationary phase, where specifically Fe, Cu, and Zn accumulate. Cu accumulation here depends inversely on the Fe concentration of the medium. Individual laboratory strains accumulate Ca, P, and Cu to different levels. All together, we identified a set of specific changes to growth rate, elemental composition, and the capacity to store Fe in response to subtle differences in culturing conditions of Chlamydomonas, affecting experimental reproducibility. Accordingly, we recommend that these variables be recorded and reported as associated metadata.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

SU-E-QI-16: Reproducibility of Computed Tomography Quantitative Structural Features Using the FDA Thoracic Phantom Image Database

Purpose: To assess the reproducibility of quantitative structural features using images from the computed tomography thoracic FDA phantom database under different scanning conditions. Methods: Development of quantitative image features to describe lesion shape and size, beyond conventional RECIST measures, is an evolving area of research in need of benchmarking standards. Gavrielides et al. (2010) scanned a FDA-developed thoracic phantom with nodules of various Hounsfield units (HU) values, shapes and sizes close to vascular structures using several scanners and varying scanning conditions/parameters; these images are in the public domain. We tested six structural features, namely, Convexity, Perimeter, Major Axis, Minor Axis, Extent Mean and Eccentricity, to characterize lung nodules. Convexity measures lesion irregularity referenced to a convex surface. Previously, we showed it to have prognostic value in lung adenocarcinoma. The above metrics and RECIST measures were evaluated on three spiculated (8mm/-300HU, 12mm/+30HU and 15mm/+30HU) and two non-spiculated (8mm/+100HU and 10mm/+100HU) nodules (from layout 2) imaged at three different mAs values: 25, 100 and 200 mAs; on a Phillips scanner (16-slice Mx8000-IDT; 3mm slice thickness). The nodules were segmented semi-automatically using a commercial software tool; the same HU range was used for all nodules. Results: Analysis showed convexity having the lowest maximum coefficient of variation (MCV): 1.1% and 0.6% for spiculated and non-spiculated nodules, respectively, much lower compared to RECIST Major and Minor axes whose MCV were 10.1% and 13.4% for spiculated, and 1.9% and 2.3% for non-spiculated nodules, respectively, across the various mAs. MCVs were consistently larger for speculated nodules. In general, the dependence of structural features on mAs (noise) was low. Conclusion: The FDA phantom CT database may be used for benchmarking of structural features for various scanners and scanning conditions; we used only a small fraction of available data. Our feature convexity outperformed other structural features including RECIST measures.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-450: How Important Is a Reproducible Breath Hold for DIBH Breast Radiotherapy?

Purpose: Deep inspiration breath hold (DIBH) for left-sided breast cancer has been shown to reduce heart dose. Surface imaging helps to ensure accurate breast positioning, but does not guarantee a reproducible breath hold (BH) at DIBH treatments. We examine the effects of variable BH positions for DIBH treatments. Methods: Twenty-Five patients with free breathing (FB) and DIBH scans were reviewed. Four plans were created for each patient: 1) FB, 2) DIBH, 3) FB-DIBH – the DIBH plans were copied to the FB images and recalculated (image registration was based on breast tissue), and 4) P-DIBH – a partial BH with the heart shifted midway between the FB and DIBH positions. The FB-DIBH plans give “worst case” scenarios for surface imaging DIBH, where the breast is aligned by surface imaging but the patient is not holding their breath. Students t-tests were used to compare dose metrics. Results: The DIBH plans gave lower heart dose and comparable breast coverage versus FB in all cases. The FB-DIBH plans showed no significant difference versus FB plans for breast coverage, mean heart dose, or maximum heart dose (p >= 0.10). The mean heart dose differed between FB-DIBH and FB by < 2 Gy for all cases, the maximum heart dose differed by < 2 Gy for 21 cases. The P-DIBH plans showed significantly lower mean heart dose than FB (p = 0.01). The mean heart doses for the P-DIBH plans were < FB for 22 cases, the maximum dose < FB for 18 cases. Conclusions: A DIBH plan delivered to a FB patient set-up with surface imaging will yield similar dosimetry to a plan created and delivered FB. A DIBH plan delivered with even a partial BH can give reduced heart dose compared to FB techniques when the breast tissue is well aligned.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

TU-AB-BRA-06: Texture Feature Reproducibility Between PET/CT and PET/MR Imaging Modalities

Purpose: Radiomics involves the extraction of texture features from different imaging modalities with the purpose of developing models to predict patient treatment outcomes. The purpose of this study is to investigate texture feature reproducibility across [18F]FDG PET/CT and [18F]FDG PET/MR imaging in patients with primary malignancies. Methods: Twenty five prospective patients with solid tumors underwent clinical [18F]FDG PET/CT scan followed by [18F]FDG PET/MR scans. In all patients the lesions were identified using nuclear medicine reports. The images were co-registered and segmented using an in-house auto-segmentation method. Fifty features, based on the intensity histogram, second and high order matrices, were extracted from the segmented regions from both image data sets. One-way random-effects ANOVA model of the intra-class correlation coefficient (ICC) was used to establish texture feature correlations between both data sets. Results: Fifty features were classified based on their ICC values, which were found in the range from 0.1 to 0.86, in three categories: high, intermediate, and low. Ten features extracted from second and high-order matrices showed large ICC ≥ 0.70. Seventeen features presented intermediate 0.5 ≤ ICC ≤ 0.65 and the remaining twenty three presented low ICC ≤ 0.45. Conclusion: Features with large ICC values could be reliable candidates for quantification as they lead to similar results from both imaging modalities. Features with small ICC indicates a lack of correlation. Therefore, the use of these features as a quantitative measure will lead to different assessments of the same lesion depending on the imaging modality from where they are extracted. This study shows the importance of the need for further investigation and standardization of features across multiple imaging modalities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-J-122: Rectal Sparing Reproducibility in Prostate Cancer Patients Treated with Hydrogel Spacer and Proton Therapy

Purpose: Rectal hydrogel spacer has been shown to improve rectal sparing in prostate radiotherapy. The purpose of this study was to determine the reproducibility of rectal sparing throughout treatment in patients undergoing proton therapy. Methods: At our facility, prostate cancer patients are treated with pencil beam scanning proton therapy, utilizing an endorectal balloon (ERB) or rectal spacer hydrogel (Gel) “SpaceOAR” implant. All patients were treated with a full bladder and empty rectum (low residue diet and stool softeners). A quality assurance CT (QACT) was performed periodically throughout treatment to ensure rectal filling consistency and sparing in 41 patients treated with Gel. The treatment planning (TP) dose was calculated on each QACT and the rectum V90%, V75%, V65%, V50%, and V40% were recorded. QACT scans were acquired on day 0, week 1, week 3, and week 5. Results: 144 QACT scans were analyzed, each patient receiving 3–4 QACTs. Rectum V90% was within +/−1% of the TP dose in 70% of the QACTs and within +/−5% in 95% of scans. From previous data analyses, our ERB rectum V90% average is 6%. This value was used as an upper threshold for the Gel QACT analysis. 5 of the 41 patients (12%), corresponding to 7 QACTs, had a rectum V90% that exceeded 6% on one or more QACTs. However, the average rectal V90% measured over multiple QACTs never exceeded 6%. 55% of the QACTs had a rectum volume within 5cc of the TPCT volume, 68% were within 10cc. Conclusion: In this study, we have shown that a majority of our prostate patients can maintain consistent rectal sparing when treated with a hydrogel spacer. QACT rectal V90% exceeding our threshold was most often related to increased rectal filling and gas, which was addressed with improved dietary compliance and the intensification of stool softeners or laxatives.

60 APPLIED LIFE SCIENCES↗