Sharing experimental data and facilities in EPOS: Updates on services for the analogue modelling community in the TCS Multi-scale Laboratories

2021 ◽  
Author(s):  
Ernst Willingshofer ◽  
Francesca Funiciello ◽  
Matthias Rosenau ◽  
Guido Schreurs ◽  
Frank Zwaan ◽  
...  
Keyword(s):  
Earth Science ◽  
International Standards ◽  
Research Centre ◽  
Data Sets ◽  
Implementation Phase ◽  
Data Services ◽  
Multi Scale ◽  
Analogue Modelling ◽  
Wide Range ◽  
Experimental Facilities

<p>EPOS, the European Plate Observing System, is a unique e-infrastructure and collaborative environment for the solid earth science community in Europe and beyond. A wide range of world-class experimental (analogue modelling and rock and melt physics) and analytical (paleomagnetic, geochemistry, microscopy) laboratory infrastructures are concerted in a “Thematic Core Service” (TCS) labelled “Multi-scale Laboratories” (MSL). Sharing experimental facilities and data on analogue modelling of tectonic processes as well as on properties and applicability of different rock analogue materials are among the thematic areas that have been achieved during the current implementation phase of EPOS. The TCS Multi-scale Laboratories offers coordination of the laboratories’ network, data services, and trans-national access to laboratory facilities.</p><p> </p><p>In the framework of Transnational Access (TNA), TCS Multi-scale laboratories’ facilities are accessible to researchers across the world, creating new opportunities for synergy, collaboration and scientific innovation, according to trans-national access rules. TNA can be realized in the form of physical access (in-situ experimenting and analysis), remote service (sample analysis) and virtual access (remote processing). After three successful TNA calls, the 2020 and 2021 TNA calls have been suspended due to Covid-19 pandemic restrictions. A TNA call is now foreseen for 2022 offering access to a variety of experimental facilities and complementary expertise.</p><p> </p><p>In the framework of data services, TCS Multi Scale Laboratories promotes FAIR (Findable-Accessible-Interoperable-Re-Usable) sharing of experimental research data sets through Open Access data publications. Data sets are assigned with digital object identifiers (DOI) and are published under open CC BY licences. They are thus citable in all relevant scientific journals. A dedicated metadata schema (following international standards that are enrichiched with disciplinary controlled community vocabulary) eases exploration of the various data sets in a TCS catalogue. With respect to analogue modelling, a growing number of analogue modelling data sets include analogue material properties (friction and rheology data) and modelling results (images, maps, graphs, animations) as well as software (visualization and analysis). The main repository for data sets is currently GFZ Data Services, a domain repository for Geosciences, hosted at GFZ German Research Centre for Geosciences, but others are planned to be implemented within the next years.</p><p> </p><p>The EPOS TCS Multiscale Laboratories framework will lay the foundation for a comprehensive database of rock analogue materials, a dedicated bibliography, and will facilitate the organization of community wide activities (eg. meetings, benchmarking, etc.) to stimulate collaboration among analogue laboratories and the exchange of know-how.</p><p> </p>

scholarly journals mtDNAcombine: tools to combine sequences from multiple studies

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Eleanor F. Miller ◽  
Andrea Manica
Keyword(s):  
Sequence Data ◽  
Data Extraction ◽  
Bayesian Skyline Plot ◽  
Model Organisms ◽  
Data Sets ◽  
Data Handling ◽  
Online Database ◽  
Genetic Studies ◽  
Wide Range ◽  
Existing Data

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.

scholarly journals Flow and Particle Modelling of Dry Powder Inhalers: Methodologies, Recent Development and Emerging Applications

Pharmaceutics ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 189
Author(s):  
Zhanying Zheng ◽  
Sharon Shui Yee Leung ◽  
Raghvendra Gupta
Keyword(s):  
Dry Powder Inhaler ◽  
Research Direction ◽  
Particle Methods ◽  
Future Research ◽  
High Dose ◽  
Dry Powder ◽  
Multi Scale ◽  
Wide Range ◽  
Computational Fluid Dynamics Cfd ◽  
Discrete Element Methods

Dry powder inhaler (DPI) is a device used to deliver a drug in dry powder form to the lungs. A wide range of DPI products is currently available, with the choice of DPI device largely depending on the dose, dosing frequency and powder properties of formulations. Computational fluid dynamics (CFD), together with various particle motion modelling tools, such as discrete particle methods (DPM) and discrete element methods (DEM), have been increasingly used to optimise DPI design by revealing the details of flow patterns, particle trajectories, de-agglomerations and depositions within the device and the delivery paths. This review article focuses on the development of the modelling methodologies of flow and particle behaviours in DPI devices and their applications to device design in several emerging fields. Various modelling methods, including the most recent multi-scale approaches, are covered and the latest simulation studies of different devices are summarised and critically assessed. The potential and effectiveness of the modelling tools in optimising designs of emerging DPI devices are specifically discussed, such as those with the features of high-dose, pediatric patient compatibility and independency of patients’ inhalation manoeuvres. Lastly, we summarise the challenges that remain to be addressed in DPI-related fluid and particle modelling and provide our thoughts on future research direction in this field.

scholarly journals MUREN: a robust and multi-reference approach of RNA-seq transcript normalization

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yance Feng ◽  
Lei M. Li
Keyword(s):  
Biological Significance ◽  
Housekeeping Genes ◽  
R Package ◽  
Data Sets ◽  
Statistical Regression ◽  
Rna Seq ◽  
Least Trimmed Squares ◽  
Standard Data ◽  
Wide Range ◽  
Multiple References

Abstract Background Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of unwanted confounding factors. Explicitly or implicitly, the justification of normalization requires a set of housekeeping genes. However, the existence of housekeeping genes common for a very large collection of samples, especially under a wide range of conditions, is questionable. Results We propose to carry out pairwise normalization with respect to multiple references, selected from representative samples. Then the pairwise intermediates are integrated based on a linear model that adjusts the reference effects. Motivated by the notion of housekeeping genes and their statistical counterparts, we adopt the robust least trimmed squares regression in pairwise normalization. The proposed method (MUREN) is compared with other existing tools on some standard data sets. The goodness of normalization emphasizes on preserving possible asymmetric differentiation, whose biological significance is exemplified by a single cell data of cell cycle. MUREN is implemented as an R package. The code under license GPL-3 is available on the github platform: github.com/hippo-yf/MUREN and on the conda platform: anaconda.org/hippo-yf/r-muren. Conclusions MUREN performs the RNA-seq normalization using a two-step statistical regression induced from a general principle. We propose that the densities of pairwise differentiations are used to evaluate the goodness of normalization. MUREN adjusts the mode of differentiation toward zero while preserving the skewness due to biological asymmetric differentiation. Moreover, by robustly integrating pre-normalized counts with respect to multiple references, MUREN is immune to individual outlier samples.

Rapid boron isotope and concentration measurements of silicate geological reference materials dissolved through sodium peroxide sintering

2021 ◽  
Author(s):  
Yue Cai ◽  
Troy E Rasbury ◽  
Kathleen M Wooton ◽  
Xin Jiang ◽  
Di Wang
Keyword(s):  
Solid Earth ◽  
Reference Materials ◽  
Earth Science ◽  
Boron Isotope ◽  
Earth System ◽  
Sodium Peroxide ◽  
Wide Range ◽  
Concentration Measurements

Understanding the movement of fluids in the solid Earth system is crucial for answering a wide range of important questions in Earth Science. Boron (B) is a perfect tracer for...

scholarly journals A Novel GIS-Based Approach for Automated Detection of Nearshore Sandbar Morphological Characteristics in Optical Satellite Imagery

2021 ◽  
Vol 13 (11) ◽  
pp. 2233
Author(s):  
Rasa Janušaitė ◽  
Laurynas Jukna ◽  
Darius Jarmalavičius ◽  
Donatas Pupienis ◽  
Gintautas Žilinskas
Keyword(s):  
Satellite Imagery ◽  
Morphological Characteristics ◽  
Unsupervised Classification ◽  
Landsat 8 ◽  
Multi Scale ◽  
Medium Resolution ◽  
Wide Range ◽  
Position Index ◽  
Local Relief ◽  
Length Width

Satellite remote sensing is a valuable tool for coastal management, enabling the possibility to repeatedly observe nearshore sandbars. However, a lack of methodological approaches for sandbar detection prevents the wider use of satellite data in sandbar studies. In this paper, a novel fully automated approach to extract nearshore sandbars in high–medium-resolution satellite imagery using a GIS-based algorithm is proposed. The method is composed of a multi-step workflow providing a wide range of data with morphological nearshore characteristics, which include nearshore local relief, extracted sandbars, their crests and shoreline. The proposed processing chain involves a combination of spectral indices, ISODATA unsupervised classification, multi-scale Relative Bathymetric Position Index (RBPI), criteria-based selection operations, spatial statistics and filtering. The algorithm has been tested with 145 dates of PlanetScope and RapidEye imagery using a case study of the complex multiple sandbar system on the Curonian Spit coast, Baltic Sea. The comparison of results against 4 years of in situ bathymetric surveys shows a strong agreement between measured and derived sandbar crest positions (R2 = 0.999 and 0.997) with an average RMSE of 5.8 and 7 m for PlanetScope and RapidEye sensors, respectively. The accuracy of the proposed approach implies its feasibility to study inter-annual and seasonal sandbar behaviour and short-term changes related to high-impact events. Algorithm-provided outputs enable the possibility to evaluate a range of sandbar characteristics such as distance from shoreline, length, width, count or shape at a relevant spatiotemporal scale. The design of the method determines its compatibility with most sandbar morphologies and suitability to other sandy nearshores. Tests of the described technique with Sentinel-2 MSI and Landsat-8 OLI data show that it can be applied to publicly available medium resolution satellite imagery of other sensors.

scholarly journals In-Situ Cosmogenic 14C: Production and Examples of its Unique Applications in Studies of Terrestrial and Extraterrestrial Processes

Radiocarbon ◽  
2001 ◽  
Vol 43 (2B) ◽  
pp. 731-742 ◽  
Author(s):  
D Lal ◽  
A J T Jull
Keyword(s):  
Half Life ◽  
Earth Science ◽  
Chemical Properties ◽  
Radioactive Isotopes ◽  
Earth’S Atmosphere ◽  
The Earth ◽  
Wide Range ◽  
History Of ◽  
Earth's Atmosphere

Nuclear interactions of cosmic rays produce a number of stable and radioactive isotopes on the earth (Lai and Peters 1967). Two of these, 14C and 10Be, find applications as tracers in a wide variety of earth science problems by virtue of their special combination of attributes: 1) their source functions, 2) their half-lives, and 3) their chemical properties. The radioisotope, 14C (half-life = 5730 yr) produced in the earth's atmosphere was the first to be discovered (Anderson et al. 1947; Libby 1952). The next longer-lived isotope, also produced in the earth's atmosphere, 10Be (half-life = 1.5 myr) was discovered independently by two groups within a decade (Arnold 1956; Goel et al. 1957; Lal 1991a). Both the isotopes are produced efficiently in the earth's atmosphere, and also in solids on the earth's surface. Independently and jointly they serve as useful tracers for characterizing the evolutionary history of a wide range of materials and artifacts. Here, we specifically focus on the production of 14C in terrestrial solids, designated as in-situ-produced 14C (to differentiate it from atmospheric 14C, initially produced in the atmosphere). We also illustrate the application to several earth science problems. This is a relatively new area of investigations, using 14C as a tracer, which was made possible by the development of accelerator mass spectrometry (AMS). The availability of the in-situ 14C variety has enormously enhanced the overall scope of 14C as a tracer (singly or together with in-situ-produced 10Be), which eminently qualifies it as a unique tracer for studying earth sciences.

scholarly journals A Visual and VAE Based Hierarchical Indoor Localization Method

Sensors ◽  
2021 ◽  
Vol 21 (10) ◽  
pp. 3406
Author(s):  
Jie Jiang ◽  
Yin Zou ◽  
Lidong Chen ◽  
Yujie Fang
Keyword(s):  
Image Retrieval ◽  
Indoor Localization ◽  
Data Sets ◽  
Indoor Environments ◽  
Global Features ◽  
Data Set ◽  
Data Annotation ◽  
Wide Range ◽  
Annotation Costs ◽  
Global And Local

Precise localization and pose estimation in indoor environments are commonly employed in a wide range of applications, including robotics, augmented reality, and navigation and positioning services. Such applications can be solved via visual-based localization using a pre-built 3D model. The increase in searching space associated with large scenes can be overcome by retrieving images in advance and subsequently estimating the pose. The majority of current deep learning-based image retrieval methods require labeled data, which increase data annotation costs and complicate the acquisition of data. In this paper, we propose an unsupervised hierarchical indoor localization framework that integrates an unsupervised network variational autoencoder (VAE) with a visual-based Structure-from-Motion (SfM) approach in order to extract global and local features. During the localization process, global features are applied for the image retrieval at the level of the scene map in order to obtain candidate images, and are subsequently used to estimate the pose from 2D-3D matches between query and candidate images. RGB images only are used as the input of the proposed localization system, which is both convenient and challenging. Experimental results reveal that the proposed method can localize images within 0.16 m and 4° in the 7-Scenes data sets and 32.8% within 5 m and 20° in the Baidu data set. Furthermore, our proposed method achieves a higher precision compared to advanced methods.

scholarly journals An Interoperability Platform Enabling Reuse of Electronic Health Records for Signal Verification Studies

2016 ◽  
Vol 2016 ◽  
pp. 1-18 ◽  
Author(s):  
Mustafa Yuksel ◽  
Suat Gonul ◽  
Gokce Banu Laleci Erturkmen ◽  
Ali Anil Sinaci ◽  
Paolo Invernizzi ◽  
...  
Keyword(s):  
Real Life ◽  
Case Series ◽  
Background Information ◽  
Data Sets ◽  
Local Data ◽  
Lombardy Region ◽  
Common Information ◽  
Spontaneous Reports ◽  
Wide Range ◽  
Common Information Model

Depending mostly on voluntarily sent spontaneous reports, pharmacovigilance studies are hampered by low quantity and quality of patient data. Our objective is to improve postmarket safety studies by enabling safety analysts to seamlessly access a wide range of EHR sources for collecting deidentified medical data sets of selected patient populations and tracing the reported incidents back to original EHRs. We have developed an ontological framework where EHR sources and target clinical research systems can continue using their own local data models, interfaces, and terminology systems, while structural interoperability and Semantic Interoperability are handled through rule-based reasoning on formal representations of different models and terminology systems maintained in the SALUS Semantic Resource Set. SALUS Common Information Model at the core of this set acts as the common mediator. We demonstrate the capabilities of our framework through one of the SALUS safety analysis tools, namely, the Case Series Characterization Tool, which have been deployed on top of regional EHR Data Warehouse of the Lombardy Region containing about 1 billion records from 16 million patients and validated by several pharmacovigilance researchers with real-life cases. The results confirm significant improvements in signal detection and evaluation compared to traditional methods with the missing background information.

scholarly journals Considerations of the Scale of Radiocarbon Offsets in the East Mediterranean, and Considering a Case for the Latest (Most Recent) Likely Date for the Santorini Eruption

Radiocarbon ◽  
2012 ◽  
Vol 54 (3-4) ◽  
pp. 449-474 ◽  
Author(s):  
Sturt W Manning ◽  
Bernd Kromer
Keyword(s):  
Time Horizon ◽  
Weighted Average ◽  
17Th Century ◽  
Data Sets ◽  
East Mediterranean ◽  
Average Value ◽  
Accuracy And Precision ◽  
Wide Range ◽  
The Impact ◽  
East Mediterranean Region

The debate over the dating of the Santorini (Thera) volcanic eruption has seen sustained efforts to criticize or challenge the radiocarbon dating of this time horizon. We consider some of the relevant areas of possible movement in the14C dating—and, in particular, any plausible mechanisms to support as late (most recent) a date as possible. First, we report and analyze data investigating the scale of apparent possible14C offsets (growing season related) in the Aegean-Anatolia-east Mediterranean region (excluding the southern Levant and especially pre-modern, pre-dam Egypt, which is a distinct case), and find no evidence for more than very small possible offsets from several cases. This topic is thus not an explanation for current differences in dating in the Aegean and at best provides only a few years of latitude. Second, we consider some aspects of the accuracy and precision of14C dating with respect to the Santorini case. While the existing data appear robust, we nonetheless speculate that examination of the frequency distribution of the14C data on short-lived samples from the volcanic destruction level at Akrotiri on Santorini (Thera) may indicate that the average value of the overall data sets is not necessarily the most appropriate14C age to use for dating this time horizon. We note the recent paper of Soter (2011), which suggests that in such a volcanic context some (small) age increment may be possible from diffuse CO2emissions (the effect is hypothetical at this stage and hasnotbeen observed in the field), and that "if short-lived samples from the same stratigraphic horizon yield a wide range of14C ages, the lower values may be the least altered by old CO2." In this context, it might be argued that a substantive “low” grouping of14C ages observable within the overall14C data sets on short-lived samples from the Thera volcanic destruction level centered about 3326–3328 BP is perhaps more representative of the contemporary atmospheric14C age (without any volcanic CO2contamination). This is a subjective argument (since, in statistical terms, the existing studies using the weighted average remain valid) that looks to support as late a date as reasonable from the14C data. The impact of employing this revised14C age is discussed. In general, a late 17th century BC date range is found (to remain) to be most likelyeven ifsuch a late-dating strategy is followed—a late 17th century BC date range is thus a robust finding from the14C evidence even allowing for various possible variation factors. However, the possibility of a mid-16th century BC date (within ∼1593–1530 cal BC) is increased when compared against previous analyses if the Santorini data are considered in isolation.

scholarly journals Multi-instrument gravity-wave measurements over Tierra del Fuego and the Drake Passage – Part 1: Potential energies and vertical wavelengths from AIRS, COSMIC, HIRDLS, MLS-Aura, SAAMER, SABER and radiosondes

2016 ◽  
Vol 9 (3) ◽  
pp. 877-908 ◽  
Author(s):  
Corwin J. Wright ◽  
Neil P. Hindley ◽  
Andrew C. Moss ◽  
Nicholas J. Mitchell
Keyword(s):  
Gravity Wave ◽  
Wave Packets ◽  
Lower Thermosphere ◽  
Lower Troposphere ◽  
Drake Passage ◽  
Tierra Del Fuego ◽  
Data Sets ◽  
Meteor Radar ◽  
Diverse Range ◽  
Wide Range

Abstract. Gravity waves in the terrestrial atmosphere are a vital geophysical process, acting to transport energy and momentum on a wide range of scales and to couple the various atmospheric layers. Despite the importance of these waves, the many studies to date have often exhibited very dissimilar results, and it remains unclear whether these differences are primarily instrumental or methodological. Here, we address this problem by comparing observations made by a diverse range of the most widely used gravity-wave-resolving instruments in a common geographic region around the southern Andes and Drake Passage, an area known to exhibit strong wave activity. Specifically, we use data from three limb-sounding radiometers (Microwave Limb Sounder, MLS-Aura; HIgh Resolution Dynamics Limb Sounder, HIRDLS; Sounding of the Atmosphere using Broadband Emission Radiometry, SABER), the Constellation Observing System for Meteorology, Ionosphere and Climate (COSMIC) GPS-RO constellation, a ground-based meteor radar, the Advanced Infrared Sounder (AIRS) infrared nadir sounder and radiosondes to examine the gravity wave potential energy (GWPE) and vertical wavelengths (λz) of individual gravity-wave packets from the lower troposphere to the edge of the lower thermosphere ( ∼  100 km). Our results show important similarities and differences. Limb sounder measurements show high intercorrelation, typically  > 0.80 between any instrument pair. Meteor radar observations agree in form with the limb sounders, despite vast technical differences. AIRS and radiosonde observations tend to be uncorrelated or anticorrelated with the other data sets, suggesting very different behaviour of the wave field in the different spectral regimes accessed by each instrument. Evidence of wave dissipation is seen, and varies strongly with season. Observed GWPE for individual wave packets exhibits a log-normal distribution, with short-timescale intermittency dominating over a well-repeated monthly-median seasonal cycle. GWPE and λz exhibit strong correlations with the stratospheric winds, but not with local surface winds. Our results provide guidance for interpretation and intercomparison of such data sets in their full context.

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