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Results for “Reproducibility”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

SU-C-19A-04: Evaluation of Patient Positioning Reproducibility with Three Supine Breast Boards

Purpose: To evaluate positioning reproducibility using three commercially available breast board immobilization systems for whole breast radiation therapy. Methods: Weekly pre-treatment cone beam CT images from 18 free-breathing breast radiotherapy patients, each immobilized with one of three breast boards, were retrospectively registered to the planning CT. Relative shifts between breast tissue and sternum/chest wall (CW), and breast tissue and spine compared to planning CT were obtained for each board. Positioning reproducibility, inter-patient variation and intra-patient variation were evaluated by group mean (M), standard deviation of group mean (Σ) and standard deviation of random shift (σ). Margins to account for setup uncertainties were calculated based on shift uncertainties in x, y, and z directions. Results: For breast positioning relative to sternum/CW, the average shift from planned positioning was 4.5mm (95% CI: 3.5 – 5.3), 3.3mm (CI: 2.9 - 3.8) and 2.6mm (CI: 1.8 - 3.5) for Breast Boards I, II, and III, respectively. The respective numbers for breast positioning relative to spine were 7.2 mm (CI: 4.1 – 10.3), 6.4 mm (CI: 4.3 – 8.3) and 4.3 mm (CI: 2.5 – 6.2). Localizing to the sternum/CW as a surrogate for the breast tissue, margins for setup uncertainties were 5.7mm, 5.5mm, and 6.0mm for Breast Board I, 5.0mm, 4.0mm and 4.3mm for Breast Board II, and 3.8mm, 3.5mm and 4.8mm for Breast Board III, in the lateral, anterior/posterior, and superior/inferior directions, respectively. Conclusion: Better patient positioning reproducibility was observed with Boards II and III compared to Board I. Inter- and intra-patient set-up uncertainties were also improved with Boards II and III, which requires smaller PTV margins. Independent of breast board, breast cancer patient positioning to the sternum/CW is a better surrogate than the spine. Our findings have potential dosimetric consequences from set-up uncertainties when employing IMRT or proton treatments, and further analyses are on-going.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-J-243: Reproducibility of Radiomics Features Through Different Voxel Discretization Levels in F18-FDG PET Images of Cervical Cancer

Purpose: Site-specific investigations of the role of Radiomics in cancer diagnosis and therapy are needed. We report of the reproducibility of quantitative image features over different discrete voxel levels in PET/CT images of cervical cancer. Methods: Our dataset consisted of the pretreatment PET/CT scans from a cohort of 76 patients diagnosed with cervical cancer, FIGO stage IB-IVA, age range 31–76 years, treated with external beam radiation therapy to a dose range between 45–50.4 Gy (median dose: 45 Gy), concurrent cisplatin chemotherapy and MRI-based Brachytherapy to a dose of 20–30 Gy (median total dose: 28 Gy). Two board certified radiation oncologists delineated Metabolic Tumor volume (MTV) for each patient. Radiomics features were extracted based on 32, 64, 128 and 256 discretization levels (DL). The 64 level was chosen to be the reference DL. Features were calculated based on Co-occurrence (COM), Gray Level Size Zone (GLSZM) and Run-Length (RLM) matrices. Mean Percentage Differences (Δ) of features for discrete levels were determined. Normality distribution of Δ was tested using Kolomogorov - Smirnov test. Bland-Altman test was used to investigate differences between feature values measured on different DL. The mean, standard deviation and upper/lower value limits for each pair of DL were calculated. Interclass Correlation Coefficient (ICC) analysis was performed to examine the reliability of repeated measures within the context of the test re-test format. Results: 3 global and 5 regional features out of 48 features showed distribution not significantly different from a normal one. The reproducible features passed the normality test. Only 5 reproducible results were reliable, ICC range 0.7 – 0.99. Conclusion: Most of the radiomics features tested showed sensitivity to voxel level discretization between (32 – 256). Only 4 GLSZM, 3 COM and 1 RLM showed insensitivity towards mentioned discrete levels.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-677: Reproducibility of Production of Ionization Chambers

Purpose: To compare the reproducibility of the production of several cylindrical and plane-parallel chambers popular in Poland in terms of a calibration coefficient. Methods: The investigation was performed for PTW30013 (20 chambers), 30001 (10 chambers), FC65-G (17 chambers) cylindrical chambers and for PPC05 (14 chambers), Roos 34001 (8 chambers) plane parallel chambers. The calibration factors were measured at the same accredited secondary standard laboratory in terms of a dose to water. All the measurements were carried out at the same laboratory, by the same staff, in accordance with the same IAEA recommendations. All the chambers were calibrated in the Co60 beam. Reproducibility was described in terms of the mean value, its standard deviation and the ratio of the maximum and minimum value of calibration factors for each set of chambers separately. The combined uncertainty budged (1SD) calculated according to the IAEA-TECDOC-1585 of the calibration factor was of 0.25%. Results: The calibration coefficients for PTW30013, 30001, and FC65-G chambers were 5.36±0.03, 5.28±0.06, 4.79±0.015 nC/Gy respectively and for PPC05, and Roos chambers were 59±2, 8.3±0.1 nC/Gy respectively. The maximum/minimum ratio of calibration factors for PTW30013, 30001, FC65-G, and for PPC05, Roos chambers were 1.03, 1.03, 1.01, 1.14 and 1.03 respectively. Conclusion: The production of all ion chambers was very reproducible except the Markus type PPC05 for which the ratio of maximum/minimum calibration coefficients of 1.14 was obtained.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

SU-F-I-31: Reproducibility of An Automatic Exposure Control Technique in the Low-Dose CT Scan of Cardiac PET/CT Exams

Purpose: Two separate low-dose CT scans are usually performed for attenuation correction of rest and stress N-13 ammonia PET/CT myocardial perfusion imaging (PET/CT). We utilize an automatic exposure control (AEC) technique to reduce CT radiation dose while maintaining perfusion image quality. Our goal is to assess the reproducibility of displayed CT dose index (CTDI) on same-day repeat CT scans (CT1 and CT2). Methods: Retrospectively, we reviewed CT images of PET/CT studies performed on the same day. Low-dose CT utilized AEC technique based on tube current modulation called Smart-mA. The scan parameters were 64 × 0.625mm collimation, 5mm slice thickness, 0.984 pitch, 1-sec rotation time, 120 kVp, and noise index 50 with a range of 10–200 mA. The scan length matched with PET field of view (FOV) with the heart near the middle of axial FOV. We identified the reference slice number (RS) for an anatomical landmark (carina) and used it to estimate axial shift between two CTs. For patient size, we measured an effective diameter on the reference slice. The effect of patient positioning to CTDI was evaluated using the table height. We calculated the absolute percent difference of the CTDI (%diff) for estimation of the reproducibility. Results: The study included 168 adults with an average body-mass index of 31.72 ± 9.10 (kg/m{sup 2}) and effective diameter was 32.72 ± 4.60 cm. The average CTDI was 1.95 ± 1.40 mGy for CT1 and 1.97 ± 1.42mGy for CT2. The mean %diff was 7.8 ± 6.8%. Linear regression analysis showed a significant correlation between the table height and %diff CTDI. (r=0.82, p<0.001) Conclusion: We have shown for the first time in human subjects, using two same-day CT images, that the AEC technique in low-dose CT is reproducible within 10% and significantly depends on the patient centering.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-J-131: Reproducibility of Positioning Error Due to Temporarily Indwelled Urethral Catheter for Urethra-Sparing Prostate IMRT

Purpose: The purpose of this study was to prospectively assess the reproducibility of positioning errors due to temporarily indwelled catheter in urethra-sparing image-guided (IG) IMRT. Methods: Ten patients received urethra-sparing prostate IG-IMRT with implanted fiducials. After the first CT scan was performed in supine position, 6-Fr catheter was indwelled into urethra, and the second CT images were taken for planning. While the PTV received 80 Gy, 5% dose reduction was applied for the urethral PRV along the catheter. Additional CT scans were also performed at 5th and 30th fraction. Positions of interests (POIs) were set on posterior edge of prostate at beam isocenter level (POI1) and cranial and caudal edge of prostatic urethra on the post-indwelled CT images. POIs were copied into the pre-indwelled, 5th and 30th fraction’s CT images after fiducial matching on these CT images. The deviation of each POI between pre- and post-indwelled CT and the reproducibility of prostate displacement due to catheter were evaluated. Results: The deviation of POI1 caused by the indwelled catheter to the directions of RL/AP/SI (mm) was 0.20±0.27/−0.64±2.43/1.02±2.31, respectively, and the absolute distances (mm) were 3.15±1.41. The deviation tends to be larger if closer to the caudal edge of prostate. Compared with the pre-indwelled CT scan, a median displacement of all POIs (mm) were 0.3±0.2/2.2±1.1/2.0±2.6 in the post-indwelled, 0.4±0.4/3.4±2.1/2.3±2.6 in 5th, and 0.5±0.5/1.7±2.2/1.9±3.1 in 30th fraction’s CT scan with a similar data distribution. There were 6 patients with 5-mm-over displacement in AP and/or CC directions. Conclusion: Reproducibility of positioning errors due to temporarily indwelling catheter was observed. Especially in case of patients with unusually large shifts by indwelling catheter at the planning process, treatment planning should be performed by using the pre-indwelled CT images with transferred contour of the urethra identified by post-indwelled CT images.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-55: Reproducibility of Interstitial HDR Brachytherapy Plans

Purpose: Treating gynecological cancers with interstitial high-dose-rate (HDR) brachytherapy requires precise reconstruction of catheter positions to obtain accurate dosimetric plans. In this study, we investigated the degree of reproducibility of dosimetric plans for Syed HDR brachytherapy. Methods: We randomly selected five patients having cervix-vaginal cancer who were recently treated in our clinic with interstitial HDR brachytherapy with a prescription dose of 25–30 Gy in five fractions. Interstitial needles/catheters were placed under fluoroscopic guidance and intra-operative 3T MRI scan was performed to confirm the desired catheter placement for adequate target volume coverage. A CT scan was performed and fused with the MRI for delineating high-risk CTV (HR-CTV), intermediate-risk CTV (IR-CTV) and OARs. HDR treatment plans were generated using Oncentra planning software. A single plan was used for all five fractions of treatment for each patient. For this study, we took the original clinical plan and removed all the reconstructed catheters from the plan keeping the original contours unchanged. Then, we manually reconstructed all the catheters and entered the same dwell time from the first original clinical plan. The dosimetric parameters studied were: D90 for HR-CTV and IR-CV, and D2cc for bladder, rectum, sigmoid and bowel. Results: The mean of absolute differences in dosimetric coverage (D90) were (range): 1.3% (1.0–2.0%) and 2.0% (0.9–3.6%) for HR-CTV and IR-CTV, respectively. In case of OARs, the mean of absolute variations in D2cc were (range): 4.7% (0.7–8.9%) for bladder, 1.60% (0.3–3.2%) for rectum, 1.6% (0–3.9%) for sigmoid, and 1.8% (0–5.1%) for bowel. Conclusion: Overall, the reproducibility of interstitial HDR plans was within clinically acceptable limit. Observed maximum variation in D2cc for bladder. If number of catchers and dwell points were relatively low or any one catheter was heavily loaded, then reproducibility of the plan was more sensitive to the accuracy of catheter reconstruction.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Breaking the reproducibility barrier with standardized protocols for plant–microbiome research

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Novak, Vlastimil↗
DOE OSTI2017

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers

Here we present Singularity Hub, a framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers. Singularity containers make it possible for scientists and developers to package reproducible software, and Singularity Hub adds automation to this workflow by building, capturing metadata for, visualizing, and serving containers programmatically. Our novel metrics, based on custom filters of content hashes of container contents, allow for comparison of an entire container, including operating system, custom software, and metadata. First we will review Singularity Hub’s primary use cases and how the infrastructure has been designed to support modern, common workflows. Next, we conduct three analyses to demonstrate build consistency, reproducibility metric and performance and interpretability, and potential for discovery. This is the first effort to demonstrate a rigorous assessment of measurable similarity between containers and operating systems. We provide these capabilities within Singularity Hub, as well as the source software singularity-python that provides the underlying functionality. Singularity Hub is available at https://singularity-hub.org, and we are excited to provide it as an openly available platform for building, and deploying scientific containers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

The Need for Reproducibility

The purpose of this presentation is to consider issues of reproducibility, specifically it determines whether bitwise reproducible computation is possible, if computational research in DOE improves its publication process, and if reproducible results can be achieved apart from the peer review process?

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2020

Reproducibility and Optimization Techniques for Evaluated Data in the Resolved Resonance Region [Slides]

This presentation discusses the experimental setup input parameters that are basic quantities for reproducibility. The goal is to increase quality of the evaluated data and decrease time needed for an evaluation. Full reproducibility should be achieved efficiently by including any type of constraints in the optimization procedure and to improve computational time to reach convergence. The goal of an automated reproducibility aligns to the goal of “certified” evaluated data, i.e., defined by a well-defined metric.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2013

Reproducibility in a multiprocessor system

Fixing a problem is usually greatly aided if the problem is reproducible. To ensure reproducibility of a multiprocessor system, the following aspects are proposed; a deterministic system start state, a single system clock, phase alignment of clocks in the system, system-wide synchronization events, reproducible execution of system components, deterministic chip interfaces, zero-impact communication with the system, precise stop of the system and a scan of the system state.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A reproducibility study of "Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space"

Nigam et al. reported a genetic algorithm (GA) utilizing the SELFIES representation and also propose an adaptive, neural network-based penalty that is supposed to improve the diversity of the generated molecules. The main claims of the paper are that this GA outperforms other generative techniques (as measured by the penalized logP) and that a neural network-based adaptive penalty increases the diversity of the generated molecules. In this work, we investigated the reproducibility of their claims. Overall, we were able to reproduce comparable results using the SELFIES-based GA, but mostly by exploiting deficiencies of the (easily optimizable) fitness function (i.e., generating long, sulfur containing chains). In addition, we reproduce results showing that the discriminator can be used to bias the generation of molecules to ones that are similar to the reference set. Lastly, we attempted to quantify the evolution of the diversity, understand the influence of some hyperparameters, and propose improvements to the adaptive penalty.

Jablonka, Kevin Maik↗
DOE OSTI2024

Image-based modeling of coupled electro-chemo-mechanical behavior of Li-ion battery cathode using an interface-modified reproducing kernel particle method

Abstract An interface-modified reproducing kernel particle method (IM-RKPM) is introduced in this work to allow for a direct model construction from image pixels of heterogeneous polycrystalline Li-ion battery microstructures. The interface-modified reproducing kernel (IM-RK) approximation is constructed through scaling of a kernel function by a regularized distance function in conjunction with strategic placement of interface node locations. This leads to RK shape functions with either weak or strong discontinuities across material interfaces, suitable for modeling various interface mechanics. With the placement of a triple junction node and distance-based scaling of kernel functions, the resulting IM-RK shape function also possesses proper discontinuities at the triple junctions. This IM-RK approximation effectively remedies the well-known Gibb’s oscillation in the smooth approximation of discontinuities. Different from the conventional meshfree approaches for interface discontinuities, this IM-RK approach is done without additional degrees of freedom associated with the enrichment functions, and it is formulated with the standard procedures in the RK shape function construction. This work focuses on identifying the accuracy and convergence properties of IM-RKPM for modeling the coupled electro-chemo-mechanical system. A linear patch test is formulated and numerically tested for the electro-chemo-mechanical coupled problem with a Butler–Volmer boundary condition representing the physical conditions in Li-ion battery microstructures. This is followed by verification of the optimal rates of convergence of IM-RKPM for solving the coupled problem with higher order solutions. The image-based modeling of Li-ion battery microstructures in the numerical examples demonstrates the applicability of the proposed method to realistic Li-ion battery materials modeling.

25 ENERGY STORAGE↗
DOE OSTI2017

Reproducible, Component-based Modeling with TopoFlow, A Spatial Hydrologic Modeling Toolkit

Modern geoscientists have online access to an abundance of different data sets and models, but these resources differ from each other in myriad ways and this heterogeneity works against interoperability as well as reproducibility. The purpose of this paper is to illustrate the main issues and some best practices for addressing the challenge of reproducible science in the context of a relatively simple hydrologic modeling study for a small Arctic watershed near Fairbanks, Alaska. This study requires several different types of input data in addition to several, coupled model components. All data sets, model components and processing scripts (e.g. for preparation of data and figures, and for analysis of model output) are fully documented and made available online at persistent URLs. Similarly, all source code for the models and scripts is open-source, version controlled and made available online via GitHub. Each model component has a Basic Model Interface (BMI) to simplify coupling and its own HTML help page that includes a list of all equations and variables used. The set of all model components (TopoFlow) has also been made available as a Python package for easy installation. Three different graphical user interfaces for setting up TopoFlow runs are described, including one that allows model components to run and be coupled as web services.

58 GEOSCIENCES↗
DOE OSTI2024

A quasi-meshfree method for constructing boundary-aware reproducing bases on geometrically complex domains using manifold geodesics

In many applications, physical domains are geometrically complex making it challenging to perform coarse-scale approximation. A defeaturing process is often used to simplify the domain in preparation for approximation and analysis at the coarse scale. In this paper, a methodology is presented for constructing a coarse-scale reproducing basis on geometrically complex domains given an initial fine-scale mesh of the fully featured domain. The initial fine-scale mesh can be of poor quality and extremely refined. The construction of the basis functions begins with a coarse-scale covering of the domain and generation of weighting functions with local support. Manifold geodesics are used to define distances within the local support for general applicability to non-convex domains. Conventional moving least squares is used to construct the coarse-scale reproducing basis. Applications in quasi-interpolation and linear elasticity are presented.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Towards an Open (Data) Science Analytics-Hub for Reproducible Multi-Model Climate Analysis at Scale

Open Science is key to future scientific research and promotes a deep transformation in the whole scientific research process encouraging the adoption of transparent and collaborative scientific approaches aimed at knowledge sharing. Open Science is increasingly gaining attention in the current and future research agenda worldwide. To effectively address Open Science goals, besides Open Access to results and data, it is also paramount to provide tools or environments to support the whole research process, in particular the design, execution and sharing of transparent and reproducible experiments, including data provenance (or lineage) tracking. This work introduces the Climate Analytics-Hub, a new component on top of the Earth System Grid Federation (ESGF), which joins big data approaches and parallel computing paradigms to provide an Open Science environment for reproducible multi-model climate change data analytics experiments at scale. An operational implementation has been set up at the SuperComputing Centre of the Euro- Mediterranean Center on Climate Change, with the main goal of becoming a reference Open Science hub in the climate community regarding the multi-model analysis based on the Coupled Model Intercomparison Project (CMIP).

analytics-hub↗
DOE OSTI2022

CUF-Links: Continuous and Ubiquitous FAIRness Linkages for Reproducible Research

Despite much creative work on methods and tools, reproducibility— the ability to repeat the computational steps used to obtain a research result—remains elusive. One reason for these difficulties is that extant tools for capturing research processes, while powerful, often fail to capture vital connections as research projects grow in extent and complexity. We explain here how these interstitial connections can be preserved via simple methods that integrate easily with current work practices to capture basic information about every data product consumed or produced in a project. By thus extending the scope of findable, accessible, interoperable, and reusable (FAIR) data in both time and space to enable the creation of a continuous chain of Continuous and Ubiquitous FAIRness linkages (CUFlinks) from inputs to outputs, such mechanisms can facilitate capture of the provenance linkages that are essential to reproducible research. Herein we give examples of mechanisms that can facilitate the use of these methods, and review how they have been applied in practice.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Planetary normal mode computation: Parallel algorithms, performance and reproducibility

This report is an extension of work entitled “Computing planetary interior normal modes with a highly parallel polynomial filtering eigensolver.” by Shi et al., [1] originally presented at the SC18 conference. A highly parallel polynomial filtered eigensolver was developed and exploited to calculate the planetary normal modes. The proposed method is ideally suited for computing interior eigenpairs for large-scale eigenvalue problems as it greatly enhances memory and computational efficiency. In this article, the second-order finite element method is used to further improve the accuracy as only the first-order finite element method was deployed in the previous work. The parallel algorithm, its parallel performance up to 20k processors, and the great computational accuracy are illustrated. The reproducibility of the previous work was successfully performed on the Student Cluster Competition at the SC19 conference by several participant teams using a completely different Mars-model dataset on different clusters. Both weak and strong scaling performances of the reproducibility by the participant teams were impressive and encouraging. The analysis and reflection of their results are demonstrated and future direction is discussed.

97 MATHEMATICS AND COMPUTING↗