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Dataset for: On the Nature of Hydrophobic Organic Compound Adsorption to Smectite Minerals Using the Example of Hexachlorobenzene-Montmorillonite Interactions
<p><br>This dataset contains all data obtained from first principle DFT calculations at the PBE-D3 DFT level<br>by the program VASP for the paper published in the journal "Minerals". Please cite this article when using the dataset.<br><br>Title: "On the Nature of Hydrophobic Organic Compound Adsorption<br>to Smectite Minerals Using the Example of Hexachlorobenzene-Montmorillonite Interactions."</p> <p>Authors: Peter Grancic, Leonard Böhm, Martin H. Gerzabek, and Daniel Tunega <br>DOI10.3390/min13020280. </p> <p><br>The model systems are Ca-montmorillonite (Ca-Mt) models with varying layer charge from the Mg/Al substitutions.<br>Calculated are interaction energies of hexachlorobenzene (HCB) with Ca-Mt models in various configurations.<br>QE.dat file is file with collected energies of all models, Collect_QE.py is a selfmade python file for the collection of energies.<br>The structure of all directories is as following:<br>HCBCaxxx directories contain optimized HCB-CaMt complexes<br>HCBCaxxx_Clay directories contain pure CaMt models<br>HCBCaxxx_HOC directories contain only HOC molecule<br>Each directory contains:<br>-input geometry data (POSCAR file)<br>-optimized geometries (CONTCAR.norm file)<br>-input parameters for VASP (INCAR file)<br>-k-points (KPOINTS file)<br>-complete output files (OUTCAR.norm and vasprun.xml.norm files)<br>POTCAR file with pseudopotentials are not provided due to copyright rights.<br>Their type can be found in OUTCAR or vasprun.xml files.</p> <p>Funding: This work has been supported by German Research Foundation (Deutsche Forschungsgemeinschaft, DFG), grant number 443637168, BO5388/1–1 and Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung, FWF), grant number I 4876–N in the bilateral project ”Clay minerals as sorbents for hydrophobic organic chemicals – ClayHOC”. The results<br>presented have been achieved using the Vienna Scientific Cluster (VSC), project number 70544.</p> <p>Terms of use: These data are provided "as is", without any warranty. This dataset is provided under the Creative Commons Attribution 4.0 International license.</p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Friedrich von Hoyningen-Huene, <a href="http://www.wikidata.org/entity/Q12362794">http://www.wikidata.org/entity/Q12362794</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Mike Imber, <a href="http://www.wikidata.org/entity/Q6847355">http://www.wikidata.org/entity/Q6847355</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by James Bowie, <a href="http://www.wikidata.org/entity/Q6130052">http://www.wikidata.org/entity/Q6130052</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Georg Hermann Wilhelm Stein, <a href="http://www.wikidata.org/entity/Q1253220">http://www.wikidata.org/entity/Q1253220</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Carl Heinrich Bescke, <a href="http://www.wikidata.org/entity/Q113622563">http://www.wikidata.org/entity/Q113622563</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Reinhard Houy, <a href="http://www.wikidata.org/entity/Q114316067">http://www.wikidata.org/entity/Q114316067</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Data from: Do genetic loci that cause reproductive isolation in the lab inhibit gene flow in nature?
<p>The genetic dissection of reproductive barriers between diverging lineages provides enticing clues into the origin of species. One strategy uses linkage analysis in experimental crosses to identify genomic locations involved in phenotypes that mediate reproductive isolation. A second framework searches for genomic regions that show reduced rates of exchange across natural hybrid zones. It is often assumed that these approaches will point to the same loci, but this assumption is rarely tested. In this perspective, we discuss the factors that determine whether loci connected to postzygotic reproductive barriers in the laboratory are inferred to reduce gene flow in nature. We synthesize data on the genetics of postzygotic isolation in house mice, one of the most intensively studied systems in speciation genetics. In a rare empirical comparison, we measure the correspondence of loci tied to postzygotic barriers via genetic mapping in the laboratory and loci at which gene flow is inhibited across a natural hybrid zone. We find no evidence that the two sets of loci overlap beyond what is expected by chance. In light of these results, we recommend avenues for empirical and theoretical research to resolve the potential incongruence between the two predominant strategies for understanding the genetics of speciation.</p>
THE NATURE OF X-RAYS FROM YOUNG STELLAR OBJECTS IN THE ORION NEBULA CLUSTER - A Chandra HETGS Legacy Project
<p><span>This first release provides the community with a first cut of confusion cleaned X-ray spectra of the Orion Nebula Cluster observed with the HETG onboard the Chandra X-ray Observatory. The data were taken starting in 1999 until 2021. <br><br>The confusion cleaning is based on several aspects of sources for confusion, which includes cluster point sources intersecting with grating dispersions, grating arms intersecting each other in CCD space, as well as grating dispersion overlaps prohibiting proper order sorting. The latter is a major effect and resulted in sometimes severe data losses. In the first release, our automated procedure took care of the vast majority of point sources and grating arm intersections. With respect to the dispersion arm overlaps, in this release we took a statistical approach optimizing the agreement of all four grating dispersion arms in the merged data to agree within a 1 sigma statistical uncertainty over 90% of the bandpass between 2 and 15 Angstrom. For that we used the zero order flux fractions of the interfering sources as the driving parameter. <br><br>There are still many caveats and rooms for improvement, which we will address in upcoming releases, which include the treatment of the increasing background at high dispersion, improve extraction efficiency, exclude observations with non-detections before confusion cleaning, include possible new detections, investigate the 5 A excess we observe in the HEG, though at low statistics, spotcheck individual observations for any residual issues. <br><br>Release 1 provides the community with an excellent starting point for addressing our identified science projects. Out of the 46 sources that were extracted, 37 resulted in valid spectral data. 7 sources have less than 1000 counts in 1st order, some of those may not yet be very useful. <br></span></p> <p> </p> <p>Each directory contains the merged cleaned spectrum and responses for<br>one source. The file "pha2" is a Type II PHA file (multiple spectra)<br>containing the four first order spectra, HEG -1, HEG +1, MEG -1, and<br>MEG +1. Headers have been edited indicate the object (OBJECT), and<br>start and stop times for the set of observations. Since the exposure<br>depends on order, due to the cleaning process, EXPOSURE is a column in<br>the data table. Some other keywords now say "MERGED" since they can<br>vary with observation.</p> <p>There is one effective area file per order (".arf" files). These have<br>also been merged by zeroing out the same regions as excluded in the<br>count spectra, and summed weighting by exposure. They also have<br>similar header edits as for the spectra.</p> <p>While the exposures in headers may say 2 Ms, the actual exposure at<br>any wavelength may be much less. This is not explicitly known, but is<br>implicit in the ignored wavelength regions in the merged counts and<br>responses.</p> <p>There is one grating response matrix (".rmf" files) per order. Since<br>all spectral extractions of all sources used the same cross-dispersion<br>region, there is no change in these files between sources. One set<br>suffices for all extractions. These are in the directory "RMFs", and<br>also for convenience have symbolic links in each source directory.</p> <p>HETG background files have also been provided, one PHA file per first<br>order, in directory HETG_Background. These have been derived from<br>long observations of blank fields. Details are provided in the<br>accompanying memo, hetg_background.pdf.</p> <p>Headers have not been designed for auto-loading of responses (that is<br>CORRFILE, RESPFILE, and BACKFILE are set to 'none').</p>
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs.
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet.
Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation.
Operating diagram of IF incubator, two identical incubators were used for eggs that were already sorted. They are made up of an isothermal enclosure and contain three tiers (100 × 60 × 17 cm). The water circulating in each tier comes from the same filtration, cooling and sterilisation device. As a result, the eggs placed in the different tiers are subject to the same temperature regime. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of IF incubator, two identical incubators were used for eggs that were already sorted. They are made up of an isothermal enclosure and contain three tiers (100 × 60 × 17 cm). The water circulating in each tier comes from the same filtration, cooling and sterilisation device. As a result, the eggs placed in the different tiers are subject to the same temperature regime.
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction.
Top view of DR1/DR2 double riffle, each section contains a spawning ground made up of eight gravel-filled trays, a rest area. The "double riffle" was designed to accommodate two groups from 25 to 50 specimens of broodstock in strictly identical conditions. The spawning grounds are equipped with waterproof, motion-sensing cameras with infrared night vision, connected to a 1000 Gb recorder. The diurnal and nocturnal activities of the two groups can therefore be simultaneously recorded over a long period. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Top view of DR1/DR2 double riffle, each section contains a spawning ground made up of eight gravel-filled trays, a rest area. The "double riffle" was designed to accommodate two groups from 25 to 50 specimens of broodstock in strictly identical conditions. The spawning grounds are equipped with waterproof, motion-sensing cameras with infrared night vision, connected to a 1000 Gb recorder. The diurnal and nocturnal activities of the two groups can therefore be simultaneously recorded over a long period.
Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day.
Operating diagram of the incubator, two tiered modules contain six independent incubators. Three shallow hatching are (220 × 60 × 17 cm) stacked on top of each other to create a compact assembly in which each tier functions independently. Eighteen trays covered with eggs can be placed in each tier, allowing the simultaneous incubation of seven to nine lays. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of the incubator, two tiered modules contain six independent incubators. Three shallow hatching are (220 × 60 × 17 cm) stacked on top of each other to create a compact assembly in which each tier functions independently. Eighteen trays covered with eggs can be placed in each tier, allowing the simultaneous incubation of seven to nine lays.
Figure 8 in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Figure 8. – Egg production as a function of age. These results were obtained from the number of eggs laid throughout the breeding season divided by the number of females that laid. The same bloodstocks (born in captivity in 2008) were used for 9 years. The maximum production was obtained at 6 years. The number of females was 17 at the beginning and 2 at the end (Tab. II).
Figure 2. – Z. asper eggs. A in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Figure 2. – Z. asper eggs. A: Mature ovum on the right and immature ovum on the left. B: Extraction of milt, this operation is done first. C: A low pressure from the abdomen towards the anus with the index finger allows the ova to be extracted. D: The yellow colour of the ova is a good indicator of their good quality. E: Water can only be added when everything is well mixed.
Linked collectors and determiners for: Collection of various insect orders, Natural History Museum, University of Oslo.
Natural history specimen data linked to collectors and determiners held within, "Collection of various insect orders, Natural History Museum, University of Oslo". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="http://bionomia.net/dataset/4cfd80a7-d630-4d7f-89fb-d2d1e749a418">https://bionomia.net/dataset/4cfd80a7-d630-4d7f-89fb-d2d1e749a418</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/4cfd80a7-d630-4d7f-89fb-d2d1e749a418">https://gbif.org/dataset/4cfd80a7-d630-4d7f-89fb-d2d1e749a418</a>. Formatted as a Frictionless Data package.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.