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At least 55 records · Page 3

A reproducible study design for the MIMIC-IV in-hospital mortality task

Open, tabular electronic health record (EHR) datasets such as MIMIC-III and MIMIC-IV have become critical resources for developing machine learning (ML) models addressing clinical prediction tasks, including hospital readmission, length of stay, and in-hospital mortality (IHM). While MIMIC-III has benefited from well-established preprocessing pipelines and standardized feature sets, MIMIC-IV remains comparatively challenging to work with because there are no standardized benchmarks to support reproducibility and comparability across studies. To address this limitation, we present a rigorously curated MIMIC-IV custom feature set optimized for IHM prediction, constructed through a reproducible preprocessing pipeline and feature selection strategy.

97 MATHEMATICS AND COMPUTING

Enhanced climate reproducibility testing with false discovery rate correction

Simulating the Earth's climate is an important and complex problem, thus climate models are similarly complex, comprised of millions of lines of code. In order to appropriately utilize the latest computational and software infrastructure advancements in Earth system models running on modern hybrid computing architectures to improve their performance, precision, accuracy, or all three; it is important to ensure that model simulations are repeatable and robust. This introduces the need for establishing statistical or non-bit-for-bit reproducibility, since bit-for-bit reproducibility may not always be achievable. Here, we propose a short-simulation ensemble-based test for an atmosphere model to evaluate the null hypothesis that modified model results are statistically equivalent to that of the original model. We implement this test in version 2 of the US Department of Energy's Energy Exascale Earth System Model (E3SM). The test evaluates a standard set of output variables across the two simulation ensembles and uses a false discovery rate correction to account for multiple testing. The false positive rates of the test are examined using re-sampling techniques on large simulation ensembles and are found to be lower than the currently implemented bootstrapping-based testing approach in E3SM. We also evaluate the statistical power of the test using perturbed simulation ensemble suites, each with a progressively larger magnitude of change to a tuning parameter. The new test is generally found to exhibit more statistical power than the current approach, being able to detect smaller changes in parameter values with higher confidence.

Kelleher, Michael E. [Oak Ridge National Laborator

Multispectral facsimile reproducer

Facsimile reproducer records spatially well-registered true-color and false-color video data on tape. Proposed optical arrangement allows light sources to be adjusted along the mirror scanning direction in such a manner that no electronic delays are required if the reproducer is operated synchronously with the camera.

Burcher, E. E.

Reproducible analyses of microbial food for advanced life support systems

The use of yeasts in controlled ecological life support systems (CELSS) for microbial food regeneration in space required the accurate and reproducible analysis of intracellular carbohydrate and protein levels. The reproducible analysis of glycogen was a key element in estimating overall content of edibles in candidate yeast strains. Typical analytical methods for estimating glycogen in Saccharomyces were not found to be entirely aplicable to other candidate strains. Rigorous cell lysis coupled with acid/base fractionation followed by specific enzymatic glycogen analyses were required to obtain accurate results in two strains of Candida. A profile of edible fractions of these strains was then determined. The suitability of yeasts as food sources in CELSS food production processes is discussed.

Petersen, Gene R.

Visual-Stratigraphic Dating of the GISP2 Ice Core: Basis, Reproducibility, and Application

Annual layers are visible in the Greenland Ice Sheet Project 2 ice core from central Greenland, allowing rapid dating of the core. Changes in bubble and grain structure caused by near-surface, primarily summertime formation of hoar complexes provide the main visible annual marker in the Holocene, and changes in "cloudiness" of the ice correlated with dustiness mark Wisconsinan annual cycles; both markers are evident and have been intercalibrated in early Holocene ice. Layer counts are reproducible between different workers and for one worker at different times, with 1% error over century-length times in the Holocene. Reproducibility is typically 5% in Wisconsinan ice-age ice and decreases with increasing age and depth. Cumulative ages from visible stratigraphy are not significantly different from independent ages of prominent events for ice older than the historical record and younger than approximately 50,000 years. Visible observations are not greatly degraded by "brittle ice" or many other core-quality problems, allowing construction of long, consistently sampled time series. High accuracy requires careful study of the core by dedicated observers.

Alley, R. B.

Reproducibility and Repeatability of Tensile and Low-Cycle Fatigue Properties in Propulsion Grade Hydrogen

Hydrogen has the potential of increased use in the future as an environmentally friendly fuel. It has, however, shown a tendency to embrittle some materials. To be used in a safe manner and to exploit its full potential, it will be necessary to develop a database of material properties in hydrogen environment. The tests needed to produce this data are costly to perform (tensile test cost 25 times more and low cycle fatigue test are 55 times as expensive). Moreover, there is presently a lack of universal test methods to ensure standardized data within the hydrogen community. Each of the industries that work with hydrogen (aerospace, petroleum, fuel cells, etc.) performs tests by their own laboratory-developed methods, thus rendering cross- comparisons of material property data highly questionable. It is extremely important that data generated in a hydrogen environment be done to a standard that reduces variance to a minimum and allows direct comparison of test results from different laboratories. Doing so will assure that all data generated can be used to further our understanding of the hydrogen effects and to make sure components/products designed for hydrogen are the safest and most reliable possible. This paper reviews the results of two 'round-robin' programs conducted by NASA-MSFC. These two programs examined the reproducibility and repeatability of tensile and low-cycle fatigue test results in high-pressure hydrogen environments. The studies indicated that even with the tightest controls available from current commercial standards, the reproducibility (between different laboratories) and repeatability (within a laboratory) results of the tensile tests exhibited five times the variance as in standard ambient air tests. The variance with the LCF tests were on the same order as with air tests, but that was due to the large variation present in the last Interlaboratory air program. The paper concludes with a recommendation for a program that would allow the development of improved test methods, leading to lower variance in the generation of mechanical property data in the future.

Vesely, E. J.

Reliability and Reproducibility of Advanced ECG Parameters in Month-to-Month and Year-to-Year Recordings in Healthy Subjects

Advanced resting ECG parameters such the spatial mean QRS-T angle and the QT variability index (QTVI) have important diagnostic and prognostic utility, but their reliability and reproducibility (R&R) are not well characterized. We hypothesized that the spatial QRS-T angle would have relatively higher R&R than parameters such as QTVI that are more responsive to transient changes in the autonomic nervous system. The R&R of several conventional and advanced ECG para-meters were studied via intraclass correlation coefficients (ICCs) and coefficients of variation (CVs) in: (1) 15 supine healthy subjects from month-to-month; (2) 27 supine healthy subjects from year-to-year; and (3) 25 subjects after transition from the supine to the seated posture. As hypothesized, for the spatial mean QRS-T angle and many conventional ECG parameters, ICCs we-re higher, and CVs lower than QTVI, suggesting that the former parameters are more reliable and reproducible.

Starc, Vito

A Long-Term and Reproducible Passive Microwave Sea Ice Concentration Data Record for Climate Studies and Monitoring

A long-term, consistent, and reproducible satellite-based passive microwave sea ice concentration climate data record (CDR) is available for climate studies, monitoring, and model validation with an initial operation capability (IOC). The daily and monthly sea ice concentration data are on the National Snow and Ice Data Center (NSIDC) polar stereographic grid with nominal 25 km × 25 km grid cells in both the Southern and Northern Hemisphere polar regions from 9 July 1987 to 31 December 2007. The data files are available in the NetCDF data format at http://nsidc.org/data/g02202.html and archived by the National Climatic Data Center (NCDC) of the National Oceanic and Atmospheric Administration (NOAA) under the satellite climate data record program (http://www.ncdc.noaa.gov/cdr/operationalcdrs.html). The description and basic characteristics of the NOAA/NSIDC passive microwave sea ice concentration CDR are presented here. The CDR provides similar spatial and temporal variability as the heritage products to the user communities with the additional documentation, traceability, and reproducibility that meet current standards and guidelines for climate data records. The data set, along with detailed data processing steps and error source information, can be found at http://dx.doi.org/10.7265/N5B56GN3.

monitoring

Evaluation of NASA's MERRA Precipitation Product in Reproducing the Observed Trend and Distribution of Extreme Precipitation Events in the United States

This study evaluates the performance of NASA's Modern-Era Retrospective Analysis for Research and Applications (MERRA) precipitation product in reproducing the trend and distribution of extreme precipitation events. Utilizing the extreme value theory, time-invariant and time-variant extreme value distributions are developed to model the trends and changes in the patterns of extreme precipitation events over the contiguous United States during 1979-2010. The Climate Prediction Center (CPC) U.S.Unified gridded observation data are used as the observational dataset. The CPC analysis shows that the eastern and western parts of the United States are experiencing positive and negative trends in annual maxima, respectively. The continental-scale patterns of change found in MERRA seem to reasonably mirror the observed patterns of change found in CPC. This is not previously expected, given the difficulty in constraining precipitation in reanalysis products. MERRA tends to overestimate the frequency at which the 99th percentile of precipitation is exceeded because this threshold tends to be lower in MERRA, making it easier to be exceeded. This feature is dominant during the summer months. MERRA tends to reproduce spatial patterns of the scale and location parameters of the generalized extreme value and generalized Pareto distributions. However, MERRA underestimates these parameters, particularly over the Gulf Coast states, leading to lower magnitudes in extreme precipitation events. Two issues in MERRA are identified: 1) MERRA shows a spurious negative trend in Nebraska and Kansas, which is most likely related to the changes in the satellite observing system over time that has apparently affected the water cycle in the central United States, and 2) the patterns of positive trend over the Gulf Coast states and along the East Coast seem to be correlated with the tropical cyclones in these regions. The analysis of the trends in the seasonal precipitation extremes indicates that the hurricane and winter seasons are contributing the most to these trend patterns in the southeastern United States. In addition, the increasing annual trend simulated by MERRA in the Gulf Coast region is due to an incorrect trend in winter precipitation extremes.

MERRA

NASA Life Sciences Portal (NLSP): Supporting Scientific Transparency and Reproducibility

NASA’s Life Sciences Ports (NLSP) serves the scientific community by providing curated data from space life science experiment. The Human Research Program (HRP) with the help of NLSP is currently transforming their life sciences data archive systems and processes to improve compliance with the FAIR principles [1]. Some of these improvements will at the same time support the twin pillars of Open Science [2]: transparency of methods and reproducibility of results. Scientific transparency is marked by the easily intelligible communication of what has been investigated: what were the procedures for collecting sample and the characteristics of samples collected? what kinds of measurements were made, what were the environmental conditions of the measurements? What were the analysis techniques of the collected data? Reproducibility of the results and findings from the investigation requires a high level of transparency for all but the simplest investigations; the slightest deviation in communicating and replicating complex experimental procedures or data analyses can often yield quite different data and even findings, thwarting their validation. One of the ways the NLSP is aiming to improve the communication of scientific information is through the use of ontology-driven metadata. Ontologies are powerful, graph-based knowledge representation structures, which can be leveraged to increase data interoperability, the area of the FAIR principles in which many data systems most lack compliance. Over the past decade, there has been a concerted effort in the biomedical community to develop modular and narrowly focused domain and application-specific ontologies in a common, open-source framework, the Open Biological and Biomedical Ontology (OBO) Foundry [3]. The open sharing and modular nature of this effort promises huge increases in harmonized data sharing for systems that leverage these models. Which is in line with the FAIR Data Principles of Findability, Accessibility, Interoperability, and Reuse for scientific data management and stewardship. 1. Wilkinson, M.D., et al., The FAIR Guiding Principles for scientific data management and stewardship. Sci Data, 2016. 3: p. 160018. 2. National Academies of Sciences, E. and Medicine, Open Science by Design: Realizing a Vision for 21st Century Research. 2018, Washington, DC: The National Academies Press. 232. 3. Smith, B., et al., The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 2007. 25(11): p. 1251-5.

Life Sciences data

NASA Life Sciences Portal (NLSP): Supporting Scientific Transparency and Reproducibility

NASA’s Life Sciences Ports (NLSP) serves the scientific community by providing curated data from space life science experiment. The Human Research Program (HRP) with the help of NLSP is currently transforming their life sciences data archive systems and processes to improve compliance with the FAIR principles [1]. Some of these improvements will at the same time support the twin pillars of Open Science [2]: transparency of methods and reproducibility of results. Scientific transparency is marked by the easily intelligible communication of what has been investigated: what were the procedures for collecting sample and the characteristics of samples collected? what kinds of measurements were made, what were the environmental conditions of the measurements? What were the analysis techniques of the collected data? Reproducibility of the results and findings from the investigation requires a high level of transparency for all but the simplest investigations; the slightest deviation in communicating and replicating complex experimental procedures or data analyses can often yield quite different data and even findings, thwarting their validation. One of the ways the NLSP is aiming to improve the communication of scientific information is through the use of ontology-driven metadata. Ontologies are powerful, graph-based knowledge representation structures, which can be leveraged to increase data interoperability, the area of the FAIR principles in which many data systems most lack compliance. Over the past decade, there has been a concerted effort in the biomedical community to develop modular and narrowly focused domain and application-specific ontologies in a common, open-source framework, the Open Biological and Biomedical Ontology (OBO) Foundry [3]. The open sharing and modular nature of this effort promises huge increases in harmonized data sharing for systems that leverage these models. Which is in line with the FAIR Data Principles of Findability, Accessibility, Interoperability, and Reuse for scientific data management and stewardship.

Life Sciences data

Quantifying the Ability of Magnetohydrodynamic Models to Reproduce Observed Birkeland Current and Auroral Electrojet Magnitudes

Although global magnetohydrodynamic (MHD) models have increased in sophistication and are now at the forefront of modeling Space Weather, there is still no clear understanding of how well these models replicate the observed ionospheric current systems. Without a full understanding and treatment of the ionospheric current systems, global models will have significant shortcomings that will limit their use. In this study we focus on reproducing observed seasonal interhemispheric asymmetry in ionospheric currents using the Space Weather Modeling Framework (SWMF). We find that SWMF does reproduce the linear relationship between the electrojets and the FACs, despite the underestimation of the currents’ magnitudes. Quantitatively, we find that at best SWMF is only capturing approximately 60% of the observed current. We also investigate how varying F10.7 effects the ionospheric potential and currents during the summer and winter. We find that simulations ran with higher F10.7 result in lower ionospheric potentials. Additionally, we find that the models do not always replicate the expected behavior of the currents with varying F10.7. This work points to a needed improvement in ionospheric conductance models.

Tre'Shunda James

Reproducible emission from nonlinear random lasers

Multiple scattering of light serves as a mechanism for feedback in random lasers. Consequently, internal spatial mode patterns, lasing wavelengths, and output directionality can all be random. Strong mode interaction can occur in such devices due to spatially overlapping modes resulting in nonlinearity with respect to the pump input power. Nevertheless, temporal coherence and lasing mode amplitude can be fixed at a constant pumping rate. This is a property desirable for applications where unique randomness is exploited but expected to be reliable over time, such as physical unclonable functions. Random lasers can also be cheaply and easily fabricated, exhibit relatively low lasing thresholds and high emission intensity. However, the precise scattering properties of such structures and fluctuations in the pump field can make device emission irreproducible, thereby limiting random laser applications. Here, in this work, we directly compare the random lasing spectra from zinc oxide samples fabricated in four distinct ways: spin-coating, sputtering, solgel deposition, and atomic layer deposition. The particular method of fabrication has a strong impact. Samples made through atomic layer deposition here exhibit both reproducibility and strong nonlinearity desirable for applications. Randomness in emission spectra persists across hundreds of repeated and averaged measurements irrespective of spatial location and is demonstrably nonlinear with respect to input signal intensity.

47 OTHER INSTRUMENTATION

Metal Foam Morphology Affects the Run to Run Reproducibility of OER Using Nickel Catalysts

Nickel (Ni) foam-based electrodes are excellent catalysts for the oxygen evolution reaction; however, we found that the random pore-size distribution of Ni foams contributes to a significant variability in electrochemically active surface area, compromising experimental reproducibility. We provide insights into quantifying this critical material property, verified by four electrochemical laboratories.

25 ENERGY STORAGE

The DIARieS Ecosystem – A Software Ecosystem to Simplify Discovery, Implementation, Analysis, Reproducibility, and Sharing of Scientific Results and Environments in Heliophysics

The infrastructure of the Heliophysics discipline has promising components but with several missing gaps, drastically reducing research and development efficiency. Developing an online discovery and analysis software ecosystem will close several of these gaps. The five main focuses on this ecosystem should be Discovery, Implementation, Analysis, Reproducibility, and Sharing of results (DIARieS). In this paper, we give a detailed description of how the proposed software ecosystem should operate, and point out the large range of possible applications to benefit many disparate groups, such as researchers, operational staff, decision-makers, and educators. The infrastructure components and technological capabilities necessary for its completion are either currently available or in development, making such an ecosystem possible for the first time. One main focus of current infrastructure investments must be to adapt and connect these pieces together into a cohesive whole to increase our research and development efficiency.

infrastructure

Kernel Manifolds: Nonlinear‐Augmentation Dimensionality Reduction Using Reproducing Kernel Hilbert Spaces

This paper generalizes recent advances on quadratic manifold (QM) dimensionality reduction by developing kernel methods-based nonlinear-augmentation dimensionality reduction. QMs, and more generally feature map-based nonlinear corrections, augment linear dimensionality reduction with a nonlinear correction term in the reconstruction map to overcome approximation accuracy limitations of purely linear approaches. While feature map-based approaches typically learn a least squares optimal polynomial correction term, we generalize this approach by learning an optimal nonlinear correction from a user-defined reproducing kernel Hilbert space. Our approach allows one to impose arbitrary nonlinear structure on the correction term, including polynomial structure, and includes feature map and radial basis function-based corrections as special cases. Furthermore, our method has relatively low training cost and has monotonically decreasing error as the latent space dimension increases. In conclusion, we compare our approach to proper orthogonal decomposition and several recent QM approaches on data from several example problems.

kernel methods

Interpretable and flexible non-intrusive reduced-order models using reproducing kernel Hilbert spaces

This paper develops an interpretable, non-intrusive reduced-order modeling technique using regularized kernel interpolation. Existing non-intrusive approaches approximate the dynamics of a reduced-order model (ROM) by solving a data-driven least-squares regression problem for low-dimensional matrix operators. Our approach instead leverages regularized kernel interpolation, which yields an optimal approximation of the ROM dynamics from a user-defined reproducing kernel Hilbert space. We show that our kernel-based approach can produce interpretable ROMs whose structure mirrors full-order model structure by embedding judiciously chosen feature maps into the kernel. The approach is flexible and allows a combination of informed structure through feature maps and closure terms via more general nonlinear terms in the kernel. We also derive a computable a posteriori error bound that combines standard error estimates for intrusive projection-based ROMs and kernel interpolants. In conclusion, the approach is demonstrated in several numerical experiments that include comparisons to operator inference using both proper orthogonal decomposition and quadratic manifold dimension reduction.

Data-driven model reduction

Overcoming Variability: A Reproducible Approach to SERS Detection of Nanodiamonds

Detonation nanodiamonds (DNDs) are formed at specific pressures and temperatures during explosions. Different explosives produce varied yields of DNDs within their detonation soot, with Composition B producing the highest yield. Raman spectroscopy (RS) is often used for the characterization of sp 2 - and sp 3 -hybridized carbon allotropes in carbonaceous materials because of distinct disorder and graphitic bands. Bulk diamond also gives a distinct Raman peak at 1332 cm –1 . Furthermore, as bulk diamond decreases in size to nanometer-sized species, the peak red-shifts and broadens, becoming increasingly difficult to detect with RS using visible excitations. Therefore, surface-enhanced Raman spectroscopy (SERS) was used to enhance the diamond peak of DNDs, enabling better detection and faster examination of DNDs within detonation soot. Previous literature of the SERS of DNDs delivered inconsistent results in spectral signatures and SERS substrates. Herein, refining of the methodology for the acquisition of SERS spectra of DNDs was achieved. Before any SERS experiments, the DNDs were first characterized with normal Raman (NR) and scanning electron microscopy. Two routes for SERS enhancement were evaluated: colloidal noble metal nanoparticles and evaporated silver films. Silver films produced the best signal enhancement of DNDs with the best signal-to-noise and peak enhancements observed at 20–30 nm thick silver films at 5% (∼300 μW) laser power. Consistent, reproducible SERS spectra were acquired of small aggregates of DNDs down to ∼500 nm. NR and SERS mapping analysis of DNDs before and after evaporation of silver films revealed the improvements in the detection capabilities of SERS compared with NR.

Carbon