Petrological microscopy data workflow – an example from Cap de Creus, NE Spain

2021 ◽  
Author(s):  
Richard Wessels ◽  
Thijmen Kok ◽  
Hans van Melick ◽  
Martyn Drury
Keyword(s):  
High Resolution ◽  
Shear Zones ◽  
Research Data ◽  
Image Correlation ◽  
Geochemical Data ◽  
Rock Composition ◽  
Meta Data ◽  
Sample Number ◽  
Thin Sections ◽  
The Impact

<p>Publishing research data in a Findable, Accessible, Interoperable, and Reusable (FAIR) manner is increasingly valued and nowadays often required by publishers and funders. Because experimental research data provide the backbone for scientific publications, it is important to publish this data as FAIRly as possible to enable reuse and citation of the data, thereby increasing the impact of research.</p><p>The structural geology group at Utrecht University is collaborating with the EarthCube-funded StraboSpot initiative to develop (meta)data schemas, templates and workflows, to support researchers in collecting and publishing petrological and microstructural data. This data will be made available in a FAIR manner through the EPOS (European Plate Observing System) data publication chain <span xml:lang="EN-GB"><span>(https://epos-msl.uu.nl/</span></span><span xml:lang="EN-GB"><span>)</span></span><span xml:lang="EN-GB"><span>.</span></span></p><p>The data workflow under development currently includes: a) collecting structural field (meta)data compliant with the StraboSpot protocols, b) creating thin sections oriented in three dimensions by applying a notch system (Tikoff et al., 2019), c) scanning and digitizing thin sections using a high-resolution scanner, d) automated mineralogy through EDS on a SEM, and e) high-resolution geochemistry using a microprobe. The purpose of this workflow is to be able to track geochemical and structural measurements and observations throughout the analytical process.</p><p>This workflow is applied to samples from the Cap de Creus region in northeast Spain. Located in the axial zone of the Pyrenees, the pre-Cambrian metasediments underwent HT-LP greenschist- to amphibolite-facies metamorphism, are intruded by pegmatitic bodies, and transected by greenschist-facies shear zones. Cap de Creus is a natural laboratory for studying the deformation history of the Pyrenees, and samples from the region are ideal to test and refine the data workflow. In particular, the geochemical data collected under this workflow is used as input for modelling the bulk rock composition using Perple_X.    </p><p>In the near future the workflow will be complimented by adding unique identifiers to the collected samples using IGSN (International Geo Sample Number), and by incorporating a StraboSpot-developed application for microscopy-based image correlation. This workflow will be refined and included in the broader correlative microscopy workflow that will be applied in the upcoming EXCITE project, an H2020-funded European collaboration of electron and x-ray microscopy facilities and researchers aimed at structural and chemical imaging of earth materials. </p>

Data, Statistics, and Controversy: Making Science Research Data Intelligible

2012 ◽  
Vol 3 (1) ◽  
Author(s):  
Nell Sedransk ◽  
Linda J. Young ◽  
Cliff Spiegelman
Keyword(s):  
Data Base ◽  
Science Research ◽  
Scientific Data ◽  
Research Data ◽  
Sufficient Information ◽  
Meta Data ◽  
Public Data ◽  
Scientific Results ◽  
Public Datasets ◽  
The Impact

Making published, scientific research data publicly available can benefit scientists and policy makers only if there is sufficient information for these data to be intelligible. Thus the necessary meta-data go beyond the scientific, technological detail and extend to the statistical approach and methodologies applied to these data. The statistical principles that give integrity to researchers’ analyses and interpretations of their data require documentation. This is true when the intent is to verify or validate the published research findings; it is equally true when the intent is to utilize the scientific data in conjunction with other data or new experimental data to explore complex questions; and it is profoundly important when the scientific results and interpretations are taken outside the world of science to establish a basis for policy, for legal precedent or for decision-making. When research draws on already public data bases, e.g., a large federal statistical data base or a large scientific data base, selection of data for analysis, whether by selection (subsampling) or by aggregating, is specific to that research so that this (statistical) methodology is a crucial part of the meta-data. Examples illustrate the role of statistical meta-data in the use and reuse of these public datasets and the impact on public policy and precedent.

scholarly journals Impact of mineral composition and distribution on the mechanical properties of porous media

2020 ◽  
Vol 205 ◽  
pp. 02006
Author(s):  
Olivia M. Brunhoeber ◽  
Dinu Arakkal ◽  
Rourou Ji ◽  
Marta Miletić ◽  
Lauren E. Beckingham
Keyword(s):  
Mechanical Properties ◽  
Porous Media ◽  
Mineral Composition ◽  
Tensile Tests ◽  
Mineral Dissolution ◽  
Image Correlation ◽  
Geological Sequestration ◽  
Thin Sections ◽  
Natural Rock ◽  
The Impact

Geological sequestration of CO2 in deep saline formations is a promising means of reducing atmospheric CO2 emissions. Once injected, CO2 dissolves into formation brine, lowering pH and creating conditions favorable for mineral dissolution. Cations released from dissolving minerals may create conditions favorable for secondary mineral precipitation, which can result in the long-term mineralogical trapping of injected CO2. These reactions may alter the natural rock mechanical properties, which can affect the safety and efficiency of geological sequestration. This work aims to investigate the impact of mineral composition and distribution on the mechanical properties of porous media. In this study, the mineralogy, mineral distribution, and mechanical properties of samples from Escambia County, AL, are evaluated. The mechanical properties of the rock samples are evaluated using the unconfined compression and indirect tensile tests in the combination with digital image correlation. The mineral composition and distribution are determined through the analysis of scanning electron microscopy backscattered electron and energy dispersive X-ray spectroscopy images of thin sections. These analyses showed that the mechanical properties vary with composition, which may have significant practical consequences for geological sequestration of CO2.

The AuScope Geochemistry Laboratory Network

2020 ◽  
Author(s):  
Alex Prent ◽  
Brent McInnes ◽  
Andy Gleadow ◽  
Suzanne O'Reilly ◽  
Samuel Boone ◽  
...  
Keyword(s):  
Earth Science ◽  
Open Data ◽  
Geochemical Data ◽  
Data Repository ◽  
Meta Data ◽  
Sample Number ◽  
Data Schema ◽  
Laboratory Network ◽  
Australian Continent ◽  
User Access

<p>AuScope is an Australian consortium of Earth Science institutes cooperating to develop national research infrastructure. AuScope received federal funding in 2019 to establish the AuScope Geochemistry Laboratory Network (AGN), with the objective of coordinating FAIR-based open data initiatives, support user access to laboratory facilities, and strengthen analytical capability on a national scale. </p><p>Activities underway include an assessment of best practices for researchers to register samples using the International Geo Sample Number (IGSN) system in combination with prescribed minima for meta-data collection. Initial activities will focus on testing meta-data schema on high value datasets such as geochronology (SHRIMP U-Pb, Curtin University), geochemistry (Hf-isotopes, Macquarie University) and low-temperature thermochronology analyses (fission track/U-He, University of Melbourne). Collectively, these datasets will lead to a geochemical data repository in the form of an Isotopic Atlas eResearch Platform that is available to the public via the AuScope Discovery Portal. Over time, the repository will aggregate a large volume of publicly funded geochemical data, providing a key resource in quantitatively understanding the evolution of Earth system processes that have shaped the Australian continent and its resources.</p>

Managing Open and FAIR Data in Geochemistry: Where are we a decade after the Editors Roundtable?

2021 ◽  
Author(s):  
Steven L Goldstein ◽  
Kerstin Lehnert ◽  
Albrecht W Hofmann
Keyword(s):  
Best Practices ◽  
Data Management ◽  
Research Data ◽  
Geochemical Data ◽  
Policy Statement ◽  
Data Repositories ◽  
Data Reporting ◽  
Reporting Practices ◽  
Space Sciences ◽  
The Impact

<p>The ultimate goal of research data management is to achieve the long-term utility and impact of data acquired by research projects. Proper data management ensures that all researchers can validate and replicate findings, and reuse data in the quest for new discoveries. Research data need to be open, consistently and comprehensively documented for meaningful evaluation and reuse following domain-specific guidelines, and available for reuse via public data repositories that make them Findable, persistently Accessible, Interoperable, and Reusable (FAIR).</p><p>In the early 2000’s, the development of geochemical databases such as GEOROC and PetDB underscored that the reporting and documenting practices of geochemical data in the scientific literature were inconsistent and incomplete. The original data could often not be recovered from the publications, and essential information about samples, analytical procedures, data reduction, and data uncertainties was missing, thus limiting meaningful reuse of the data and reproducibility of the scientific findings. In order to avoid that such poor scientific practice might potentially damage the health of the entire discipline, we launched the Editors Roundtable in 2007, an initiative to bring together editors, publishers, and database providers to implement consistent publication practices for geochemical data. Recognizing that mainstream scientific journals were the most effective agents to rectify problems in data reporting and implement best practices, members of the Editors Roundtable created and signed a policy statement that laid out ‘Requirements for the Publication of Geochemical Data’ (Goldstein et al. 2014, http://dx.doi.org/10.1594/IEDA/100426). This presentation will examine the impact of this initial policy statement, assess the current status of best practices for geochemical data management, and explore what actions are still needed. </p><p>While the Editors Roundtable policy statement led to improved data reporting practices in some journals, and provided the basis for data submission policies and guidelines of the EarthChem Library (ECL), data reporting practices overall remained inconsistent and inadequate. Only with the formation of the Coalition for Publishing Data in the Earth and Space Sciences (COPDESS, www.copdess.org), which extended the Editors Roundtable to include publishers and data facilities across the entire Earth and Space Sciences, along with the subsequent AGU project ‘Enabling FAIR Data’, has the implementation of new requirements by publishers, funders, and data repositories progressed and led to significant compliance with the FAIR Data Principles. Submission of geochemical data to open and FAIR repositories has increased substantially. Nevertheless, standard guidelines for documenting geochemical data and standard protocols for exchanging geochemical data among distributed data systems still need to be defined, and structures to govern such standards need to be identified by the global geochemistry community. Professional societies such as the Geochemical Society, the European Association of Geochemistry, and the International Association of GeoChemistry can and should take a leading role in this process.</p>

The High Resolution Appearance of Biological Substrates

1969 ◽  
Vol 27 ◽  
pp. 416-417
Author(s):  
Glen B. Haydon
Keyword(s):  
High Resolution ◽  
Phase Image ◽  
Biological Structure ◽  
Electron Microscopic ◽  
Thin Sections ◽  
Resolution Electron ◽  
Discrete Structures ◽  
Large Phase ◽  
Biological Substrates ◽  
High Resolution Electron Micrographs

High resolution electron microscopic study of negatively stained macromolecules and thin sections of tissue embedded in a variety of media are difficult to interpret because of the superimposed phase image granularity. Although all of the information concerning the biological structure of interest may be present in a defocused electron micrograph, the high contrast of large phase image granules produced by the substrate makes it impossible to distinguish the phase ‘points’ from discrete structures of the same dimensions. Theory predicts the findings; however, it does not allow an appreciation of the actual appearance of the image under various conditions. Therefore, though perhaps trivial, training of the cheapest computer produced by mass labor has been undertaken in order to learn to appreciate the factors which affect the appearance of the background in high resolution electron micrographs.

The ultrastructure of the double membrane-bound bodies and endoplasmic reticulum in serial sections of wheat spot mosaic-affected wheat plants

1990 ◽  
Vol 48 (3) ◽  
pp. 694-695
Author(s):  
M. H. Chen ◽  
C. Hiruki
Keyword(s):  
Endoplasmic Reticulum ◽  
High Resolution ◽  
Membrane Structure ◽  
Mosaic Disease ◽  
Serial Sections ◽  
Thin Sections ◽  
Double Membrane ◽  
Southern Alberta ◽  
Membrane Bound ◽  
Scanning Em

Wheat spot mosaic disease was first discovered in southern Alberta, Canada, in 1956. A hitherto unidentified disease-causing agent, transmitted by the eriophyid mite, caused chlorosis, stunting and finally severe necrosis resulting in the death of the affected plants. Double membrane-bound bodies (DMBB), 0.1-0.2 μm in diameter were found to be associated with the disease.Young tissues of leaf and root from 4-wk-old infected wheat plants were fixed, dehydrated, and embedded in Spurr’s resin. Serial sections were collected on slot copper grids and stained. The thin sections were then examined with a Hitachi H-7000 TEM at 75 kV. The membrane structure of the DMBBs was studied by numbering them individually and tracing along the sections to see any physical connection with endoplasmic reticulum (ER) membranes. For high resolution scanning EM, a modification of Tanaka’s method was used. The specimens were examined with a Hitachi Model S-570 SEM in its high resolution mode at 20 kV.

Atomic resolution characterisation of interface structures by Electron Energy Loss Spectroscopy

1993 ◽  
Vol 51 ◽  
pp. 576-577
Author(s):  
N. D. Browning ◽  
M. M. McGibbon ◽  
M. F. Chisholm ◽  
S. J. Pennycook
Keyword(s):  
High Resolution ◽  
Energy Loss ◽  
Electron Energy ◽  
Electron Energy Loss Spectroscopy ◽  
Imaging Technique ◽  
Atomic Scale ◽  
Atomic Resolution ◽  
Reference Image ◽  
The Impact ◽  
Electron Energy Loss

The recent development of the Z-contrast imaging technique for the VG HB501 UX dedicated STEM, has added a high-resolution imaging facility to a microscope used mainly for microanalysis. This imaging technique not only provides a high-resolution reference image, but as it can be performed simultaneously with electron energy loss spectroscopy (EELS), can be used to position the electron probe at the atomic scale. The spatial resolution of both the image and the energy loss spectrum can be identical, and in principle limited only by the 2.2 Å probe size of the microscope. There now exists, therefore, the possibility to perform chemical analysis of materials on the scale of single atomic columns or planes.In order to achieve atomic resolution energy loss spectroscopy, the range over which a fast electron can cause a particular excitation event, must be less than the interatomic spacing. This range is described classically by the impact parameter, b, which ranges from ~10 Å for the low loss region of the spectrum to <1Å for the core losses.

scholarly journals The Interactions between Polyphenols and Microorganisms, Especially Gut Microbiota

Antioxidants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 188
Author(s):  
Małgorzata Makarewicz ◽  
Iwona Drożdż ◽  
Tomasz Tarko ◽  
Aleksandra Duda-Chodak
Keyword(s):  
Intestinal Bacteria ◽  
Research Data ◽  
Bioactive Metabolites ◽  
Human Organism ◽  
Comprehensive Knowledge ◽  
Bidirectional Relationship ◽  
The Matrix ◽  
Intestinal Pathogens ◽  
The Impact

This review presents the comprehensive knowledge about the bidirectional relationship between polyphenols and the gut microbiome. The first part is related to polyphenols’ impacts on various microorganisms, especially bacteria, and their influence on intestinal pathogens. The research data on the mechanisms of polyphenol action were collected together and organized. The impact of various polyphenols groups on intestinal bacteria both on the whole “microbiota” and on particular species, including probiotics, are presented. Moreover, the impact of polyphenols present in food (bound to the matrix) was compared with the purified polyphenols (such as in dietary supplements) as well as polyphenols in the form of derivatives (such as glycosides) with those in the form of aglycones. The second part of the paper discusses in detail the mechanisms (pathways) and the role of bacterial biotransformation of the most important groups of polyphenols, including the production of bioactive metabolites with a significant impact on the human organism (both positive and negative).

scholarly journals Full-Field Operational Modal Analysis of an Aircraft Composite Panel from the Dynamic Response in Multi-Impact Test

Sensors ◽  
2021 ◽  
Vol 21 (5) ◽  
pp. 1602
Author(s):  
Ángel Molina-Viedma ◽  
Elías López-Alba ◽  
Luis Felipe-Sesé ◽  
Francisco Díaz
Keyword(s):  
Modal Analysis ◽  
Energy Absorption ◽  
High Speed ◽  
Operational Modal Analysis ◽  
Modal Identification ◽  
Image Correlation ◽  
Composite Panel ◽  
Impact Excitation ◽  
Full Field ◽  
The Impact

Experimental characterization and validation of skin components in aircraft entails multiple evaluations (structural, aerodynamic, acoustic, etc.) and expensive campaigns. They require different rigs and equipment to perform the necessary tests. Two of the main dynamic characterizations include the energy absorption under impact forcing and the identification of modal parameters through the vibration response under any broadband excitation, which also includes impacts. This work exploits the response of a stiffened aircraft composite panel submitted to a multi-impact excitation, which is intended for impact and energy absorption analysis. Based on the high stiffness of composite materials, the study worked under the assumption that the global response to the multi-impact excitation is linear with small strains, neglecting the nonlinear behavior produced by local damage generation. Then, modal identification could be performed. The vibration after the impact was measured by high-speed 3D digital image correlation and employed for full-field operational modal analysis. Multiple modes were characterized in a wide spectrum, exploiting the advantages of the full-field noninvasive techniques. These results described a consistent modal behavior of the panel along with good indicators of mode separation given by the auto modal assurance criterion (Auto-MAC). Hence, it illustrates the possibility of performing these dynamic characterizations in a single test, offering additional information while reducing time and investment during the validation of these structures.

High-Resolution Climate Change Impact Analysis on Expected Future Water Availability in the Upper Jordan Catchment and the Middle East

2014 ◽  
Vol 15 (4) ◽  
pp. 1517-1531 ◽  
Author(s):  
Gerhard Smiatek ◽  
Harald Kunstmann ◽  
Andreas Heckl
Keyword(s):  
Climate Change ◽  
High Resolution ◽  
Water Availability ◽  
Impact Analysis ◽  
River Flow ◽  
Climate Model ◽  
Mesoscale Model ◽  
Global Climate Model ◽  
Full Range ◽  
The Impact

Abstract The impact of climate change on the future water availability of the upper Jordan River (UJR) and its tributaries Dan, Snir, and Hermon located in the eastern Mediterranean is evaluated by a highly resolved distributed approach with the fifth-generation Pennsylvania State University–NCAR Mesoscale Model (MM5) run at 18.6- and 6.2-km resolution offline coupled with the Water Flow and Balance Simulation Model (WaSiM). The MM5 was driven with NCEP reanalysis for 1971–2000 and with Hadley Centre Coupled Model, version 3 (HadCM3), GCM forcings for 1971–2099. Because only one regional–global climate model combination was applied, the results may not give the full range of possible future projections. To describe the Dan spring behavior, the hydrological model was extended by a bypass approach to allow the fast discharge components of the Snir to enter the Dan catchment. Simulation results for the period 1976–2000 reveal that the coupled system was able to reproduce the observed discharge rates in the partially karstic complex terrain to a reasonable extent with the high-resolution 6.2-km meteorological input only. The performed future climate simulations show steadily rising temperatures with 2.2 K above the 1976–2000 mean for the period 2031–60 and 3.5 K for the period 2070–99. Precipitation trends are insignificant until the middle of the century, although a decrease of approximately 12% is simulated. For the end of the century, a reduction in rainfall ranging between 10% and 35% can be expected. Discharge in the UJR is simulated to decrease by 12% until 2060 and by 26% until 2099, both related to the 1976–2000 mean. The discharge decrease is associated with a lower number of high river flow years.

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