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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

MOSAIC: a joint modeling methodology for combined circadian and non-circadian analysis of multi-omics data

Abstract Motivation Circadian rhythms are approximately 24-h endogenous cycles that control many biological functions. To identify these rhythms, biological samples are taken over circadian time and analyzed using a single omics type, such as transcriptomics or proteomics. By comparing data from these single omics approaches, it has been shown that transcriptional rhythms are not necessarily conserved at the protein level, implying extensive circadian post-transcriptional regulation. However, as proteomics methods are known to be noisier than transcriptomic methods, this suggests that previously identified arrhythmic proteins with rhythmic transcripts could have been missed due to noise and may not be due to post-transcriptional regulation. Results To determine if one can use information from less-noisy transcriptomic data to inform rhythms in more-noisy proteomic data, and thus more accurately identify rhythms in the proteome, we have created the Multi-Omics Selection with Amplitude Independent Criteria (MOSAIC) application. MOSAIC combines model selection and joint modeling of multiple omics types to recover significant circadian and non-circadian trends. Using both synthetic data and proteomic data from Neurospora crassa, we showed that MOSAIC accurately recovers circadian rhythms at higher rates in not only the proteome but the transcriptome as well, outperforming existing methods for rhythm identification. In addition, by quantifying non-circadian trends in addition to circadian trends in data, our methodology allowed for the recognition of the diversity of circadian regulation as compared to non-circadian regulation. Availability and implementation MOSAIC’s full interface is available at https://github.com/delosh653/MOSAIC. An R package for this functionality, mosaic.find, can be downloaded at https://CRAN.R-project.org/package=mosaic.find. Supplementary information Supplementary data are available at Bioinformatics online.

De los Santos, Hannah↗
DOE OSTI2025

MINE: maximally informative next experiment—toward a new GWAS experimental design and methodology

Abstract The computational methodology of Genome Wide Association Studies (GWAS) currently has several limitations: (i) the number of observations (rows) on a quantitative trait tends to be smaller than the number of single nucleotide polymorphisms (SNPs) (columns) in the design matrix; (ii) each SNP is usually modeled separately, failing to acknowledge interaction between each other (ie epistasis); (iii) there is implicit linkage disequilibrium (LD) between neighboring SNPs due to their linkage. To overcome these issues, we developed a tool that uses ensemble methods to fit mixed linear models to GWAS data, and these ensemble methods include the development of a new experimental design approach in GWAS, which uses the resultant models and data to select the next informative experiment over time. This new adaptive and staged approach for GWAS experimental design was developed and tested in a 3 yr adaptive model-guided discovery experiment against a fixed classical design. In Sorghum bicolor a total of 79, 86, and 78 accessions were tested in years 1, 2, and 3, respectively out of 343 accessions available in the Bioenergy Association Panel (BAP) each identified for 232,303 SNPs, 1 every 2–3 kb in the genomes. We demonstrated the feasibility of MINE enacted with 8 people in the field per year over 3 yr vs in 1 large classical design enacted with 20 people in 1 yr. The MINE results for chromosomal regions identified controlling dry weight were confirmed against results from previous sorghum GWAS experiments and 1 large classical design for the BAP panel.

Genetics & Heredity↗
DOE OSTI2022

Source scaling comparison and validation in Central Italy: data intensive direct S waves versus the sparse data coda envelope methodology

SUMMARY Robustness of source parameter estimates is a fundamental issue in understanding the relationships between small and large events; however, it is difficult to assess how much of the variability of the source parameters can be attributed to the physical source characteristics or to the uncertainties of the methods and data used to estimate the values. In this study, we apply the coda method by Mayeda et al. using the coda calibration tool (CCT), a freely available Java-based code (https://github.com/LLNL/coda-calibration-tool) to obtain a regional calibration for Central Italy for estimating stable source parameters. We demonstrate the power of the coda technique in this region and show that it provides the same robustness in source parameter estimation as a data-driven methodology [generalized inversion technique (GIT)], but with much fewer calibration events and stations. The Central Italy region is ideal for both GIT and coda approaches as it is characterized by high-quality data, including recent well-recorded seismic sequences such as L'Aquila (2009) and Amatrice–Norcia–Visso (2016–2017). This allows us to apply data-driven methods such as GIT and coda-based methods that require few, but high-quality data. The data set for GIT analysis includes ∼5000 earthquakes and more than 600 stations, while for coda analysis we used a small subset of 39 events spanning 3.5 < Mw < 6.33 and 14 well-distributed broad-band stations. For the common calibration events, as well as an additional 247 events (∼1.7 < Mw < ∼5.0) not used in either calibration, we find excellent agreement between GIT-derived and CCT-derived source spectra. This confirms the ability of the coda approach to obtain stable source parameters even with few calibration events and stations. Even reducing the coda calibration data set by 75 per cent, we found no appreciable degradation in performance. This validation of the coda calibration approach over a broad range of event size demonstrates that this procedure, once extended to other regions, represents a powerful tool for future routine applications to homogeneously evaluate robust source parameters on a national scale. Furthermore, the coda calibration procedure can homogenize the Mw estimates for small and large events without the necessity of introducing any conversion scale between narrow-band measures such as local magnitude (ML) and Mw, which has been shown to introduce significant bias.

Morasca, Paola (ORCID:0000000265254867)↗
DOE OSTI2022

Integrating Data From In Vitro New Approach Methodologies for Developmental Neurotoxicity

Abstract In vivo developmental neurotoxicity (DNT) testing is resource intensive and lacks information on cellular processes affected by chemicals. To address this, DNT new approach methodologies (NAMs) are being evaluated, including: the microelectrode array neuronal network formation assay; and high-content imaging to evaluate proliferation, apoptosis, neurite outgrowth, and synaptogenesis. This work addresses 3 hypotheses: (1) a broad screening battery provides a sensitive marker of DNT bioactivity; (2) selective bioactivity (occurring at noncytotoxic concentrations) may indicate functional processes disrupted; and, (3) a subset of endpoints may optimally classify chemicals with in vivo evidence for DNT. The dataset was comprised of 92 chemicals screened in all 57 assay endpoints sourced from publicly available data, including a set of DNT NAM evaluation chemicals with putative positives (53) and negatives (13). The DNT NAM battery provides a sensitive marker of DNT bioactivity, particularly in cytotoxicity and network connectivity parameters. Hierarchical clustering suggested potency (including cytotoxicity) was important for classifying positive chemicals with high sensitivity (93%) but failed to distinguish patterns of disrupted functional processes. In contrast, clustering of selective values revealed informative patterns of differential activity but demonstrated lower sensitivity (74%). The false negatives were associated with several limitations, such as the maximal concentration tested or gaps in the biology captured by the current battery. This work demonstrates that this multi-dimensional assay suite provides a sensitive biomarker for DNT bioactivity, with selective activity providing possible insight into specific functional processes affected by chemical exposure and a basis for further research.

Carstens, Kelly E.↗
DOE OSTI2025

Comment on “Hermitian stochastic methodology for x-ray superfluorescence”

This comment critically examines the paper “Hermitian stochastic methodology for x-ray superfluorescence” by Chuchurka, Sukharnikov, and Rohringer [Phys. Rev. A 109, 063705 (2024)]. Here, the paper proposes a Hermitian framework based on the positive-𝑃 stochastic equations (PPSEs), claimed to be derived “from first principles,” through a redefinition of physical variables without a clear rationale. However, because the original PPSEs cannot satisfy Hermiticity under any stochastic-diffusion-gauge transformation, the framework necessarily employs representations beyond this gauge freedom, thereby contradicting the original PPSEs and their ensemble-average predictions. The resulting equations have close structural similarities with the previously established Hermitian formalism of stochastic Maxwell-Bloch equations [arXiv:2305.04653 and Phys. Rev. A 110, 023724 (2024)].

Park, Jeong-Wan [Argonne National Laboratory (ANL)↗
DOE OSTI2021

Efficient First-Principles Methodology for the Calculation of the All-Phonon Inelastic Scattering in Solids

Inelastic scattering experiments are key methods for mapping the full dispersion of fundamental excitations of solids in the ground as well as nonequilibrium states. A quantitative analysis of inelastic scattering in terms of phonon excitations requires identifying the role of multiphonon processes. Here, we develop an efficient first-principles methodology for calculating the all-phonon quantum mechanical structure factor of solids. We demonstrate our method by obtaining excellent agreement between measurements and calculations of the diffuse scattering patterns of black phosphorus, showing that multiphonon processes play a substantial role. The present approach constitutes a step towards the interpretation of static and time-resolved electron, x-ray, and neutron inelastic scattering data.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Wave Excitation Force Prediction Methodology Based on Autoregressive Filters for Real Time Control

This paper presents a wave excitation force prediction methodology for a slider crank power take-off system (PTOS) based on autoregressive filters. This study shows the feasibility of half period and zero crossing prediction of the irregular ocean waves to keep phase lock condition between the generator and the wave excitation force. This is critically important for unidirectional continuous rotation of the generator to maximize energy extraction. Results from the prediction with different filter orders are analyzed to accommodate real time processing requirements. It has been shown that 10th order filter provides the good compromise of accuracy and timely processing.

16 TIDAL AND WAVE POWER↗
DOE OSTI2021

SYMBIOSYS: A Methodology for Performance Analysis of Composable HPC Data Services

Microservices are a powerful new way of building, customizing, and deploying distributed services owing to their flexibility and maintainability. Several large-scale distributed platforms have emerged to serve the growing needs of data-centric workloads and services in commercial computing. Concurrently, high-performance computing (HPC) systems and software are rapidly evolving to meet the demands of diversified applications and heterogeneity. The interplay of hardware factors, software configuration parameters, and the flexibility offered with a microservice architecture makes it nontrivial to estimate the optimal service instantiation for a given application workload. Further, this problem is exacerbated when considering that these services operate in a dynamic and heterogeneous HPC environment. An optimally integrated service can be vastly more performant than a haphazardly integrated one. Existing performance tools for HPC either fail to understand the request-response model of communication inherent to microservices or they operate within a narrow scope, limiting the insight that can be gleaned from employing them in isolation. We propose a methodology for integrated performance analysis of HPC microservices frameworks and applications called SYMBIOSYS. We describe its design and implementation within the context of the Mochi framework. This integration is achieved by combining distributed callpath profiling and tracing with a performance data exchange strategy that collects fine-grained, low-level metrics from the RPC communication library and network layers. The result is a portable, low-overhead performance analysis setup that provides a holistic profile of the dependencies among microservices and how they interact with the Mochi RPC software stack. Using HEPnOS, a production-quality Mochi data service, we demonstrate the low-overhead operation of SYMBIOSYS at scale and use it to identify the root causes of poorly performing service configurations.

microservices↗
DOE OSTI2019

Quasi-Static Time-Series PV Hosting Capacity Methodology and Metrics

Distributed photovoltaic systems (DPV) can cause adverse grid impacts, including voltage or thermal violations. The installed capacity at which violations first occur and above which would require system upgrades is called the hosting capacity. Current methods for determining hosting capacity tend to be conservative by either only considering infrequent worst-case snapshots in time and/or only capturing coarse time and spatial resolution. Additionally, current hosting capacity methods do not accurately capture the time-dependence making them unable to capture the behavior of voltage regulating equipment and of some advanced controls mitigations. This can trigger delays from unnecessary engineering analysis or deter solar installations in areas that are actually suitable. We propose a quasi-static-time-series (QSTS) based PV hosting capacity methodology to address these issues. With this approach, we conduct power flow analysis over the course of a full year, to capture time-varying parameters and control device actions explicitly. We show that this approach can more fully capture grid impacts of DPV than traditional methods.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2015

Interconnection Assessment Methodology and Cost Benefit Analysis for High-Penetration PV Deployment in the Arizona Public Service System

In an effort to better understand the impacts of high penetrations of photovoltaic (PV) generators on distribution systems, Arizona Public Service and its partners completed a multi-year project to develop the tools and knowledge base needed to safely and reliably integrate high penetrations of utility- and residential-scale PV. Building upon the APS Community Power Project-Flagstaff Pilot, this project investigates the impact of PV on a representative feeder in northeast Flagstaff. To quantify and catalog the effects of the estimated 1.3 MW of PV that will be installed on the feeder (both smaller units at homes and large, centrally located systems), high-speed weather and electrical data acquisition systems and digital 'smart' meters were designed and installed to facilitate monitoring and to build and validate comprehensive, high-resolution models of the distribution system. These models are being developed to analyze the impacts of PV on distribution circuit protection systems (including coordination and anti-islanding), predict voltage regulation and phase balance issues, and develop volt/VAr control schemes. This paper continues from a paper presented at the 2014 IEEE PVSC conference that described feeder model evaluation and high penetration advanced scenario analysis, specifically feeder reconfiguration. This paper presents results from Phase 5 of the project. Specifically, the paper discusses tool automation; interconnection assessment methodology and cost benefit analysis.

14 SOLAR ENERGY↗
DOE OSTI2017

Building Modelling Methodologies for Virtual District Heating and Cooling Networks

District heating and cooling systems (DHC) are a proven energy solution that has been deployed for many years in a growing number of urban areas worldwide. They comprise a variety of technologies that seek to develop synergies between the production and supply of heat, cooling, domestic hot water and electricity. Although the benefits of DHC systems are significant and have been widely acclaimed, yet the full potential of modern DHC systems remains largely untapped. There are several opportunities for development of energy efficient DHC systems, which will enable the effective exploitation of alternative renewable resources, waste heat recovery, etc., in order to increase the overall efficiency and facilitate the transition towards the next generation of DHC systems. This motivated the need for modelling these complex systems. Large-scale modelling of DHC-networks is challenging, as it has several components interacting with each other. In this paper we present two building methodologies to model the consumer buildings. These models will be further integrated with network model and the control system layer to create a virtual test bed for the entire DHC system. The model is validated using data collected from a real life DHC system located at Lulea, a city on the coast of northern Sweden. The test bed will be then used for simulating various test cases such as peak energy reduction, overall demand reduction etc.

Saurav, Kumar↗
DOE OSTI2018

Insider Threat Cybersecurity Framework Webtool & Methodology: Defending Against Complex Cyber-Physical Threats

The paper demonstrates how the Insider Threat Cybersecurity Framework (ITCF) web tool and methodology help provide a more dynamic, defense-in-depth security posture against insider cyber-physical threats. ITCF includes over 30 cyber-physical security best practices to help organizations identify, protect, detect, respond and recover to sophisticated insider threats and vulnerabilities. The following paper tests the efficacy of this approach and helps validate and verify ITCF’s capabilities and features through various insider attacks use-cases. Three different investment scenarios and explored to determine how an organization can most efficiently leverage ICTF to increase their overall security posture against insider attacks. ITCF also facilitates implementation of the goals outlined in Presidential Executive Order (EO) on Strengthening the Cybersecurity of Federal Networks and Critical Infrastructure (May 2017): To help owners and operators of critical infrastructure identify, protect, detect, respond, and recover cyber threats. ITCF helps organizations with the following features: provides an easy to use rapid assessment tool to perform an insider threat self-assessment; determines the current insider threat cybersecurity posture; defines investment based goals to achieve a target state; connects the cybersecurity posture with business processes, functions, and continuity; and finally, helps develop plans to answer critical organizational cybersecurity questions. In this paper, the webtool and its core capabilities are depicted by performing an extensive comparative assessment over two different high-profile insider threat incidents.

Mylrea, Michael E.↗
DOE OSTI2018

Design of Distributed Cyber-Physical Systems for Connected and Automated Vehicles with Implementing Methodologies

With the development of communication and control technology, intelligent transportation systems have received increasing attention from both industry and academia. Intelligent transportation systems are supported by the Internet of Things, Cyber-Physical System, Artificial Intelligence, Cloud Computing and many other technologies, which supply fundamental information for connected and automated vehicles. Although plenty of studies have provided different formulations for intelligent transportation systems, many of them depend on Master Control Center. However, a centralized control mode requires a huge amount of data transmission and high level of hardware configuration and may cause communication delay and privacy leak. Some distributed architectures have been proposed to overcome the above problems but systematized technologies to collect and exchange information, process large amounts of data, model the dynamics of vehicles, and safely control the connected and automated vehicles are not explored in detail. In this paper, we proposed a novel distributed cyber-physical system for connected and automated vehicles in which every vehicle is modeled as a double-integrator using edge computing to analyze information collected from its nearest neighbors. The vehicles are supposed to travel along a desired trajectory and to maintain a rigid formation geometry. Related methodologies for the proposed system are illustrated and experiments are conducted showing that the performance of the connected and automated vehicles matches very well with analytic predictions. Some design guidelines and open questions are provided for the future study.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23

Ensemble docking is now commonly used in early-stage in silico drug discovery and can be used to attack difficult problems such as finding lead compounds which can disrupt protein–protein interactions. We give an example of this methodology here, as applied to fibroblast growth factor 23 (FGF23), a protein hormone that is responsible for regulating phosphate homeostasis. The first small-molecule antagonists of FGF23 were recently discovered by combining ensemble docking with extensive experimental target validation data (Science Signaling, 9, 2016, ra113). Here, we provide a detailed account of how ensemble-based high-throughput virtual screening was used to identify the antagonist compounds discovered in reference (Science Signaling, 9, 2016, ra113). Moreover, we perform further calculations, redocking those antagonist compounds identified in reference (Science Signaling, 9, 2016, ra113) that performed well on drug-likeness filters, to predict possible binding regions. These predicted binding modes are rescored with the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) approach to calculate the most likely binding site. Furthermore, our findings suggest that the antagonist compounds antagonize FGF23 through the disruption of protein–protein interactions between FGF23 and fibroblast growth factor receptor (FGFR).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Prospective Environmental Analyses of Emerging Technology: A Critique, a Proposed Methodology, and a Case Study on Incremental Sheet Forming

Summary Prospective environmental assessment of emerging technology is necessary in order to inform designers of beneficial changes early in a technology's development, and policy makers looking to fund projects and nudge manufacturers toward the most sustainable application of a technology. Existing analyses often have shortcomings such as failing to consider the environmental impacts in all stages of a product's life cycle; implicitly assuming that the emerging technology will be cost‐effective wherever it is technically viable; and assuming optimistic application scenarios that discontinue long‐established trends in human behavior. In this article, we propose a new approach, complementary to the prospective and anticipatory life cycle assessment literature, addressing the above concerns and attempting to make sense of the large uncertainties inherent in such analyses by using distributions to model all the inputs. The paper focuses on emerging manufacturing technologies, such as incremental sheet forming (ISF), but the issues examined are also applicable to new end‐use products, such as autonomous vehicles. This paper makes use of approaches (such as Bass modeling and product cannibalization considerations) familiar to those in the business community who anticipate market diffusion of a new technology and the effect on existing technology sales. The proposed methodology is demonstrated by estimating the potential environmental impacts in the U.S. car industry by 2030 of an emerging double‐sided ISF process. Energy and cost models of ISF and drawing are used to estimate potential mean savings of around 100 TJ primary and 60 million U.S. dollars per year by 2030.

Cooper, Daniel R.↗
DOE OSTI2016

Methodology for Estimating Thermal and Neutron Embrittlement of Cast Austenitic Stainless Steels During Service in Light Water Reactors

Cast austenitic stainless steel (CASS) materials, which have a duplex structure consisting of austenite and ferrite phases, are susceptible to thermal embrittlement during reactor service. In addition, the prolonged exposure of these materials, which are used in reactor core internals, to neutron irradiation changes their microstructure and microchemistry, and these changes degrade their fracture properties even further. This paper presents a revision of the procedure and correlations presented in NUREG/CR-4513, Rev. 1 (Aug. 1994) for predicting the change in fracture toughness and tensile properties of CASS components due to thermal aging during service in light water reactors (LWRs) at 280–330 °C (535–625 °F). The methodology is applicable to CF-3, CF-3M, CF-8, and CF-8M materials with a ferrite content of up to 40%. The fracture toughness, tensile strength, and Charpy-impact energy of aged CASS materials are estimated from known material information. Embrittlement is characterized in terms of room-temperature (RT) Charpy-impact energy. The extent or degree of thermal embrittlement at “saturation” (i.e., the minimum impact energy that can be achieved for a material after long-term aging) is determined from the chemical composition of the material. Charpy-impact energy as a function of the time and temperature of reactor service is estimated from the kinetics of thermal embrittlement, which are also determined from the chemical composition. The fracture toughness J-R curve for the aged material is then obtained by correlating RT Charpy-impact energy with fracture toughness parameters. A common “predicted lower-bound” J-R curve for CASS materials of unknown chemical composition is also defined for a given grade of material, range of ferrite content, and temperature. In addition, guidance is provided for evaluating the combined effects of thermal and neutron embrittlement of CASS materials used in the reactor core internal components. The correlations for estimating the change in tensile strength, including the Ramberg/Osgood parameters for strain hardening, are also described.

Chopra, O. K.↗
DOE OSTI2014

Low sheet resistance titanium nitride films by low-temperature plasma-enhanced atomic layer deposition using design of experiments methodology

A design of experiments methodology was used to optimize the sheet resistance of titanium nitride (TiN) films produced by plasma-enhanced atomic layer deposition (PE-ALD) using a tetrakis(dimethylamino)titanium precursor in a N{sub 2}/H{sub 2} plasma at low temperature (250 °C). At fixed chamber pressure (300 mTorr) and plasma power (300 W), the plasma duration and N{sub 2} flow rate were the most significant factors. The lowest sheet resistance values (163 Ω/sq. for a 20 nm TiN film) were obtained using plasma durations ∼40 s, N{sub 2} flow rates >60 standard cubic centimeters per minute, and purge times ∼60 s. Time of flight secondary ion mass spectroscopy data revealed reduced levels of carbon contaminants in the TiN films with lowest sheet resistance (163 Ω/sq.), compared to films with higher sheet resistance (400–600 Ω/sq.) while transmission electron microscopy data showed a higher density of nanocrystallites in the low-resistance films. Further significant reductions in sheet resistance, from 163 Ω/sq. to 70 Ω/sq. for a 20 nm TiN film (corresponding resistivity ∼145 μΩ·cm), were achieved by addition of a postcycle Ar/N{sub 2} plasma step in the PE-ALD process.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

SU-D-16A-02: A Novel Methodology for Accurate, Semi-Automated Delineation of Oral Mucosa for Radiation Therapy Dose-Response Studies

Purpose: The significant morbidity caused by radiation-induced acute oral mucositis means that studies aiming to elucidate dose-response relationships in this tissue are a high priority. However, there is currently no standardized method for delineating the mucosal structures within the oral cavity. This report describes the development of a methodology to delineate the oral mucosa accurately on CT scans in a semi-automated manner. Methods: An oral mucosa atlas for automated segmentation was constructed using the RayStation Atlas-Based Segmentation (ABS) module. A radiation oncologist manually delineated the full surface of the oral mucosa on a planning CT scan of a patient receiving radiotherapy (RT) to the head and neck region. A 3mm fixed annulus was added to incorporate the mucosal wall thickness. This structure was saved as an atlas template. ABS followed by model-based segmentation was performed on four further patients sequentially, adding each patient to the atlas. Manual editing of the automatically segmented structure was performed. A dose comparison between these contours and previously used oral cavity volume contours was performed. Results: The new approach was successful in delineating the mucosa, as assessed by an experienced radiation oncologist, when applied to a new series of patients receiving head and neck RT. Reductions in the mean doses obtained when using the new delineation approach, compared with the previously used technique, were demonstrated for all patients (median: 36.0%, range: 25.6% – 39.6%) and were of a magnitude that might be expected to be clinically significant. Differences in the maximum dose that might reasonably be expected to be clinically significant were observed for two patients. Conclusion: The method developed provides a means of obtaining the dose distribution delivered to the oral mucosa more accurately than has previously been achieved. This will enable the acquisition of high quality dosimetric data for use in dose-response studies. We would like to thank the Engineering and Physical Sciences Research Council for funding. We acknowledge support from the NIHR RM/ICR Biomedical Research Centre. RayStatation was used under an evaluation agreement with RaySearch Laboratories AB.

60 APPLIED LIFE SCIENCES↗