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Changes in flood types across Europe
Data set contains annual and seasonal counts of different flood events classified by their generating process for five different regions of Europe as well as for the entire European domain. Furthermore summaries of a trend significance test for each region, season, and flood type is included. Further description and content of each data file is available in the included metadata.
Spatial flood events and process types
Spatially clustered flood events from peak flows identified at selected GRDC sations. The data also shows the stations affected by each of the clustered eevents. The clustered events were classified into four different process types. Furthermore, five regions were defined across Europe and the regions affected by each flood event are identified. Further description and content of each data file can be seen in the included metadata.
A Single Walled Carbon Nanotube of the (6,5) Type
<p>The files show a rotating single walled carbon nanotube as a continuos gif file. The Pictures also show a commonly used Polymer (PFO-Bpy) as it adsorbes on the carbon nanotube surfaces.</p> <p>* CNT created with Avogadro's CNT building tool.</p> <p>* PFO-Bpy and Toluene created with ChemBioDraw as molecular files and imported to Avogadro</p> <p>* Export from Avogadro to xyz file</p> <p>* import to blender using [molecular blender](https://github.com/smparker/molecular-blender)</p> <p>* Gif creation using [Bligify](https://github.com/doakey3/Bligify)</p>
The Sonora Substellar Atmosphere Models. IV. Elf Owl: Atmospheric Mixing and Chemical Disequilibrium with Varying Metallicity and C/O Ratios (T- type Models)
<ul> <li><strong>Overview of V2: "The Sonora Substellar Atmosphere Models. V: A Correction to the Disequilibrium Abundance of CO2 for Sonora Elf Owl"</strong></li> </ul> <p> Version 2 of the Sonora Elf Owl Models updates the CO2 and PH3 abundances and spectra. As described in the Wogan et al. (2024) research note (URL OF NOTE GOES HERE), Version 1 of the models did not apply the CO2 quench approximation properly resulting in predicted CO2 abundances that were too small by several orders of magintude in some cases. Version 2 fixes this mistake, updating CO2 abundances and the emission spectra to reflect the new CO2 abundances. Version 2 also removes all spectra contributions of PH3 because Version 1 consistently contained too much PH3 absorption when compared to JWST data (Veiler et al. 2024, <a href="http://doi.org/10.3847/1538-4357/ad6759" target="_blank" rel="noopener noreferrer">http://doi.org/10.3847/1538-4357/ad6759</a>).</p> <p> </p> <ul> <li><strong>Overview of V1</strong></li> </ul> <p> The Sonora Elf Owl Models is a successor to the <a href="../records/5063476#:~:text=This%20particular%20set%20of%20model,g%20are%200.25%20or%200.5.">Sonora Bobcat</a> and <a href="../records/4450269">Sonora Cholla</a> models. The Sonora Elf Owl model grid includes cloud-free radiative-convective equilibrium model atmospheres with vertical mixing induced disequilibrium chemistry with sub-solar to super-solar atmospheric metallicities and Carbon-to-Oxygen ratio. The atmospheric models have been computed using the open-source radiative-convective equilibrium model <a href="https://natashabatalha.github.io/picaso/">PICASO</a>. The parameters included within this grid are effective temperature (<strong><em>Teff</em></strong>), gravity (<strong><em>log(g)</em></strong>), vertical eddy diffusion coefficient (<strong><em>log(Kzz)</em></strong>), atmospheric metallicity (<strong><em>[M/H]</em></strong>), and Carbon-to-Oxygen ratio (<strong><em>C/O</em></strong>).</p> <p>The ranges and increments of these parameters are described in the published paper.<br><br></p> <ul> <li><strong>Three grids available on three links</strong></li> </ul> <p><strong> The model grid has been presented using three Zenodo repositories. This repository has all the models between 575 to 1200 K (applicable for T- type objects). The models for Teff between 275 to 550 K (applicable for Y- type objects) are available in the Zenodo DOI :- <a href="../records/10381250">https://zenodo.org/records/10381250</a>. The models for Teff between 1300 to 2400 K (applicable for L- type objects) are available in the Zenodo DOI :- <a href="../records/10385987">https://zenodo.org/records/10385987</a>.</strong></p> <p> </p> <ul> <li><strong> File types and how to use them</strong></li> </ul> <p> The models have been presented in the Xarray format so that all the atmospheric properties including the T(P) profile, atmospheric chemistry, and thermal emission spectra can be accessed within the same files. A python based Jupyter notebook named "Reading and plotting Elf Owl Models.ipynb" has been also supplied which demonstrates how to open and use these files.</p> <ul> <li> <strong>Spectra</strong></li> </ul> <p> The emission spectra for each atmospheric model has been computed between 0.6 to 15 microns. The reported flux is in the units of erg/s/cm<sup>2</sup>/cm. Note that these fluxes need to be multiplied with R<sup>2</sup>/D<sup>2</sup> before comparing them with the typically observed flux of brown dwarfs/exoplanets. R is the radius of the object, and D is the distance here.</p> <div> </div> <div> <ul> <li><strong>Note on CH4</strong></li> </ul> </div> <p> As stated in <a href="https://ui.adsabs.harvard.edu/abs/2023ApJ...942...71M/abstract">Mukherjee et al. 2023 </a>our CH4 opacity is derived using the <a href="https://iopscience.iop.org/article/10.3847/1538-4365/ab7a1a">Hargreaves et al. 2020</a> HITEMP line list and computed using the HAPI code (<a href="https://www.sciencedirect.com/science/article/abs/pii/S0022407315302466">Kochanov et al. 2016</a>). HAPI automatically pre-weights the isotopologues according to earth abundances that are listed on the HITRAN website (<a href="https://hitran.org/lbl/2?6=on" target="_blank" rel="noopener noreferrer">see here for CH4</a>). Therefore, users should note that there will be minor features of CH3D included in the models. Given the general absence of deuterated molecules in brown dwarfs (Teff>~300) we will include a second posting of models which includes the Elf Owl grid with <strong>only</strong> the major CH4 isotopologue (12C-H4).</p> <div> <ul> <li><strong>Note on PH3</strong></li> </ul> </div> <p> PH3 abundance is treated separately from the general disequilibrium scheme. This is because of the current non-detection of PH3 in many brown dwarf atmospheres (see citations in paper). The current PH3 treatment uses the chemical equilibrium treatment described in Visscher et al. However, after publishing this grid and using the model for analysis of high precision JWST data, we noticed that even the simple chemical equilibrium treatment which reduces the abundance, introduces a noticeable PH3 feature. Therefore in our v2 of this model grid we will further diminish the abundance.</p>
The Sonora Substellar Atmosphere Models. IV. Elf Owl: Atmospheric Mixing and Chemical Disequilibrium with Varying Metallicity and C/O Ratios (L- type Models)
<ul> <li><strong>Overview of V2: "The Sonora Substellar Atmosphere Models. V: A Correction to the Disequilibrium Abundance of CO2 for Sonora Elf Owl"</strong></li> </ul> <p> Version 2 of the Sonora Elf Owl Models updates the CO2 and PH3 abundances and spectra. As described in the Wogan et al. (2024) research note (URL OF NOTE GOES HERE), Version 1 of the models did not apply the CO2 quench approximation properly resulting in predicted CO2 abundances that were too small by several orders of magintude in some cases. Version 2 fixes this mistake, updating CO2 abundances and the emission spectra to reflect the new CO2 abundances. Version 2 also removes all spectra contributions of PH3 because Version 1 consistently contained too much PH3 absorption when compared to JWST data (Veiler et al. 2024, <a href="http://doi.org/10.3847/1538-4357/ad6759" target="_blank" rel="noopener noreferrer">http://doi.org/10.3847/1538-4357/ad6759</a>).</p> <p> </p> <ul> <li><strong>Overview of V1</strong></li> </ul> <p> The Sonora Elf Owl Models is a successor to the <a href="../records/5063476#:~:text=This%20particular%20set%20of%20model,g%20are%200.25%20or%200.5.">Sonora Bobcat</a> and <a href="../records/4450269">Sonora Cholla</a> models. The Sonora Elf Owl model grid includes cloud-free radiative-convective equilibrium model atmospheres with vertical mixing induced disequilibrium chemistry with sub-solar to super-solar atmospheric metallicities and Carbon-to-Oxygen ratio. The atmospheric models have been computed using the open-source radiative-convective equilibrium model <a href="https://natashabatalha.github.io/picaso/">PICASO</a>. The parameters included within this grid are effective temperature (<strong><em>Teff</em></strong>), gravity (<strong><em>log(g)</em></strong>), vertical eddy diffusion coefficient (<strong><em>log(Kzz)</em></strong>), atmospheric metallicity (<strong><em>[M/H]</em></strong>), and Carbon-to-Oxygen ratio (<strong><em>C/O</em></strong>).</p> <p>The ranges and increments of these parameters are described in the published paper.<br><br></p> <ul> <li><strong>Three grids available on three links</strong></li> </ul> <p><strong> The model grid has been presented using three Zenodo repositories. This repository has all the models between 1300 to 2400 K (applicable for L- type objects). The models for Teff between 275 to 550 K (applicable for Y- type objects) are available in the Zenodo DOI :- <a href="../records/10381250">https://zenodo.org/records/10381250</a>. The models for Teff between 575 to 1200 K (applicable for T- type objects) are available in the Zenodo DOI :- <a href="../records/10385821">https://zenodo.org/records/10385821</a>.</strong></p> <p> </p> <ul> <li><strong> File types and how to use them</strong></li> </ul> <p> The models have been presented in the Xarray format so that all the atmospheric properties including the T(P) profile, atmospheric chemistry, and thermal emission spectra can be accessed within the same files. A python based Jupyter notebook named "Reading and plotting Elf Owl Models.ipynb" has been also supplied which demonstrates how to open and use these files.</p> <ul> <li> <strong>Spectra</strong></li> </ul> <p> The emission spectra for each atmospheric model has been computed between 0.6 to 15 microns. The reported flux is in the units of erg/s/cm<sup>2</sup>/cm. Note that these fluxes need to be multiplied with R<sup>2</sup>/D<sup>2</sup> before comparing them with the typically observed flux of brown dwarfs/exoplanets. R is the radius of the object, and D is the distance here.</p> <div> </div> <div> <ul> <li><strong>Note on CH4</strong></li> </ul> </div> <p> As stated in <a href="https://ui.adsabs.harvard.edu/abs/2023ApJ...942...71M/abstract">Mukherjee et al. 2023 </a>our CH4 opacity is derived using the <a href="https://iopscience.iop.org/article/10.3847/1538-4365/ab7a1a">Hargreaves et al. 2020 </a>HITEMP line list and computed using the HAPI code (<a href="https://www.sciencedirect.com/science/article/abs/pii/S0022407315302466">Kochanov et al. 2016</a>). HAPI automatically pre-weights the isotopologues according to earth abundances that are listed on the HITRAN website (<a href="https://hitran.org/lbl/2?6=on" target="_blank" rel="noopener noreferrer">see here for CH4</a>). Therefore, users should note that there will be minor features of CH3D included in the models. Given the general absence of deuterated molecules in brown dwarfs (Teff>~300) we will include a second posting of models which includes the Elf Owl grid with <strong>only</strong> the major CH4 isotopologue (12C-H4).</p> <div> <ul> <li><strong>Note on PH3</strong></li> </ul> </div> <p> In v1, PH3 abundance was treated separately from the general disequilibrium scheme. This is because of the current non-detection of PH3 in many brown dwarf atmospheres (see citations in paper). The current PH3 treatment uses the chemical equilibrium treatment described in Visscher et al. However, after publishing this grid and using the model for analysis of high precision JWST data, we noticed that even the simple chemical equilibrium treatment which reduces the abundance, introduces a noticeable PH3 feature. In v2 we completely remove the contribution of PH3. </p>
Type-II kinase inhibitors that target Parkinson's Disease-associated LRRK2
<p>This dataset includes all of the tabular data used in the tables and figures in the article. Additionally, we provide a table with key resources for data aquisition.</p> <p>Aberrant increases in kinase activity of leucine-rich repeat kinase 2 (LRRK2) are associated with Parkinson’s disease (PD). Numerous LRRK2-selective type-I kinase inhibitors have been developed and some have entered clinical trials. In this study, we present the first LRRK2-selective type-II kinase inhibitors. Targeting the inactive conformation of LRRK2 is functionally distinct from targeting the active-like conformation using type-I inhibitors. We designed these inhibitors using a combinatorial chemistry approach fusing selective LRRK2 type-I and promiscuous type-II inhibitors by iterative cycles of synthesis supported by structural biology and activity testing. Our current lead structures are selective and potent LRRK2 inhibitors. Through cellular assays, cryo-electron microscopy structural analysis, and in vitro motility assays, we show that our inhibitors stabilize the open, inactive kinase conformation. These new conformation-specific compounds will be invaluable as tools to study LRRK2’s function and regulation, and expand the potential therapeutic options for PD.</p>
FragGT: Fragment-based Evolutionary Molecule Generation using Gene Types
<p>This directory contains data requires to run frag-gt (Meyers and Brown, 2023), a fragment-based evolutionary algorithm for generating optimal molecules released as part of the guacamol_baselines GitHub repository – https://github.com/BenevolentAI/guacamol_baselines.</p><p>Scripts for generating the data are available from github. The compressed data directory contains (A) Processed and filtered SMILES derived from ChEMBL v.33 produced by `download_chembl_smiles` and (B) fragment stores generated by `generate_fragstore` and `filter_fragstore` for both the above file in (A) and the original GuacaMol dataset.</p><p>smiles_files and fragstores were derived from molecule data downloaded from ChEMBL (https://www.ebi.ac.uk/chembl).</p><p>Liability: We do not represent and/or warrant that no third party rights exist which might prevent the use of the database or that no third party rights would be infringed by said use.</p><p>(data updated for frag-gt version 0.0.2)</p>
JSTOR plant type specimens linked to GBIF occurrences
<p>A mapping between URLs for type specimens in JSTOR Global Plants and the corresponding occurrence in the Global Biodiversity Information Facility (GBIF).</p><p>Guide to fields:</p><ul><li><strong>doi</strong>: JSTOR identifier</li><li><strong>code</strong>: Barcode:</li><li><strong>gbif</strong>: GBIF occurrence id</li><li><strong>occurrenceUrl</strong>: URL to specimen in original herbarium database</li><li><strong>occurrenceID</strong>: occurrenceID stored in GBIF</li><li><strong>title</strong>: Title of specimen in JSTOR</li><li><strong>resource_type</strong>: Type of resource</li><li><strong>canonical</strong>: Canonical taxonomic name</li><li><strong>stored_under_name</strong>: Taxonomic name specimen is stored under</li><li><strong>type_status</strong>: What kind of type</li><li><strong>family</strong>: Family plant species belongs to</li><li><strong>collector</strong>: Collector</li><li><strong>date</strong>: Date of collection</li><li><strong>country</strong>: Country of collection</li><li><strong>herbarium</strong>: Herbarium where specimen is stored</li><li><strong>names</strong>: All taxonomic names associated with specimen as JSON array</li><li><strong>url</strong>: JSTOR URL</li><li><strong>thumbnailUrl</strong>: URL to thumbnail of image in JSTOR</li></ul>
Phase Diagram of Kob-Andersen-Type Binary Lennard-Jones Mixtures
<p>This data repository contains data related to the paper Phase Diagram of Kob-Andersen-Type Binary Lennard-Jones Mixtures, Phys. Rev. Lett. 120, 165501 (2018), DOI: <a href="https://doi.org/10.1103/PhysRevLett.120.165501">10.1103/PhysRevLett.120.165501 </a>by Ulf R. Pedersen, Thomas B. Schrøder, and Jeppe C. Dyre.</p><p> </p><p>Abstract of the paper:</p><p>The binary Kob-Andersen (KA) Lennard-Jones mixture is the standard model for computational studies of viscous liquids</p><p>and the glass transition. For very long simulations, the viscous KA system crystallizes, however, by phase separating</p><p>into a pure A particle phase forming a fcc crystal. We present the thermodynamic phase diagram for KA-type mixtures</p><p>consisting of up to 50% small (B) particles showing, in particular, that the melting temperature of the standard KA</p><p>system at liquid density 1.2 is 1.028(3) in A particle Lennard-Jones units. At large B particle concentrations, the</p><p>system crystallizes into the CsCl crystal structure. The eutectic corresponding to the fcc and CsCl structures is cutoff</p><p>in a narrow interval of B particle concentrations around 26% at which the bipyramidal orthorhombic PuBr3 structure is</p><p>the thermodynamically stable phase. The melting temperature's variation with B particle concentration at two constant</p><p>pressures, as well as at the constant density 1.2, is estimated from simulations at pressure 10.19 using isomorph</p><p>theory. Our data demonstrate approximate identity between the melting temperature and the onset temperature below which</p><p>viscous dynamics appears. Finally, the nature of the solid-liquid interface is briefly discussed.</p>
Inhibition of Parkinson's Disease-related LRRK2 by type-I and type-II kinase inhibitors: activity and structures
<p>Mutations in Leucine Rich Repeat Kinase 2 (LRRK2) are a common cause of familial Parkinson’s Disease (PD), and a risk factor for the sporadic form. Increased kinase activity has been shown in both familial and sporadic PD patients. This has made LRRK2 kinase inhibitors a major focus of drug development efforts in PD. Although significant progress has been made in understanding the structural biology of LRRK2, there are no available structures of LRRK2 inhibitor complexes. To this end, we solved cryo-EM structures of LRRK2, wild-type and PD-linked mutants, bound to the LRRK2-specific type-I inhibitor MLi-2 and the broad-spectrum type-II inhibitor GZD-824. Our structures revealed LRRK2’s kinase in the active-like state, stabilized by type-I inhibitor interactions, and an inactive DYG-out type-II inhibitor complex. The structures also showed how inhibitor-induced conformational changes are affected by the N-terminal half of LRRK2. The structural models provide a template for the rational development of LRRK2 kinase inhibitors covering both canonical inhibitor binding modes.</p>
The Effect of Typing Efficiency and Suggestion Accuracy on Usage of Word Suggestions and Entry Speed
<p>Data collected during our experiments investigating the effect of suggestion accuracy and typing efficiency on usage of word suggestions, and entry speed</p>
FIGURE 10 in Convergent Evolution of a Eusuchian-Type Secondary Palate within Shartegosuchidae
FIGURE 10. Simplified phylogenetic tree mapping the stages in the evolution of the secondary palate in Crocodylomorpha. Palatal bones are colored as follows: maxilla, blue; palatine, pink; ectopterygoid, red; pterygoid, brown; and vomer, yellow.
FIGURE 5 in Convergent Evolution of a Eusuchian-Type Secondary Palate within Shartegosuchidae
FIGURE 5. CT scan cross sections through the pterygoid of Shartegosuchus (IGM 200/50). The blue line demarcates the boundary of the pterygoid. A. anterior to palatal fenestra; B. posterior to palatal fenestra; C. through palatal fenestra; D. through choana. Abbreviations: ch, choana; in cav, internal cavity; pal fen, palatal fenestra.
FIGURE 4 in Convergent Evolution of a Eusuchian-Type Secondary Palate within Shartegosuchidae
FIGURE 4. Digital reconstructions and line drawings of Shartegosuchus asperapalatum (IGM 200/50) in A. left lateral view, B. right lateral view of Shartegosuchus asperapalatum (IGM 200/50). Abbreviations: ang, angular; ant fos, antorbital fossa; d, dentary; ect, ectopterygoid; j, jugal; lac, lacrimal; m, maxilla; n, nasal; pf, prefrontal; pm, premaxilla; pty, pterygoid; sp, splenial.
FIGURE 1. A in Convergent Evolution of a Eusuchian-Type Secondary Palate within Shartegosuchidae
FIGURE 1. A. Map of Mongolia with marker indicating the locality of Shartegosuchus asperapalatum (IGM 200/50). B. Photograph of locality of Shartegosuchus asperapalatum (IGM 200/50) with arrow indicating the position the specimen was recovered from.
FIGURE 8 in Convergent Evolution of a Eusuchian-Type Secondary Palate within Shartegosuchidae
FIGURE 8. The five most parsimonious trees from the analyses (length = 897). Red circles indicate the node Shartegosuchoidea and blue circles indicate the node Shartegosuchidae.
FIGURE 6 in Convergent Evolution of a Eusuchian-Type Secondary Palate within Shartegosuchidae
FIGURE 6. Line drawings of the mandible Shartegosuchus asperopalatum (IGM 200/50) in A. dorsal view, B. left lateral view, and C. right lateral view. Abbreviations: ang, angular; d, dentary; sp, splenial.
Fig. 3 in Repatriation of knowledge about insects and types through the DORSA virtual museum (Digital Orthoptera Specimen Access)
Fig. 3: Orthoptera (crickets and grasshoppers) collections in Germany – number of holotypes in major museums. A similar distributed pattern is observed for type material of other groups of organisms housed in German museums or research institutions.
Fig. 4 in Repatriation of knowledge about insects and types through the DORSA virtual museum (Digital Orthoptera Specimen Access)
Fig. 4: Documentation of DORSA specimen data on the internet. Left: species page in SYSTAX (red arrows mark scrolling down); top right: species page in OSF; middle right: image and sound file pages in SYSTAX; bottom right: distribution map from a map server (Canadian Biodiversity Information Facility). External links are marked by yellow arrows, internal links by green arrows.
Fig. 2 in Repatriation of knowledge about insects and types through the DORSA virtual museum (Digital Orthoptera Specimen Access)
Fig. 2: Species group names of Orthoptera worldwide (valid names and synonyms) and types specimens in German collections. The category holotype includes also syntypes, lectotypes and neotypes. [From Ingrisch et al. 2004a].
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.